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| Entry | Database: PDB / ID: 7r5k | |||||||||
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| Title | Human nuclear pore complex (constricted) | |||||||||
 Components |
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 Keywords | TRANSPORT PROTEIN / multiprotein complex / nucleocytoplasmic transport | |||||||||
| Function / homology |  Function and homology informationcytoplasmic 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 |  Homo sapiens (human) | |||||||||
| Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 12 Å | |||||||||
 Authors | Mosalaganti, S. / Obarska-Kosinska, A. / Siggel, M. / Taniguchi, R. / Turonova, B. / Zimmerli, C.E. / Buczak, K. / Schmidt, F.H. / Margiotta, E. / Mackmull, M.T. ...Mosalaganti, S. / Obarska-Kosinska, A. / Siggel, M. / Taniguchi, R. / Turonova, B. / Zimmerli, C.E. / Buczak, K. / Schmidt, F.H. / Margiotta, E. / Mackmull, M.T. / Hagen, W.J.H. / Hummer, G. / Kosinski, J. / Beck, M. | |||||||||
| Funding support | European Union,  Germany, 2items
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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
| Structure viewer | Molecule: MolmilJmol/JSmol |
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Downloads & links
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| PDBx/mmCIF format | 7r5k.cif.gz | 13.1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb7r5k.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 7r5k.json.gz | Tree view | PDBx/mmJSON format | |
| Others |  Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/7r5kftp://data.pdbj.org/pub/pdb/validation_reports/r5/7r5k | HTTPS FTP |
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-Related structure data
| Related structure data |  14322MC  7r1yC  7r5jC M: map data used to model this data C: citing same article ( |
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| Similar structure data |
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PDBj
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Assembly
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-Components
-Protein , 12 types, 41 molecules 00010203044041B0B1E0E1F0F1F2F3H0H1H2H3I0I1I2I3N0N1N2N3O0O1O2...
| #1: Protein | Mass: 358654.375 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)References: UniProt: P49792, Transferases; Acyltransferases; Aminoacyltransferases #3: Protein | Mass: 59635.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRG9#5: Protein | Mass: 196256.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5SRE5#8: Protein | Mass: 76377.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BTX1#9: Protein | Mass: 34805.664 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NFH5#10: Protein | Mass: 55491.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z3B4#11: Protein | Mass: 60941.480 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BVL2#16: Protein | Mass: 35578.438 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55735#17: Protein | Mass: 39700.566 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EE3#19: Protein | Mass: 42195.652 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NFH3#21: Protein | Mass: 36748.512 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NFH4#22: Protein | Mass: 252807.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WYP5 |
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-Nuclear pore ... , 13 types, 60 molecules 1011121314151617A0A1A2A3A4A5A6C0C1C2C3C4D0D1D2D3D4D5J0J1J2J3...
| #2: Protein | Mass: 205314.406 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TEM1#4: Protein | Mass: 93599.102 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N1F7#6: Protein | Mass: 228172.875 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92621#7: Protein | Mass: 155357.281 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75694#12: Protein | Mass: 53289.574 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37198#13: Protein | Mass: 129108.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUM0#14: Protein | Mass: 106504.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P57740#15: Protein | Mass: 106039.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52948#18: Protein | Mass: 75105.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW27#20: Protein | Mass: 162280.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12769#23: Protein | Mass: 91760.117 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52948#24: Protein | | Mass: 213784.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35658#25: Protein | | Mass: 83644.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99567 |
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-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: CELL / 3D reconstruction method: subtomogram averaging |
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Sample preparation
| Component | Name: Nuclear pore complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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| Molecular weight | Value: 120 MDa / Experimental value: YES |
| Source (natural) | Organism: Homo sapiens (human) |
| Buffer solution | pH: 7.5 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE |
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Electron microscopy imaging
| Experimental equipment |  Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source:  FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
| Image recording | Electron dose: 2.93 e/Å2 / Avg electron dose per subtomogram: 120 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
| EM software | Name: SerialEM / Category: image acquisition |
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| CTF correction | Type: PHASE FLIPPING ONLY |
| Symmetry | Point symmetry: C1 (asymmetric) |
| 3D reconstruction | Resolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7711 / Symmetry type: POINT |
| EM volume selection | Num. of tomograms: 554 / Num. of volumes extracted: 7711 |
