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| Open AccessStructure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5
Pdr5 is an ABC transporter conferring multidrug resistance to pathogenic fungi. Here, structural analysis of Pdr5 provides insights into the transport mechanism featuring asymmetric movements of Pdr5 domain and enabling efflux of a broad spectrum of compounds.
- Andrzej Harris
- , Manuel Wagner
- & Lutz Schmitt
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Article
| Open AccessStructural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens
Chimeric antigen receptor T cells in the clinic currently target cell-type-specific extracellular antigens on malignant cells. Here, authors engineer tumor-specific chimeric antigen receptor T cells that target human leukocyte antigen-presented neoantigens derived from mutant intracellular proteins.
- Michael S. Hwang
- , Michelle S. Miller
- & Sandra B. Gabelli
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Article
| Open AccessBinding of regulatory proteins to nucleosomes is modulated by dynamic histone tails
The intrinsic disorder of histone tails poses challenges in their characterization. Here the authors apply extensive molecular dynamics simulations of the full nucleosome to show reversible binding to DNA with specific binding modes of different types of histone tails, where charge-altering modifications suppress tail-DNA interactions and may boost interactions between nucleosomes and nucleosome-binding proteins.
- Yunhui Peng
- , Shuxiang Li
- & Anna R. Panchenko
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Article
| Open AccessStructure of the native pyruvate dehydrogenase complex reveals the mechanism of substrate insertion
The pyruvate dehydrogenase complex (PDHc) is a large multienzyme complex that converts pyruvate into acetyl-coenzyme A and in E. coli the core of the PDHc is formed by 24 copies of dihydrolipoyl transacetylase. Here, the authors present the cryo-EM structure of the E. coli dihydrolipoyl transacetylase 24-mer core in a native resting state including lipoyl domains, and discuss the mechanism of substrate shuttling by the lipoyl domains.
- Jana Škerlová
- , Jens Berndtsson
- & Pål Stenmark
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Article
| Open AccessThe cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB
M. tuberculosis cytochrome bd oxidase is of interest as a TB drug target. Here, the authors present the 2.5 Å cryo-EM structure of M. tuberculosis cytochrome bd oxidase and identify a disulfide bond within the canonical quinol binding and oxidation domain (Q-loop) and a menaquinone-9 binding site at heme b595.
- Schara Safarian
- , Helen K. Opel-Reading
- & Hartmut Michel
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Article
| Open AccessStructure of the human marker of self 5-transmembrane receptor CD47
CD47 is a transmembrane receptor involved in the regulation of various signalling pathways and a promising target for immuno-oncology therapeutics. Here, the authors present the crystal structure of full-length human CD47 and provide insights into the molecular mechanism of CD47-mediated signalling.
- Gustavo Fenalti
- , Nicolas Villanueva
- & Kandasamy Hariharan
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Article
| Open AccessProcessive dynamics of the usher assembly platform during uropathogenic Escherichia coli P pilus biogenesis
Escherichia coli form pili structures in order to initiate infection of the urinary tract. Here, Thanassi et al., have solved the structures of pili assembly intermediates and provided insights into their biogenesis and assembly.
- Minge Du
- , Zuanning Yuan
- & David G. Thanassi
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Article
| Open AccessA quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions
m6A RNA post-transcriptional modification changes RNA hybridization kinetics. Here the authors show that the methylamino group can adopt syn-conformation pairing with uridine with a mismatch-like conformation in RNA duplex. They also develop a quantitative model that predicts how m6A affects the kinetics of hybridization.
- Bei Liu
- , Honglue Shi
- & Hashim M. Al-Hashimi
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Article
| Open AccessThe structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding
ParA is an ATPase involved in the segregation of newly replicated DNA in bacteria. Here, structures of a ParA filament bound to DNA and of ParA in various nucleotide states offer insight into its conformational changes upon DNA binding and filament assembly, including the basis for ParA’s cooperative binding to DNA.
