Articles

  • Article |

    TET2 promotes the conversion of 5-methylcytosine to 5-hydroxymethylcytosine on tRNAs and affects the processing or stability of different classes of tRNA fragments.

    • Chongsheng He
    • , Julianna Bozler
    • , Kevin A. Janssen
    • , Jeremy E. Wilusz
    • , Benjamin A. Garcia
    • , Andrea J. Schorn
    •  & Roberto Bonasio
  • Article |

    Cryo-EM structures, along with transport assays with proteoliposomes and bacterial growth analyses, show that the Escherichia coli Mla complex mediates ATP-dependent retrograde transport of phospholipids.

    • Xiaodi Tang
    • , Shenghai Chang
    • , Wen Qiao
    • , Qinghua Luo
    • , Yuejia Chen
    • , Zhiying Jia
    • , James Coleman
    • , Ke Zhang
    • , Ting Wang
    • , Zhibo Zhang
    • , Changbin Zhang
    • , Xiaofeng Zhu
    • , Xiawei Wei
    • , Changjiang Dong
    • , Xing Zhang
    •  & Haohao Dong
  • Article |

    Ultra-low-input native ChIP-seq analyses of genome-wide histone H3.3 distribution during early mouse development reveal a CAF-1-dependent transition from a non-canonical pattern in the oocyte and zygote to a canonical distribution at the two-cell stage.

    • Takashi Ishiuchi
    • , Shusaku Abe
    • , Kimiko Inoue
    • , Wan Kin Au Yeung
    • , Yuka Miki
    • , Atsuo Ogura
    •  & Hiroyuki Sasaki
  • Article |

    Cryo-EM and liposome assays reveal that Atg9 functions as a lipid scramblase, transporting phospholipids between inner and outer liposome leaflets. Analyses of mutants in yeast support a role for this activity in autophagy.

    • Kazuaki Matoba
    • , Tetsuya Kotani
    • , Akihisa Tsutsumi
    • , Takuma Tsuji
    • , Takaharu Mori
    • , Daisuke Noshiro
    • , Yuji Sugita
    • , Norimichi Nomura
    • , So Iwata
    • , Yoshinori Ohsumi
    • , Toyoshi Fujimoto
    • , Hitoshi Nakatogawa
    • , Masahide Kikkawa
    •  & Nobuo N. Noda
  • Article |

    Cryo-EM analyses together with liposome and cellular assays reveal that human ATG9A forms a trimer that mediates phospholipid flipping and promotes autophagosome membrane expansion.

    • Shintaro Maeda
    • , Hayashi Yamamoto
    • , Lisa N. Kinch
    • , Christina M. Garza
    • , Satoru Takahashi
    • , Chinatsu Otomo
    • , Nick V. Grishin
    • , Stefano Forli
    • , Noboru Mizushima
    •  & Takanori Otomo
  • Article |

    A new cryo-EM structure of human DNA-PKcs in complex with a Ku70/80 heterodimer and DNA reveals how Ku80–DNA-PKcs interactions create a scaffold to mediate DNA double-strand break repair.

    • Amanda K. Chaplin
    • , Steven W. Hardwick
    • , Shikang Liang
    • , Antonia Kefala Stavridi
    • , Ales Hnizda
    • , Lee R. Cooper
    • , Taiana Maia De Oliveira
    • , Dimitri Y. Chirgadze
    •  & Tom L. Blundell
  • Article |

    The solid-state NMR structure of an amyloid fiber formed by human hormone β-endorphin reveals a protonated Glu8 in the fibrillar core. Under neutral conditions, deprotonation of Glu8 would contribute to fibril disassembly and hormone peptide release.

    • Carolin Seuring
    • , Joeri Verasdonck
    • , Julia Gath
    • , Dhimam Ghosh
    • , Nadezhda Nespovitaya
    • , Marielle Aulikki Wälti
    • , Samir K. Maji
    • , Riccardo Cadalbert
    • , Peter Güntert
    • , Beat H. Meier
    •  & Roland Riek
  • Article |

    Proteomic definition of the telomeric PARylome combined with genetic and histone H3.3 deposition assays at telomeres reveals that PAR-regulated HIRA activity compensates for loss of ATRX in ALT cells.

