+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14322 | |||||||||
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Title | Human nuclear pore complex (constricted) | |||||||||
Map data | Structure of the human nuclear pore complex from isolated nuclear envelopes | |||||||||
Sample |
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Function / homology | Function and homology information nuclear pore transmembrane ring / cytoplasmic side of nuclear pore / positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / centriole assembly / HuR (ELAVL1) binds and stabilizes mRNA / cytoplasmic periphery of the nuclear pore complex / regulation of protein import into nucleus / positive regulation of centriole replication ...nuclear pore transmembrane ring / cytoplasmic side of nuclear pore / positive regulation of mitotic cytokinetic process / GATOR2 complex / nephron development / centriole assembly / HuR (ELAVL1) binds and stabilizes mRNA / cytoplasmic periphery of the nuclear pore complex / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / SUMO ligase activity / Seh1-associated complex / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / protein exit from endoplasmic reticulum / SUMO ligase complex / COPII-coated vesicle budding / annulate lamellae / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / nuclear pore localization / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / COPII-coated vesicle cargo loading / nuclear pore organization / nuclear pore complex assembly / nuclear pore outer ring / homologous chromosome pairing at meiosis / atrial cardiac muscle cell action potential / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / somite development / COPII vesicle coat / nuclear export signal receptor activity / Nuclear Pore Complex (NPC) Disassembly / positive regulation of protein localization to centrosome / nuclear inclusion body / nuclear pore nuclear basket / paraxial mesoderm development / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Amino acids regulate mTORC1 / miRNA processing / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / negative regulation of Ras protein signal transduction / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / microtubule bundle formation / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / nuclear export / positive regulation of mRNA splicing, via spliceosome / structural constituent of nuclear pore / Transferases; Acyltransferases; Aminoacyltransferases / Rev-mediated nuclear export of HIV RNA / fertilization / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Flemming body / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / negative regulation of programmed cell death / mitotic centrosome separation / SUMO transferase activity / centrosome cycle / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / neural tube development / COPII-mediated vesicle transport / poly(A)+ mRNA export from nucleus / lamellipodium assembly / centrosome localization / Viral Messenger RNA Synthesis / nuclear localization sequence binding / positive regulation of epidermal growth factor receptor signaling pathway / PTB domain binding / NLS-bearing protein import into nucleus / regulation of gluconeogenesis / mitotic metaphase chromosome alignment / macrophage chemotaxis / female gonad development / negative regulation of epidermal growth factor receptor signaling pathway / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / cellular response to nutrient levels / ribosomal small subunit export from nucleus / positive regulation of SMAD protein signal transduction / SUMOylation of DNA replication proteins / protein sumoylation / Signaling by ALK fusions and activated point mutants / ribosomal large subunit export from nucleus / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / mitotic spindle assembly Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Mosalaganti S / Obarska-Kosinska A / Siggel M / Taniguchi R / Turonova B / Zimmerli CE / Buczak K / Schmidt FH / Margiotta E / Mackmull MT ...Mosalaganti S / Obarska-Kosinska A / Siggel M / Taniguchi R / Turonova B / Zimmerli CE / Buczak K / Schmidt FH / Margiotta E / Mackmull MT / Hagen WJH / Hummer G / Kosinski J / Beck M | |||||||||
Funding support | European Union, Germany, 2 items
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Citation | Journal: Science / Year: 2022 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 | emd_14322.map.gz | 306.2 MB | EMDB map data format | |
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Header (meta data) | emd-14322-v30.xml emd-14322.xml | 55.2 KB 55.2 KB | Display Display | EMDB header |
Images | emd_14322.png | 40 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14322 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14322 | HTTPS FTP |
-Related structure data
Related structure data | 7r5kMC 7tbjM 7tblM 7r1yC 7r5jC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14322.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-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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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.93 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Extraction | Number tomograms: 554 / Number images used: 7711 |
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Final angle assignment | Type: OTHER |
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 |