- Alexandra V. Parker
- , Daniel Mann
- & Julien R. C. Bergeron
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Article
| Open AccessT cell receptor recognition of hybrid insulin peptides bound to HLA-DQ8
Epitopes formed by fusion of more than one self peptide, such as proinsulin and other β cell proteins, can result in the formation of non-self hybrid peptides that can potentially trigger autoimmune responses. Here the authors show how TRBV5 + T cell receptors are geared towards recognition of HLA-DQ8 bound hybrid peptides in patients with type 1 diabetes.
- Mai T. Tran
- , Pouya Faridi
- & Hugh H. Reid
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Article
| Open AccessPD-L1 degradation is regulated by electrostatic membrane association of its cytoplasmic domain
The cytoplasmic domain of PD-L1 (PD-L1-CD) is involved in regulating PD-L1 stability and degradation. Here the authors show that membrane binding of PD-L1-CD mediates the cellular levels of PD-L1, while metformin can disrupt the interaction between PD-L1-CD and the membrane to reduce PD-L1 levels.
- Maorong Wen
- , Yunlei Cao
- & Bo OuYang
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Article
| Open AccessDeciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC
KdpFABC is a high-affinity bacterial K+ pump which combines the ion channel-like KdpA and the P-type ATPase KdpB. Here, the authors elucidate the mechanisms underlying transport and the coupling to ATP hydrolysis, and provide evidence that ions are transported via an intersubunit tunnel through KdpA and KdpB.
- Jakob M. Silberberg
- , Robin A. Corey
- & Inga Hänelt
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Article
| Open AccessAn ester bond underlies the mechanical strength of a pathogen surface protein
Bacterial surface adhesion proteins are characterized by unusual mechanical properties. Here, the authors use atomic force microscopy-based technique to study a surface-anchoring protein Cpe0147 from Clostridium perfringens and show that an ester bond can withstand considerable mechanical forces and prevent complete protein unfolding.
- Hai Lei
- , Quan Ma
- & Yi Cao
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Article
| Open AccessThe antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter
Vilazodone (VLZ) is a drug for the treatment of major depressive disorders that targets the serotonin transporter (SERT). Here, the authors combine pharmacology measurements and cryo-EM structural analysis to characterize VLZ binding to SERT and observe that VLZ exhibits non-competitive inhibition of serotonin transport and binds with nanomolar affinity to an allosteric site in SERT.
- Per Plenge
- , Dongxue Yang
- & Claus J. Loland
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Article
| Open AccessMolecular recognition of an acyl-peptide hormone and activation of ghrelin receptor
Ghrelin is a gastric peptide hormone and its acylation is required for binding to and activation of the ghrelin receptor in the brain, which initiates appetite. Here, the authors present cryo-EM structures of the Gq-coupled ghrelin receptor bound to ghrelin and the synthetic agonist GHRP-6 and they describe how the acylated peptide hormone is recognised by the receptor, which is of interest for drug design.
- Yue Wang
- , Shimeng Guo
- & Yi Jiang
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Article
| Open AccessUbiD domain dynamics underpins aromatic decarboxylation
Understanding the structure and dynamics of enzymes is important for a number of applications. Here, the authors report on the crystal structure of vanillic acid decarboxylase, and show how the dynamics of the UbiD superfamily enzymes relate to the covalent catalysis of aromatic (de)carboxylation.
- Stephen A. Marshall
- , Karl A. P. Payne
- & David Leys
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Article
| Open AccessStructural basis for proficient oxidized ribonucleotide insertion in double strand break repair
The authors previously showed that pol μ lacks discrimination against oxidized dGTP (8-oxo-dGTP). Here they reveal the structural basis for proficient oxidized ribonucleotide (8-oxo-rGTP) incorporation during double strand break repair by pol μ.