    • Song My Hoang
    • , Nicole Kaminski
    • , Ragini Bhargava
    • , Jonathan Barroso-González
    • , Michelle L. Lynskey
    • , Laura García-Expósito
    • , Justin L. Roncaioli
    • , Anne R. Wondisford
    • , Callen T. Wallace
    • , Simon C. Watkins
    • , Dominic I. James
    • , Ian D. Waddell
    • , Donald Ogilvie
    • , Kate M. Smith
    • , Felipe da Veiga Leprevost
    • , Dattatreya Mellacharevu
    • , Alexey I. Nesvizhskii
    • , Jianfeng Li
    • , Dominique Ray-Gallet
    • , Robert W. Sobol
    • , Genevieve Almouzni
    •  & Roderick J. O’Sullivan
  • Article |

    A new X-ray crystal structure and supporting biochemical analyses of the human cardiac calsequestrin polymer reveal the basis of filament assembly and map disease-associated mutations to the multimerization interface.

    • Erron W. Titus
    • , Frederick H. Deiter
    • , Chenxu Shi
    • , Julianne Wojciak
    • , Melvin Scheinman
    • , Natalia Jura
    •  & Rahul C. Deo
  • Article |

    Atomic force microscopy imaging of yeast condensin indicates that condensin may extrude DNA by switching conformation between open O and collapsed B shapes, indicative of a type of scrunching model.

    • Je-Kyung Ryu
    • , Allard J. Katan
    • , Eli O. van der Sluis
    • , Thomas Wisse
    • , Ralph de Groot
    • , Christian H. Haering
    •  & Cees Dekker
  • Article |

    The effects of four antibodies on the aggregation pathway of Aβ are examined via an in-depth kinetics approach, revealing the specific molecular steps affected by each antibody.

    • Sara Linse
    • , Tom Scheidt
    • , Katja Bernfur
    • , Michele Vendruscolo
    • , Christopher M. Dobson
    • , Samuel I. A. Cohen
    • , Eimantas Sileikis
    • , Martin Lundqvist
    • , Fang Qian
    • , Tiernan O’Malley
    • , Thierry Bussiere
    • , Paul H. Weinreb
    • , Catherine K. Xu
    • , Georg Meisl
    • , Sean R. A. Devenish
    • , Tuomas P. J. Knowles
    •  & Oskar Hansson
  • Article |

    Crystal structures of BAK core domain dimers suggest a mechanism by which lipids contribute to the oligomerization of BAK, which is essential for BAK-mediated permeabilization of the mitochondrial outer membrane.

    • Angus D. Cowan
    • , Nicholas A. Smith
    • , Jarrod J. Sandow
    • , Eugene A. Kapp
    • , Yepy H. Rustam
    • , James M. Murphy
    • , Jason M. Brouwer
    • , Jonathan P. Bernardini
    • , Michael J. Roy
    • , Ahmad Z. Wardak
    • , Iris K. Tan
    • , Andrew I. Webb
    • , Jacqueline M. Gulbis
    • , Brian J. Smith
    • , Gavin E. Reid
    • , Grant Dewson
    • , Peter M. Colman
    •  & Peter E. Czabotar
  • Article |

    Cryo-EM structures of the entire mammalian F1Fo ATPase reveal several new features and details on the proton translocation pathway and suggest a model for the opening of the permeability transition pore.

    • Gergely Pinke
    • , Long Zhou
    •  & Leonid A. Sazanov
  • Article |

    Cryo-EM structural analysis reveals the mechanism by which the SARS-CoV-2 protein Nsp1 inhibits global translation.

    • Katharina Schubert
    • , Evangelos D. Karousis
    • , Ahmad Jomaa
    • , Alain Scaiola
    • , Blanca Echeverria
    • , Lukas-Adrian Gurzeler
    • , Marc Leibundgut
    • , Volker Thiel
    • , Oliver Mühlemann
    •  & Nenad Ban
  • Article |

    Structures of HIV-1 capsid protein (CA) in tubular assemblies, determined by MAS-NMR, reveal the basis of CA’s conformational plasticity.

