+Open data
-Basic information
Entry | Database: PDB / ID: 7peq | ||||||||||||
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Title | Model of the outer rings of the human nuclear pore complex | ||||||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Nuclear Pore Complex / NPC | ||||||||||||
Function / homology | Function and homology information GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-coated vesicle cargo loading / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly ...GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / COPII-coated vesicle cargo loading / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / somite development / COPII vesicle coat / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / paraxial mesoderm development / nuclear pore nuclear basket / 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 / 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 / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / neural tube development / COPII-mediated vesicle transport / lamellipodium assembly / Viral Messenger RNA Synthesis / SUMOylation of chromatin organization proteins / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / female gonad development / SUMOylation of ubiquitinylation proteins / macrophage chemotaxis / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / positive regulation of TOR signaling / mRNA transport / cellular response to nutrient levels / neurogenesis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of TORC1 signaling / Resolution of Sister Chromatid Cohesion / positive regulation of TORC1 signaling / MHC class II antigen presentation / serine-type peptidase activity / cellular response to amino acid starvation / HCMV Late Events / nuclear periphery / molecular condensate scaffold activity / chromosome segregation / promoter-specific chromatin binding / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / HCMV Early Events / ER to Golgi transport vesicle membrane / kinetochore / ISG15 antiviral mechanism / spindle / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / protein transport / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / defense response to Gram-positive bacterium / nuclear speck / ribonucleoprotein complex / cell division / lysosomal membrane / intracellular membrane-bounded organelle Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 35 Å | ||||||||||||
Authors | Schuller, A.P. / Wojtynek, M. / Mankus, D. / Tatli, M. / Kronenberg-Tenga, R. / Regmi, S.G. / Dasso, M. / Weis, K. / Medalia, O. / Schwartz, T.U. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: Nature / Year: 2021 Title: The cellular environment shapes the nuclear pore complex architecture. Authors: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / ...Authors: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / Karsten Weis / Ohad Medalia / Thomas U Schwartz / Abstract: Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about ...Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7peq.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7peq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7peq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7peq_validation.pdf.gz | 981.4 KB | Display | wwPDB validaton report |
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Full document | 7peq_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7peq_validation.xml.gz | 313.3 KB | Display | |
Data in CIF | 7peq_validation.cif.gz | 548.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/7peq ftp://data.pdbj.org/pub/pdb/validation_reports/pe/7peq | HTTPS FTP |
-Related structure data
Related structure data | 12814MC 7perC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10700 (Title: Cryo electron tomography of FIB-milled lamella of human DLD-1 cells Data size: 8.0 Data #1: Un-aligned tilt series of FIB-lamella of human DLD-1 cells [tilt series]) EMPIAR-10701 (Title: Cryo electron tomography of FIB-milled lamella of human DLD-1 cells Data size: 8.0 Data #1: Un-aligned tilt series of FIB-milled lamella of Nup96-depleted human DLD-1 cells [tilt series]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Nuclear pore complex protein ... , 5 types, 20 molecules ACBCCCDCADBDCDDDAEBECEDEAHBHCHDHAJBJCJDJ
#1: Protein | Mass: 129108.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUM0 #2: Protein | Mass: 106504.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P57740 #3: Protein | Mass: 106039.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52948 #6: Protein | Mass: 75105.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW27 #8: Protein | Mass: 162280.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12769 |
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-Protein , 4 types, 16 molecules AFBFCFDFAGBGCGDGAIBICIDIAKBKCKDK
#4: Protein | Mass: 35578.438 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55735 #5: Protein | Mass: 39700.566 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EE3 #7: Protein | Mass: 42195.652 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NFH3 #9: Protein | Mass: 36748.512 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NFH4 |
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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: Nup96::Neon-AID DLD-1 / Type: CELL / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: cryo-FIB milled sections of DLD1 cells |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 2.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||
Symmetry | Point symmetry: C8 (8 fold cyclic) | ||||||||||||
3D reconstruction | Resolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1252 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||
EM volume selection | Num. of tomograms: 54 / Num. of volumes extracted: 1552 | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||
Atomic model building | PDB-ID: 5A9Q Accession code: 5A9Q / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||
Displacement parameters | Biso max: 78.15 Å2 / Biso mean: 0.9902 Å2 / Biso min: 0 Å2 |