- Joonas A. Jamsen
- , Akira Sassa
- & Samuel H. Wilson
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Article
| Open AccessA simple pressure-assisted method for MicroED specimen preparation
Micro-crystal electron diffraction (MicroED) has shown great potential for the structure determination of crystals that are too small for X-ray diffraction but MicroED sample preparation remains challenging. Here, the authors present Preassis, a pressure-assisted method for the preparation of MicroED specimens and demonstrate that Preassis can be applied to a wide range of protein crystal suspensions with low and high viscosities, as well as those with low crystal concentrations.
- Jingjing Zhao
- , Hongyi Xu
- & Xiaodong Zou
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Article
| Open AccessStructures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD
The ER chaperone BiP is regulated by FICD-mediated AMPylation and deAMPylation. Here, the authors characterise the structure of mammalian AMPylated BiP bound to FICD, by X-ray crystallography and neutron scattering, providing insights into the mechanism of BiP AMPylation and deAMPylation.
- Luke A. Perera
- , Steffen Preissler
- & David Ron
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Article
| Open AccessStructural basis for the inhibition of HTLV-1 integration inferred from cryo-EM deltaretroviral intasome structures
Human T-cell lymphotropic virus type 1 (HTLV-1) is an oncogenic deltaretrovirus. Here the authors provide structural characterization of the binding mechanism of novel integrase strand transfer inhibitor (INSTI) candidates to limit HTLV-1 infection.
- Michal S. Barski
- , Teresa Vanzo
- & Goedele N. Maertens
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Article
| Open AccessIn situ ultrastructures of two evolutionarily distant apicomplexan rhoptry secretion systems
The rhoptry is an apical secretory organelle of apicomplexan parasites that is essential for host cell invasion. Here, Mageswaran et al. provide in situ ultrastructures of rhoptries from two pathogens, revealing a conserved architecture including luminal filaments and a distinct docking mechanism.
- Shrawan Kumar Mageswaran
- , Amandine Guérin
- & Yi-Wei Chang
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Article
| Open AccessStructural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization
Bone morphogenetic protein (BMP) receptors are single pass transmembrane serine/threonine kinases that form tetrameric complexes comprised of two type I and two type II BMP receptors. Here the authors characterize a structure of an active type I/type II kinase tetramer providing insight into molecular mechanism driving ligand-induced signaling.
- Christopher Agnew
- , Pelin Ayaz
- & Natalia Jura
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Article
| Open AccessStructures of tmRNA and SmpB as they transit through the ribosome
Trans-translation, mediated by small protein B (SmpB) and transfer-messenger RNA (tmRNA), enables recycling of the ribosomes stalled on defective mRNAs in bacteria. Here, the authors report structures of the ribosome during trans-translation that reveal a translocation intermediate and elucidate the movements of the tmRNA-SmpB complex in the ribosome.
- Charlotte Guyomar
- , Gaetano D’Urso
- & Reynald Gillet
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Article
| Open AccessThe conformational stability of pro-apoptotic BAX is dictated by discrete residues of the protein core
The pro-apoptotic BAX protein is a monomer under homeostatic conditions and, in response to stress, transforms into oligomers that induce apoptosis. Here, the authors characterize structural features of BAX that individually stabilize the monomer while collectively contributing to oligomerization.
- Noah B. Bloch
- , Thomas E. Wales
- & Loren D. Walensky
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Article
| Open AccessCryo-EM structures of the TTYH family reveal a novel architecture for lipid interactions
The human Tweety homologue (TTYH) family of transmembrane proteins have been suggested to act as chloride channels. Here the authors present cryo-EM structures of the 3 human TTYH paralogs that do not display the expected features of an anion channel, and instead appear to interact with lipid-like compounds residing in the membrane; suggesting an involvement in lipid-associated processes.