    • Manman Lu
    • , Ryan W. Russell
    • , Alexander J. Bryer
    • , Caitlin M. Quinn
    • , Guangjin Hou
    • , Huilan Zhang
    • , Charles D. Schwieters
    • , Juan R. Perilla
    • , Angela M. Gronenborn
    •  & Tatyana Polenova
  • Article |

    ERV-specific enhancer-based networks regulate species-specific transcriptomes in mammalian spermatogenesis.

    • Akihiko Sakashita
    • , So Maezawa
    • , Kazuki Takahashi
    • , Kris G. Alavattam
    • , Masashi Yukawa
    • , Yueh-Chiang Hu
    • , Shohei Kojima
    • , Nicholas F. Parrish
    • , Artem Barski
    • , Mihaela Pavlicev
    •  & Satoshi H. Namekawa
  • Article |

    In situ cryo-ET analyses of Borrelia burgdorferi flagellar motors locked in clockwise or counterclockwise rotation provide insights into rotational switching.

    • Yunjie Chang
    • , Kai Zhang
    • , Brittany L. Carroll
    • , Xiaowei Zhao
    • , Nyles W. Charon
    • , Steven J. Norris
    • , Md A. Motaleb
    • , Chunhao Li
    •  & Jun Liu
  • Article |

    Cryo-EM, X-ray crystallography and mutational analyses reveal how Dengue and Zika virus protein NS5 suppresses STAT2 activity and interferon response in host cells.

    • Boxiao Wang
    • , Stephanie Thurmond
    • , Kang Zhou
    • , Maria T. Sánchez-Aparicio
    • , Jian Fang
    • , Jiuwei Lu
    • , Linfeng Gao
    • , Wendan Ren
    • , Yanxiang Cui
    • , Ethan C. Veit
    • , HeaJin Hong
    • , Matthew J. Evans
    • , Seán E. O’Leary
    • , Adolfo García-Sastre
    • , Z. Hong Zhou
    • , Rong Hai
    •  & Jikui Song
  • Article |

    A combination of structural and protein-chemistry approaches along with phylogenetic analyses provide insights into the specific activities of mouse tubulin tyrosine ligase-like enzymes as initiases or elongases of glutamylation.

    • Kishore K. Mahalingan
    • , E. Keith Keenan
    • , Madeleine Strickland
    • , Yan Li
    • , Yanjie Liu
    • , Haydn L. Ball
    • , Martin E. Tanner
    • , Nico Tjandra
    •  & Antonina Roll-Mecak
  • Article |

    A combination of cell-based and biochemical approaches reveals how oncogenic fusion protein SS18-SSX directs BAF complexes to H2AK119Ub-modified nucleosomes to remodel chromatin at cancer-specific gene targets.

    • Matthew J. McBride
    • , Nazar Mashtalir
    • , Evan B. Winter
    • , Hai T. Dao
    • , Martin Filipovski
    • , Andrew R. D’Avino
    • , Hyuk-Soo Seo
    • , Neil T. Umbreit
    • , Roodolph St. Pierre
    • , Alfredo M. Valencia
    • , Kristin Qian
    • , Hayley J. Zullow
    • , Jacob D. Jaffe
    • , Sirano Dhe-Paganon
    • , Tom W. Muir
    •  & Cigall Kadoch
  • Article |

    The SARS-CoV-2 spike glycoprotein is flexible, and its receptor-binding domain (RBD) fluctuates between open and closed conformations. Disulfide bonds are engineered into the spike ectodomain to lock the RBD in the closed state, leading to a construct with high thermostability.

