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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 informationnuclear 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 assemblySimilarity 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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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 | Aladdin (disambiguation) / AdracalinMass: 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 | Nuclear pore / 93 kDa nucleoporin / Nucleoporin Nup93Mass: 93599.102 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N1F7#6: Protein | Nuclear pore / 205 kDa nucleoporin / Nucleoporin Nup205Mass: 228172.875 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92621#7: Protein | Nuclear pore / 155 kDa nucleoporin / Nucleoporin Nup155Mass: 155357.281 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75694#12: Protein | / 62 kDa nucleoporin / Nucleoporin Nup62 / NUCLEAR PORE COMPLEX PROTEIN NUP62Mass: 53289.574 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37198#13: Protein | / 133 kDa nucleoporin / Nucleoporin Nup133Mass: 129108.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUM0#14: Protein | Nuclear pore / 107 kDa nucleoporin / Nucleoporin Nup107Mass: 106504.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P57740#15: Protein | Nuclear pore / 96 kDa nucleoporin / Nucleoporin Nup96 / Nup96Mass: 106039.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52948#18: Protein | Nuclear pore / 85 kDa nucleoporin / FROUNT / Nucleoporin Nup75 / Nucleoporin Nup85 / Pericentrin-1Mass: 75105.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW27#20: Protein | Nuclear pore / 160 kDa nucleoporin / Nucleoporin Nup160Mass: 162280.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12769#23: Protein | Nuclear pore / 98 kDa nucleoporin / Nucleoporin Nup98 / Nup98Mass: 91760.117 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52948#24: Protein | | Nuclear pore / 214 kDa nucleoporin / Nucleoporin Nup214 / Protein CANMass: 213784.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P35658#25: Protein | | Nuclear pore / 88 kDa nucleoporin / Nucleoporin Nup88Mass: 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 complexNuclear pore / 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 FIELDBright-field microscopy / 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 |