- Anastasiia Sukalskaia
- , Monique S. Straub
- & Raimund Dutzler
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Article
| Open AccessStructure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase
The SARS-CoV-2 NSP13 helicase is essential for viral replication and of interest as a drug target. Here, the authors present the crystal structures of NSP13 in the apo form and bound to either phosphate or the non-hydrolysable ATP analog AMP-PNP and discuss the helicase mechanism. They also perform a crystallographic fragment screening and identify 65 bound fragments, which could help in the design of new antiviral agents.
- Joseph A. Newman
- , Alice Douangamath
- & Opher Gileadi
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Article
| Open AccessStructural basis for Ca2+ activation of the heteromeric PKD1L3/PKD2L1 channel
Hetero-oligomeric TRP-like channels such as PKD1L3/PKD2L1 play crucial roles in a range of physiological and pathophysiological processes. Here, the authors present the cryo-EM structures of a minimal functional murine PKD1L3/PKD2L1 complex in the absence and presence of calcium and further supported through structure-guided mutagenic studies, they discuss the mechanism of calcium-induced channel activation.
- Qiang Su
- , Mengying Chen
- & Yigong Shi
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Article
| Open AccessPolyclonal antibody responses to HIV Env immunogens resolved using cryoEM
Here, the authors present cryoEMPEM, a method for high-resolution structural analysis of vaccine-elicited polyclonal antibody responses. They apply cryoEMPEM in combination with standard serology experiments to characterize the polyclonal antibody (pAb) responses elicited in rhesus macaques by HIV Env trimer immunogens and were able to determine up to 8 different polyclonal antibody structures in complex with their respective antigen from a single cryoEM dataset.
- Aleksandar Antanasijevic
- , Leigh M. Sewall
- & Andrew B. Ward
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Article
| Open AccessCryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin
The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here, the authors employ an approach that uses cryo-EM single particle analysis to track the number and distribution of nucleotides bound to each subunit in the homo-oligomeric MmCpn archaeal chaperonin complex and observe that ATP binds in a statistically random manner to MmCpn both within a ring and across the rings, which shows that there is no cooperativity in ATP binding to archaeal group II chaperonins under the conditions used in this study.
- Yanyan Zhao
- , Michael F. Schmid
- & Wah Chiu
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Article
| Open AccessThe intervening domain is required for DNA-binding and functional identity of plant MADS transcription factors
MADS transcription factors regulate multiple aspects of plant development. Here the authors show that the intervening I domain is conserved in both type I and type II plant MADS lineages and contributes to the functional identity of the protein by influencing both DNA binding activity and dimerisation specificity.
- Xuelei Lai
- , Rosario Vega-Léon
- & Chloe Zubieta
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Article
| Open AccessCharacterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA
The cyanophage S-2L incorporates 2-aminoadenine (Z) instead of adenine into its DNA, which still pairs with thymine forming a triple hydrogen bond. Here, the authors identify a third gene mazZ located between purZ and datZ that is required for 2-aminoadenine biosynthesis and determine the crystal structures of MazZ and PurZ. They further show that co-expression of these three genes in E.coli enables 2-aminoadenine incorporation into the bacterial genome.
- Dariusz Czernecki
- , Frédéric Bonhomme
- & Marc Delarue
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Article
| Open AccessThe middle lipin domain adopts a membrane-binding dimeric protein fold
Lipins need to bind cell membranes before they can function as phosphatidic acid phosphatases. Here, the authors elucidate the structural basis of lipin membrane-association and identify a lipin domain with a novel protein fold that is critical for membrane binding and full functionality of lipins.
- Weijing Gu
- , Shujuan Gao
- & Michael V. Airola
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Article
| Open AccessSwitching at the ribosome: riboswitches need rProteins as modulators to regulate translation
Translational regulation by riboswitches is an important mechanism for the modulation of gene expression in bacteria. Here the authors show that the ligand-induced allosteric switch in the adenine-sensing riboswitch from V. vulnificus is insufficient and leads only to a partial opening of the ribosome binding site and requires interaction with 30S-bound ribosomal protein S1, which acts as an RNA chaperone.