    • Xiaoli Xiong
    • , Kun Qu
    • , Katarzyna A. Ciazynska
    • , Myra Hosmillo
    • , Andrew P. Carter
    • , Soraya Ebrahimi
    • , Zunlong Ke
    • , Sjors H. W. Scheres
    • , Laura Bergamaschi
    • , Guinevere L. Grice
    • , Ying Zhang
    • , John Bradley
    • , Paul A. Lyons
    • , Kenneth G. C. Smith
    • , Mark Toshner
    • , Anne Elmer
    • , Carla Ribeiro
    • , Jenny Kourampa
    • , Sherly Jose
    • , Jane Kennet
    • , Jane Rowlands
    • , Anne Meadows
    • , Criona O’Brien
    • , Rebecca Rastall
    • , Cherry Crucusio
    • , Sarah Hewitt
    • , Jane Price
    • , Jo Calder
    • , Laura Canna
    • , Ashlea Bucke
    • , Hugo Tordesillas
    • , Julie Harris
    • , Valentina Ruffolo
    • , Jason Domingo
    • , Barbara Graves
    • , Helen Butcher
    • , Daniela Caputo
    • , Emma Le Gresley
    • , Benjamin J. Dunmore
    • , Jennifer Martin
    • , Ekaterina Legchenko
    • , Carmen Treacy
    • , Christopher Huang
    • , Jennifer Wood
    • , Rachel Sutcliffe
    • , Josh Hodgson
    • , Joy Shih
    • , Stefan Graf
    • , Zhen Tong
    • , Federica Mescia
    • , Tobias Tilly
    • , Ciara O’Donnell
    • , Kelvin Hunter
    • , Linda Pointon
    • , Nicole Pond
    • , Marta Wylot
    • , Emma Jones
    • , Stuart Fawke
    • , Ben Bullman
    • , Laura Bergamaschi
    • , Lori Turner
    • , Isobel Jarvis
    • , Ommar Omarjee
    • , Aloka De Sa
    • , Joe Marsden
    • , Ariana Betancourt
    • , Marianne Perera
    • , Maddie Epping
    • , Nathan Richoz
    • , Georgie Bower
    • , Rahul Sharma
    • , Francesca Nice
    • , Oisin Huhn
    • , Hannah Stark
    • , Neil Walker
    • , Kathy Stirrups
    • , Nigel Ovington
    • , Eleanor Dewhust
    • , Emily Li
    • , Sofia Papadia
    • , James A. Nathan
    • , Stephen Baker
    • , Leo C. James
    • , Helen E. Baxendale
    • , Ian Goodfellow
    • , Rainer Doffinger
    •  & John A. G. Briggs
  • Article |

    EY6A, a neutralizing antibody isolated from a patient convalescing from COVID-19, binds the receptor binding domain of the SARS-CoV-2 spike glycoprotein with high affinity, at a location away from the binding site for the ACE2 receptor, similar to the one recognized by CR3022.

    • Daming Zhou
    • , Helen M. E. Duyvesteyn
    • , Cheng-Pin Chen
    • , Chung-Guei Huang
    • , Ting-Hua Chen
    • , Shin-Ru Shih
    • , Yi-Chun Lin
    • , Chien-Yu Cheng
    • , Shu-Hsing Cheng
    • , Yhu-Chering Huang
    • , Tzou-Yien Lin
    • , Che Ma
    • , Jiandong Huo
    • , Loic Carrique
    • , Tomas Malinauskas
    • , Reinis R. Ruza
    • , Pranav N. M. Shah
    • , Tiong Kit Tan
    • , Pramila Rijal
    • , Robert F. Donat
    • , Kerry Godwin
    • , Karen R. Buttigieg
    • , Julia A. Tree
    • , Julika Radecke
    • , Neil G. Paterson
    • , Piyada Supasa
    • , Juthathip Mongkolsapaya
    • , Gavin R. Screaton
    • , Miles W. Carroll
    • , Javier Gilbert-Jaramillo
    • , Michael L. Knight
    • , William James
    • , Raymond J. Owens
    • , James H. Naismith
    • , Alain R. Townsend
    • , Elizabeth E. Fry
    • , Yuguang Zhao
    • , Jingshan Ren
    • , David I. Stuart
    •  & Kuan-Ying A. Huang
  • Article |

    A crystal structure of bacterial multidrug transporter LmrP reveals the presence of a lipid inside the substrate binding cavity, with MD simulations and mutational analyses suggesting it could be involved in broad substrate specificity.

