+Open data
-Basic information
Entry | Database: PDB / ID: 7r5j | |||||||||
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Title | Human nuclear pore complex (dilated) | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / nucleocytoplasmic transport / multiprotein complex | |||||||||
Function / homology | Function and homology information cytoplasmic side of nuclear pore / nuclear pore transmembrane ring / 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 ...cytoplasmic side of nuclear pore / nuclear pore transmembrane ring / 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 / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear envelope organization / nuclear pore localization / nuclear pore central transport channel / telomere tethering at nuclear periphery / regulation of nucleocytoplasmic transport / COPII-coated vesicle cargo loading / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / homologous chromosome pairing at meiosis / atrial cardiac muscle cell action potential / somite development / COPII vesicle coat / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / nuclear export signal receptor activity / positive regulation of protein localization to centrosome / Nuclear Pore Complex (NPC) Disassembly / paraxial mesoderm development / nuclear inclusion body / nuclear pore nuclear basket / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / miRNA processing / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / attachment of mitotic spindle microtubules to kinetochore / negative regulation of Ras protein signal transduction / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / microtubule bundle formation / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / Transferases; Acyltransferases; Aminoacyltransferases / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / fertilization / SUMOylation of RNA binding proteins / nuclear export / Flemming body / Nuclear import of Rev protein / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / negative regulation of programmed cell death / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / mitotic centrosome separation / centrosome cycle / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / neural tube development / COPII-mediated vesicle transport / poly(A)+ mRNA export from nucleus / nucleocytoplasmic transport / lamellipodium assembly / centrosome localization / Viral Messenger RNA Synthesis / positive regulation of epidermal growth factor receptor signaling pathway / PTB domain binding / nuclear localization sequence 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 / positive regulation of SMAD protein signal transduction / ribosomal small subunit export from nucleus / SUMOylation of DNA replication proteins / protein sumoylation / Signaling by ALK fusions and activated point mutants / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / ribosomal large subunit export from nucleus / mitotic spindle assembly Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 50 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
-Download
PDBx/mmCIF format | 7r5j.cif.gz | 13.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7r5j.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7r5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/7r5j ftp://data.pdbj.org/pub/pdb/validation_reports/r5/7r5j | HTTPS FTP |
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-Related structure data
Related structure data | 14321MC 7r1yC 7r5kC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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 |
-Sample preparation
Component | Name: Human nuclear pore complex from HEK cellsNuclear pore / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE-PROPANE / Humidity: 99 % / Chamber temperature: 300 K |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 3.15 e/Å2 / Avg electron dose per subtomogram: 130 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 50 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 150 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 8 / Num. of volumes extracted: 30 |