- Vanessa de Jesus
- , Nusrat S. Qureshi
- & Boris Fürtig
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Article
| Open AccessPotent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes
Highly potent neutralizing nanobodies (Nbs) are of great interest as potential COVID-19 therapeutics. Here, the authors show that potent neutralizing Nbs targeting the receptor binding domain (RBD) of the SARS-CoV-2 spike protein are also effective against convergent variants of concern of the virus. They determine eight Nb-bound spike protein cryo-EM structures, classify the binding epitopes of the Nbs and discuss their neutralization mechanisms.
- Dapeng Sun
- , Zhe Sang
- & Yi Shi
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Article
| Open AccessMechanism of LolCDE as a molecular extruder of bacterial triacylated lipoproteins
In Gram-negative bacteria, lipoproteins are transported from the inner membrane (IM) to the outer membrane (OM) by the ATP-binding cassette (ABC) transporter LolCDE. Here the authors present cryo-EM structures of nanodisc-embedded LolCDE in different states, providing mechanistic insight into the transport mechanism.
- Stuti Sharma
- , Ruoyu Zhou
- & Maofu Liao
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Article
| Open AccessThe six steps of the complete F1-ATPase rotary catalytic cycle
F1Fo ATP synthase works using a rotary catalysis mechanism. Here, the authors report cryo-EM structures of Bacillus PS3 F1-ATPase encompassing the complete set of six states taken up during the catalytic cycle, including the binding- and catalytic-dwell states.
- Meghna Sobti
- , Hiroshi Ueno
- & Alastair G. Stewart
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Article
| Open AccessCryo-EM structure of mycobacterial cytochrome bd reveals two oxygen access channels
Cytochromes bd oxidase (Cyt-bd) catalyzes the reduction of oxygen to water and is the terminal oxidase in the respiratory chain of prokaryotes. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Cyt-bd and identify two potential oxygen access channels in the structure, which is of interest for the development of novel antituberculosis drugs.
- Weiwei Wang
- , Yan Gao
- & Hongri Gong
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Article
| Open AccessStructural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation
Translational frameshifting is a mechanism that expands the coding capabilities of mRNA. Here, structures of 70S ribosome complexes with GTPase elongation factor G (EF-G), a +1-frameshifting-prone mRNA and tRNAs reveal the cooperation between the ribosome and EF-G to induce +1 frameshifting during the translocation step.
- Gabriel Demo
- , Howard B. Gamper
- & Andrei A. Korostelev
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Article
| Open AccessStructural evidence for extracellular silica formation by diatoms
Silica formation in diatoms is of interest for a range of different subjects from biomimetics to oceanography. Here the authors study the formation of silicified extensions in diatoms and find that unlike cell wall elements, that form in the cytoplasm, the extensions have a different formation mechanism outside the cytoplasm.
- Boaz Mayzel
- , Lior Aram
- & Assaf Gal
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Article
| Open AccessA synthetic nanobody targeting RBD protects hamsters from SARS-CoV-2 infection
Here, the authors report the engineering, structural and biological characterization of synthetic nanobodies (sybodies) that display potent therapeutic activity against SARS-CoV-2 infection in animal models via targeting the virus receptor-binding domain.
- Tingting Li
- , Hongmin Cai
- & Dianfan Li
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Article
| Open AccessCorrelative multi-scale cryo-imaging unveils SARS-CoV-2 assembly and egress
In this study, Peijun Zhang and colleagues use cryoFIB/SEM volume imaging and soft x-ray cryo-tomography with cryo-electron tomography (cryoET) of cellular periphery, lamellae, and subtomogram averaging to place critical structural events in the SARS-CoV-2 infection cycle in the context of whole-cell images.
