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Open data
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Basic information
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Title | Human nuclear pore complex (constricted) | |||||||||
![]() | Structure of the human nuclear pore complex from isolated nuclear envelopes | |||||||||
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![]() | multiprotein complex / nucleocytoplasmic transport / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() cytoplasmic side of nuclear pore / nuclear pore transmembrane ring / GATOR2 complex / nephron development / centriole assembly / positive regulation of centriole replication / cytoplasmic periphery of the nuclear pore complex / regulation of protein import into nucleus / regulation of Ras protein signal transduction / HuR (ELAVL1) binds and stabilizes mRNA ...cytoplasmic side of nuclear pore / nuclear pore transmembrane ring / GATOR2 complex / nephron development / centriole assembly / positive regulation of centriole replication / cytoplasmic periphery of the nuclear pore complex / regulation of protein import into nucleus / regulation of Ras protein signal transduction / HuR (ELAVL1) binds and stabilizes mRNA / positive regulation of mitotic cytokinetic process / Seh1-associated complex / SUMO ligase complex / SUMO ligase activity / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / annulate lamellae / nuclear pore localization / regulation of nucleocytoplasmic transport / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / atrial cardiac muscle cell action potential / homologous chromosome pairing at meiosis / somite development / COPII vesicle coat / positive regulation of protein localization to centrosome / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear export signal receptor activity / paraxial mesoderm development / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / nuclear pore nuclear basket / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / miRNA processing / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / negative regulation of Ras protein signal transduction / NLS-bearing protein import into nucleus / protein-containing complex localization / microtubule bundle formation / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Flemming body / SUMOylation of RNA binding proteins / nuclear export / fertilization / mitotic centrosome separation / NEP/NS2 Interacts with the Cellular Export Machinery / kinase activator activity / Transport of Mature mRNA derived from an Intron-Containing Transcript / Transferases; Acyltransferases; Aminoacyltransferases / centrosome cycle / tRNA processing in the nucleus / RNA export from nucleus / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / negative regulation of programmed cell death / lamellipodium assembly / neural tube development / nucleocytoplasmic transport / centrosome localization / positive regulation of epidermal growth factor receptor signaling pathway / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / regulation of gluconeogenesis / PTB domain binding / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / female gonad development / Vpr-mediated nuclear import of PICs / negative regulation of epidermal growth factor receptor signaling pathway / macrophage chemotaxis / protein sumoylation / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of SMAD protein signal transduction / ribosomal large subunit export from nucleus / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of TOR signaling Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 12.0 Å | |||||||||
![]() | Mosalaganti S / Obarska-Kosinska A | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Authors: Shyamal Mosalaganti / Agnieszka Obarska-Kosinska / Marc Siggel / Reiya Taniguchi / Beata Turoňová / Christian E Zimmerli / Katarzyna Buczak / Florian H Schmidt / Erica Margiotta / Marie- ...Authors: Shyamal Mosalaganti / Agnieszka Obarska-Kosinska / Marc Siggel / Reiya Taniguchi / Beata Turoňová / Christian E Zimmerli / Katarzyna Buczak / Florian H Schmidt / Erica Margiotta / Marie-Therese Mackmull / Wim J H Hagen / Gerhard Hummer / Jan Kosinski / Martin Beck / ![]() ![]() Abstract: INTRODUCTION The eukaryotic nucleus pro-tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate ...INTRODUCTION The eukaryotic nucleus pro-tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ∼120 MDa, the human NPC is one of the larg-est protein complexes. Its ~1000 proteins are taken in multiple copies from a set of about 30 distinct nucleoporins (NUPs). They can be roughly categorized into two classes. Scaf-fold NUPs contain folded domains and form a cylindrical scaffold architecture around a central channel. Intrinsically disordered NUPs line the scaffold and extend into the central channel, where they interact with cargo complexes. The NPC architecture is highly dynamic. It responds to changes in nuclear envelope tension with conforma-tional breathing that manifests in dilation and constriction movements. Elucidating the scaffold architecture, ultimately at atomic resolution, will be important for gaining a more precise understanding of NPC function and dynamics but imposes a substantial chal-lenge for structural biologists. RATIONALE Considerable progress has been made toward this