ArticleMolecular & cellular proteomics : MCP2014
Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.
Article in Molecular & cellular proteomics : MCP, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers.
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118 citing papers in PubMed.
- Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS.Nature communications · 2026Article
- Structural basis for the recruitment and selective phosphorylation of Akt by mTORC2.Science (New York, N.Y.) · 2026Article
- RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.Nucleic acids research · 2026Article
- Bound or unbound: mapping and monitoring receptor oligomerization by time-resolved fluorescence live-cell imaging.Frontiers in molecular biosciences · 2026Article
- MolViewSpec: a Mol* extension for describing and sharing molecular visualizations.Nucleic acids research · 2025Article
- Tutorial on integrative spatiotemporal modeling by integrative modeling platform.Protein science : a publication of the Protein Society · 2025Article
- Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex.Communications chemistry · 2024Article
- IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.Journal of molecular biology · 2024Article
- Progress in mass spectrometry approaches to profiling protein-protein interactions in the studies of the innate immune system.Journal of proteins and proteomics · 2024Article
- An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II.Molecular cell · 2024Article
- Optimizing representations for integrative structural modeling using Bayesian model selection.Bioinformatics (Oxford, England) · 2024Article
- Article
- The Cytotoxic Mycobacteriophage Protein Phaedrus gp82 Interacts with and Modulates the Activity of the Host ATPase, MoxR.Journal of molecular biology · 2023Article
- All-in-One Pseudo-MSJournal of the American Society for Mass Spectrometry · 2023Article
- Implications of a multiscale structure of the yeast nuclear pore complex.Molecular cell · 2023Article
- MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows at High Sensitivity and Specificity.Journal of proteome research · 2023Article
- Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae.Nucleic acids research · 2023Article
- Integrative structure determination of histones H3 and H4 using genetic interactions.The FEBS journal · 2023Article
- Exploring an Alternative Cysteine-Reactive Chemistry to Enable Proteome-Wide PPI Analysis by Cross-Linking Mass Spectrometry.Analytical chemistry · 2023Article
- Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future.Biophysical reviews · 2022Review
58 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼ 600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope.
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