- Luiza Mendonça
- , Andrew Howe
- & Peijun Zhang
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Article
| Open AccessBRCA2 binding through a cryptic repeated motif to HSF2BP oligomers does not impact meiotic recombination
BRCA2 and its interactor HSF2BP are required for meiotic recombination. Here, the authors define the interaction structurally, revealing that a repeat in BRCA2 binds two HSF2BP units, increasing the affinity. This region is, however, not essential for mouse meiosis.
- Rania Ghouil
- , Simona Miron
- & Alex N. Zelensky
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Article
| Open AccessAntibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W
UBE2W catalyzes the ubiquitination of protein N-termini but its substrate spectrum is largely unknown. Here, the authors discover mAbs selective for peptides derived from N-terminally ubiquitinated proteins, solve the structure of a peptide-bound mAb and apply the mAbs to map endogenous UBE2W substrates by proteomics.
- Christopher W. Davies
- , Simon E. Vidal
- & James T. Koerber
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Article
| Open AccessPALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis
The polycomb repressive complex 2 (PRC2) is a histone methyltransferase regulating cell differentiation and identity. Here, the authors show that the vertebrate-specific PRC2 accessory subunit PALI1 facilitates substrate binding by the complex and elucidate the allosteric mechanism of PALI1- mediated PRC2 activation.
- Qi Zhang
- , Samuel C. Agius
- & Chen Davidovich
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Article
| Open AccessMechanistic insights into the three steps of poly(ADP-ribosylation) reversal
PARG and ARH3 are the main hydrolases to reverse serine poly(ADP-ribosylation) yet their activities in the process differ. Here, the authors synthesise linear and branched poly(ADP-ribose) molecules, perform structure-function analysis and elucidate the mechanistic differences between PARG and ARH3.
- Johannes Gregor Matthias Rack
- , Qiang Liu
- & Ivan Ahel
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Article
| Open AccessStructural basis for genome packaging, retention, and ejection in human cytomegalovirus
Human cytomegalovirus (HCMV) is the prototypical member of the β-herpesvirinae subfamily and the leading viral cause of congenital infections that can lead to birth defects and it can also cause life-threatening disease in immunocompromised individuals. Here, the authors present the in-situ cryo-EM structures of the symmetry-mismatched portal and the capsid vertex-specific components (CVSCs) of HCMV and discuss the mechanistic implications for genome package, retention and ejection.
- Zhihai Li
- , Jingjing Pang
- & Xuekui Yu
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Article
| Open AccessAn enzymatic activation of formaldehyde for nucleotide methylation
The bacterial thymidylate synthase ThyX catalyzes the reductive methylation of deoxyuridylate (dUMP) into deoxythymidylate (dTMP) and requires both folate and flavin for activity. Here, the authors combine biochemical experiments, spectroscopic measurements and flavin synthesis chemistry to show that formaldehyde (CH2O) can replace the natural methylene donor of ThyX in a CH2O-shunt reaction, yielding a carbinolamine intermediate with the reduced flavin coenzyme, and they present the crystal structure of this intermediate.
- Charles Bou-Nader
- , Frederick W. Stull
- & Djemel Hamdane
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Article
| Open AccessA distinct assembly pathway of the human 39S late pre-mitoribosome
Assembly of the mitoribosome requires assistance from numerous specialized factors. Here, structures of the human 39S late assembly intermediates identify several assembly factors which keep the 16S rRNA in immature conformations, and reveal deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly.
- Jingdong Cheng
- , Otto Berninghausen
- & Roland Beckmann
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Article
| Open AccessCryo-EM structure of human Wntless in complex with Wnt3a
The transmembrane protein Wntless (WLS) is essential for the secretion of Wnt proteins, which are signaling molecules of the Wnt signaling pathways. Here, the authors present the 2.2 Å cryo-EM structure of human WLS in complex with Wnt3a and discuss mechanistic implications for the palmitoleoylation of Wnt3a that is required for WLS mediated Wnt secretion.
- Qing Zhong
- , Yanyu Zhao
- & Dan Ma