goal by a joint effort in the field. A synergistic combination of complementary approaches has turned out to be critical. In situ structural biology techniques were used to reveal the overall layout of the NPC scaffold that defines the spatial reference for molecular modeling. High-resolution structures of many NUPs were determined in vitro. Proteomic analysis and extensive biochemical work unraveled the interaction network of NUPs. Integra-tive modeling has been used to combine the different types of data, resulting in a rough outline of the NPC scaffold. Previous struc-tural models of the human NPC, however, were patchy and limited in accuracy owing to several challenges: (i) Many of the high-resolution structures of individual NUPs have been solved from distantly related species and, consequently, do not comprehensively cover their human counterparts. (ii) The scaf-fold is interconnected by a set of intrinsically disordered linker NUPs that are not straight-forwardly accessible to common structural biology techniques. (iii) The NPC scaffold intimately embraces the fused inner and outer nuclear membranes in a distinctive topol-ogy and cannot be studied in isolation. (iv) The conformational dynamics of scaffold NUPs limits the resolution achievable in structure determination. RESULTS In this study, we used artificial intelligence (AI)-based prediction to generate an exten-sive repertoire of structural models of human NUPs and their subcomplexes. The resulting models cover various domains and interfaces that so far remained structurally uncharac-terized. Benchmarking against previous and unpublished x-ray and cryo-electron micros-copy structures revealed unprecedented accu-racy. We obtained well-resolved cryo-electron tomographic maps of both the constricted and dilated conformational states of the hu-man NPC. Using integrative modeling, we fit-ted the structural models of individual NUPs into the cryo-electron microscopy maps. We explicitly included several linker NUPs and traced their trajectory through the NPC scaf-fold. We elucidated in great detail how mem-brane-associated and transmembrane NUPs are distributed across the fusion topology of both nuclear membranes. The resulting architectural model increases the structural coverage of the human NPC scaffold by about twofold. We extensively validated our model against both earlier and new experimental data. The completeness of our model has enabled microsecond-long coarse-grained molecular dynamics simulations of the NPC scaffold within an explicit membrane en-vironment and solvent. These simulations reveal that the NPC scaffold prevents the constriction of the otherwise stable double-membrane fusion pore to small diameters in the absence of membrane tension. CONCLUSION Our 70-MDa atomically re-solved model covers >90% of the human NPC scaffold. It captures conforma-tional changes that occur during dilation and constriction. It also reveals the precise anchoring sites for intrinsically disordered NUPs, the identification of which is a prerequisite for a complete and dy-namic model of the NPC. Our study exempli-fies how AI-based structure prediction may accelerate the elucidation of subcellular ar-chitecture at atomic resolution. [Figure: see text]. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 306.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 56.8 KB 56.8 KB | Display Display | ![]() |
Images | ![]() | 40 KB | ||
Filedesc metadata | ![]() | 22.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r5kMC ![]() 7tbjM ![]() 7tblM ![]() 7r1yC ![]() 7r5jC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Structure of the human nuclear pore complex from isolated nuclear envelopes | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.37 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Nuclear pore complex
+Supramolecule #1: Nuclear pore complex
+Macromolecule #1: E3 SUMO-protein ligase RanBP2
+Macromolecule #2: Nuclear pore membrane glycoprotein 210
+Macromolecule #3: Aladin
+Macromolecule #4: Nuclear pore complex protein Nup93
+Macromolecule #5: Nucleoporin NUP188 homolog
+Macromolecule #6: Nuclear pore complex protein Nup205
+Macromolecule #7: Nuclear pore complex protein Nup155
+Macromolecule #8: Nucleoporin NDC1
+Macromolecule #9: Nucleoporin NUP35
+Macromolecule #10: Nucleoporin p54
+Macromolecule #11: Nucleoporin p58/p45
+Macromolecule #12: Nuclear pore glycoprotein p62
+Macromolecule #13: Nuclear pore complex protein Nup133
+Macromolecule #14: Nuclear pore complex protein Nup107
+Macromolecule #15: Nuclear pore complex protein Nup96
+Macromolecule #16: Protein SEC13 homolog
+Macromolecule #17: Nucleoporin SEH1
+Macromolecule #18: Nuclear pore complex protein Nup85
+Macromolecule #19: Nucleoporin Nup43
+Macromolecule #20: Nuclear pore complex protein Nup160
+Macromolecule #21: Nucleoporin Nup37
+Macromolecule #22: Protein ELYS
+Macromolecule #23: Nuclear pore complex protein Nup98
+Macromolecule #24: Nuclear pore complex protein Nup214
+Macromolecule #25: Nuclear pore complex protein Nup88
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.93 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 7711 |
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Extraction | Number tomograms: 554 / Number images used: 7711 |
Final angle assignment | Type: OTHER |