Volume 18 Issue 12, December 2011

The editors of Nature Structural & Molecular Biology have assembled a special Essay Collection, coinciding with the 40th anniversary of the Protein Data Bank, to reflect on the history and future of structural biology. These personal accounts collectively tell the history of structural biology and provide perspectives on the direction of the field and challenges that it faces.

Until recently, few potent and broadly neutralizing HIV-specific antibodies had been identified, but recent findings have inspired optimism that an effective HIV vaccine can finally be developed. Here we review these studies, which used state-of-the-art high-throughput techniques to collectively describe hundreds of new potent and broad HIV-neutralizing antibodies isolated from HIV-infected individuals.

The mechanism by which the noncanonical E1-like enzyme Atg7 activates ubiquitin-like Atg8 to trigger autophagy has not been well understood. The crystal structures of the N-terminal domain of Atg7 alone and C-terminal domain of Atg7 in complex with Atg8 show that this probably proceeds without the need for dramatic conformational rearrangements by Atg7, distinct from other E1 enzymes.

Oncogenic activation can generate replicative stress, leading to activation of ATR and Chk1. The hypothesis that these events could be exploited to selectively kill cancer cells is now demonstrated in vivo, using mouse models for cancer development. Myc-driven tumors are shown to be sensitive to ATR deficiency or inhibition of Chk1.

Restoration of p53 activity is a promising chemotherapeutic approach, and because of the high binding affinity between HAUSP, MDM2 and p53, blocking HAUSP activity should have the net effect of robust p53 stabilization. HAUSP is inhibited by belt-like binding of vIRF4 from Kaposi's sarcoma–associated herpesvirus. Two peptides derived from vIRF4 can additively inhibit HAUSP, leading to p53-dependent cell cycle arrest and xenograft tumor regression.

The E3 ubiquitin ligases RNF8 and RNF168 are required for recruitment of tumor surpressor 53BP1 to sites of DNA double-strand breaks. The reasons for this have been unclear, as 53BP1 recognizes histone mark H4K20me2. Now the AAA-ATPase VCP and cofactors are shown to be recruited in a ubiquitination-dependent manner to double-strand break sites, where they remove polycomb protein L3MBTL1 from chromatin.

The RITS complex links the RNAi pathway with centromeric heterochromatin formation in fission yeast and comprises the chromodomain protein Chp1, the GW protein Tas3 and the argonaute protein Ago1. X-ray analysis of the structured core of the Chp1–Tas3 subcomplex reveals the presence of a C-terminal PIN domain in Chp1, which contributes to post-transcriptional gene silencing of subtelomeric transcripts independently of RNAi.

Histone acetyltransferase Tip60 is required to activate several target genes of ERα. Now Tip60 is shown to interact directly with ERα and to recognize the enhancer marker H3K4me1, leading to transcriptional activation in response to estrogen.

The enzyme Rubisco has a central role in atmospheric CO₂ fixation. Rubisco can be inactivated if its sugar substrate is bound prior to carbamylation of a residue in the active site. The structure of tobacco Rca, the enzyme that removes the bound sugar substrate and activates Rubisco, is now presented, offering insight into this process.

Telomerase uses its associated RNA as a template for processive addition of telomeric DNA repeats. Biochemistry and smFRET analysis are now used to investigate how the RNA template moves along the active site, revealing an accordion mechanism whereby the regions flanking the template alternate between extended and compacted forms.

SRP-type GTPases deviate from other GTPases in that they are not activated by GTPase-activating proteins (GAPs). New studies show that the MinD-type protein YlxH activates the SRP-GTPase FlhF, which is involved in flagellar biosynthesis. The crystal structure of the Bacillus subtilis FlhF–effector complex reveals the mechanism of activation, the general concept of which may also apply to RNA-mediated activation of the SRP-GTPases Ffh and FtsY.

NSP and Cas family proteins form multidomain signaling platforms that integrate signals to mediate cell migration and invasion. Structural analyses show that the C-terminal domain of human NSP protein BCAR3 adopts the Cdc25-homology fold of Ras GTPase exchange factors, but in a closed conformation incompatible with enzymatic activity. Instead, this closed conformation is instrumental for interactions with Cas proteins.

The EGFR receptor tyrosine kinase is frequently mutated in lung cancer, but the mechanism by which mutations activate kinase activity are not clear. Using purified, nearly full-length EGFR, it is now seen that mutations drive activation and resistance to inhibitors through the formation of the asymmetric kinase domain dimer.

What happens to histones during transcription is not well understood. Atomic force microscopy snapshots of RNA polymerase II (Pol II)-nucleosome complexes before, during and after transcription show the presence of looped transcriptional intermediates. In addition, a fraction of transcribed histones are remodeled to hexasomes, and the size of this fraction depends on the elongation rate of Pol II.

Rnf8 is an E3 ligase involved in the DNA damage response, adding ubiquitin moieties to histones H2A and H2AX at sites of DNA damage. Now Rnf8 is found to modify shelterin subunit Tpp1, and this is important for its stability and retention at telomeres. Cells lacking Rnf8 show telomere shortening and chromosome fusions.

In fission yeast, the DNA damage kinases Tel1 (ATM) and Rad3 (ATR) are required to recruit telomerase to telomere. The relevant target for these kinases is now identified: shelterin subunit Ccq1 is phosphorylated at Thr93 in a Tel1/Rad3-dependent manner, and this modification is essential for Ccq1 to interact with telomerase subunit Est1.

Dimethylated arginine (DMA) marks are recognized by Tudor domain–containing proteins and play a role in the assembly of ribonucleoprotein complexes. Structural analysis of prototypic Tudor domains from SMN and SPF30 in complex with DMA reveals the recognition mode of DMA, enabling the design of an optimized binding pocket.

Common fragile sites (CFSs) can drive genomic instability. The basis for their fragile nature is not clear, but lymphocyte CFSs have been mapped to regions with low replication initiation events and late replication completion. These features are now used to rapidly identify CFSs in different fibroblast cells.

The surface glycoprotein of the distinct ebolavirus responsible for the largest outbreak yet described (Sudan Gulu) has been crystallized in complex with a novel, neutralizing antibody. The crystal structure and accompanying in vitro and in vivo experiments demonstrate that the antibody functions after virus entry and illustrates a key hotspot for ebolavirus neutralization.

The FET family proteins FUS, EWSR1 and TAF15 are RNA-binding proteins with diverse nuclear functions. PAR-CLIP analyses now reveal the genome-wide RNA targets of all three human FET proteins and of two FUS mutants that cause amyotrophic lateral sclerosis. Although the RNA-binding properties of the mutants remain unchanged, the spectrum of RNA targets is altered because of the changed subcellular localization of the mutants.

The Fanconi anemia (FA) DNA-repair pathway is important in processing of DNA interstrand cross-links and in resistance to exogenously added aldehyde. Genetic analyses now reveal the synthetic lethality of deficiencies in the FA pathway and formaldehyde catabolism, indicting that this pathway repairs lesions caused by endogenous formaldehyde.

Co-transcriptional splicing has been seen in lower eukaryotes as well as for a few mammalian genes, but the extent to which it affects mammalian gene regulation has been unclear. RNA sequencing now shows that co-transcriptional splicing is widespread in human cells and particularly abundant in the human brain.