    • Vincent Debruycker
    • , Andrew Hutchin
    • , Matthieu Masureel
    • , Emel Ficici
    • , Chloé Martens
    • , Pierre Legrand
    • , Richard A. Stein
    • , Hassane S. Mchaourab
    • , José D. Faraldo-Gómez
    • , Han Remaut
    •  & Cédric Govaerts
  • Article |

    Massively parallel reporter assays from a synthetic mRNA library identify sequence features of 5′ UTRs that control mRNA translatability and reveal ribosome-dependent and ribosome-independent mRNA-surveillance pathways.

    • Longfei Jia
    • , Yuanhui Mao
    • , Quanquan Ji
    • , Devin Dersh
    • , Jonathan W. Yewdell
    •  & Shu-Bing Qian
  • Article |

    Crystallography and mutagenesis analyses examine how HIV-1 Nef interacts with AP2 to enable CD4 binding and downregulation and reveal the role of a Nef pocket that is also involved in downregulation of class I MHC.

    • Yonghwa Kwon
    • , Robyn M. Kaake
    • , Ignacia Echeverria
    • , Marissa Suarez
    • , Mohammad Karimian Shamsabadi
    • , Charlotte Stoneham
    • , Peter W. Ramirez
    • , Jacob Kress
    • , Rajendra Singh
    • , Andrej Sali
    • , Nevan Krogan
    • , John Guatelli
    •  & Xiaofei Jia
  • Article |

    The SARS-CoV-2 spike glycoprotein is flexible, and its receptor-binding domain (RBD) fluctuates between up or down conformations. Mutations engineered into the spike ectodomain either lock the RBD in the down state or make it adopt the up conformation more readily.

    • Rory Henderson
    • , Robert J. Edwards
    • , Katayoun Mansouri
    • , Katarzyna Janowska
    • , Victoria Stalls
    • , Sophie M. C. Gobeil
    • , Megan Kopp
    • , Dapeng Li
    • , Rob Parks
    • , Allen L. Hsu
    • , Mario J. Borgnia
    • , Barton F. Haynes
    •  & Priyamvada Acharya
  • Article |

    Two nanobodies that bind SARS-CoV-2 spike RBD are shown to block interaction with receptor ACE2 and thus neutralize the virus, and have an additive effect with antibody CR3022.

    • Jiangdong Huo
    • , Audrey Le Bas
    • , Reinis R. Ruza
    • , Helen M. E. Duyvesteyn
    • , Halina Mikolajek
    • , Tomas Malinauskas
    • , Tiong Kit Tan
    • , Pramila Rijal
    • , Maud Dumoux
    • , Philip N. Ward
    • , Jingshan Ren
    • , Daming Zhou
    • , Peter J. Harrison
    • , Miriam Weckener
    • , Daniel K. Clare
    • , Vinod K. Vogirala
    • , Julika Radecke
    • , Lucile Moynié
    • , Yuguang Zhao
    • , Javier Gilbert-Jaramillo
    • , Michael L. Knight
    • , Julia A. Tree
    • , Karen R. Buttigieg
    • , Naomi Coombes
    • , Michael J. Elmore
    • , Miles W. Carroll
    • , Loic Carrique
    • , Pranav N. M. Shah
    • , William James
    • , Alain R. Townsend
    • , David I. Stuart
    • , Raymond J. Owens
    •  & James H. Naismith
  • Article |

    Live-cell single-molecule imaging reveals that the rate-limiting step in AGO2-mediated mRNA cleavage frequently involves unmasking of target sites by translating ribosomes.

    • Suzan Ruijtenberg
    • , Stijn Sonneveld
    • , Tao Ju Cui
    • , Ive Logister
    • , Dion de Steenwinkel
    • , Yao Xiao
    • , Ian J. MacRae
    • , Chirlmin Joo
    •  & Marvin E. Tanenbaum
  • Article |

    Disulfide-bond formation between a cysteine pair at the groove and C-terminal α-helix of the anti-apoptotic protein BFL-1 operates as a redox switch that controls the accessibility of the protein’s anti-apoptotic pocket, which is important for the regulation of pro-apoptotic BCL-2 family members.

    • Kyle J. Korshavn
    • , Thomas E. Wales
    • , Gregory H. Bird
    • , John R. Engen
    •  & Loren D. Walensky