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- PDB-5ijn: Composite structure of the inner ring of the human nuclear pore c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ijn | ||||||
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Title | Composite structure of the inner ring of the human nuclear pore complex (32 copies of Nup205) | ||||||
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![]() | TRANSPORT PROTEIN / Nuclear pore complex / Nucleocytoplasmic transport | ||||||
Function / homology | ![]() centriole assembly / positive regulation of centriole replication / regulation of protein import into nucleus / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...centriole assembly / positive regulation of centriole replication / regulation of protein import into nucleus / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / nuclear pore inner ring / nuclear envelope organization / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / atrial cardiac muscle cell action potential / nuclear pore organization / positive regulation of protein localization to centrosome / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / miRNA processing / Transport of the SLBP independent Mature mRNA / NS1 Mediated Effects on Host Pathways / Transport of the SLBP Dependant Mature mRNA / negative regulation of Ras protein signal transduction / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / nuclear localization sequence binding / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Flemming body / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / mitotic centrosome separation / NEP/NS2 Interacts with the Cellular Export Machinery / centrosome cycle / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of programmed cell death / nucleocytoplasmic transport / positive regulation of epidermal growth factor receptor signaling pathway / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / PTB domain binding / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / negative regulation of epidermal growth factor receptor signaling pathway / SUMOylation of DNA replication proteins / positive regulation of SMAD protein signal transduction / Regulation of HSF1-mediated heat shock response / mRNA transport / regulation of signal transduction / nuclear pore / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / Hsp70 protein binding / positive regulation of mitotic nuclear division / SH2 domain binding / nuclear periphery / regulation of mitotic spindle organization / SUMOylation of chromatin organization proteins / HCMV Late Events / ubiquitin binding / Hsp90 protein binding / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / phospholipid binding / HCMV Early Events / spindle pole / protein import into nucleus / mitotic spindle / cellular senescence / nuclear envelope / protein transport / signaling receptor complex adaptor activity / snRNP Assembly / nuclear membrane / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / ribonucleoprotein complex / negative regulation of cell population proliferation / centrosome / chromatin binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 21.4 Å | ||||||
![]() | Kosinski, J. / Mosalaganti, S. / von Appen, A. / Beck, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular architecture of the inner ring scaffold of the human nuclear pore complex. Authors: Jan Kosinski / Shyamal Mosalaganti / Alexander von Appen / Roman Teimer / Amanda L DiGuilio / William Wan / Khanh Huy Bui / Wim J H Hagen / John A G Briggs / Joseph S Glavy / Ed Hurt / Martin Beck / ![]() ![]() ![]() Abstract: Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these ...Nuclear pore complexes (NPCs) are 110-megadalton assemblies that mediate nucleocytoplasmic transport. NPCs are built from multiple copies of ~30 different nucleoporins, and understanding how these nucleoporins assemble into the NPC scaffold imposes a formidable challenge. Recently, it has been shown how the Y complex, a prominent NPC module, forms the outer rings of the nuclear pore. However, the organization of the inner ring has remained unknown until now. We used molecular modeling combined with cross-linking mass spectrometry and cryo-electron tomography to obtain a composite structure of the inner ring. This architectural map explains the vast majority of the electron density of the scaffold. We conclude that despite obvious differences in morphology and composition, the higher-order structure of the inner and outer rings is unexpectedly similar. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.5 MB | Display | ![]() |
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PDB format | ![]() | 10.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 6.9 MB | Display | |
Data in XML | ![]() | 2.2 MB | Display | |
Data in CIF | ![]() | 3.4 MB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Number of models | 8 |
Symmetry | Point symmetry: (Schoenflies symbol: C8 (8 fold cyclic)) |
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Components
-NUCLEAR PORE COMPLEX PROTEIN ... , 5 types, 22 molecules ABEKQWCIOUDJPVFLRXGMSY
#1: Protein | Mass: 155357.281 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 93599.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein | Mass: 228172.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Protein | Mass: 55491.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Protein | Mass: 60941.480 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Protein , 1 types, 4 molecules HNTZ
#6: Protein | Mass: 53289.574 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
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Sample preparation
Component | Name: Nuclear envelope / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 23 MDa / Experimental value: NO |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE-PROPANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / Space group name: P1 / Space group num: 1 | ||||||||||||||||
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 21.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8400 / Symmetry type: POINT | ||||||||||||||||
EM volume selection | Num. of tomograms: 101 / Num. of volumes extracted: 1112 | ||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT Details: this pdb structure includes unambiguous fits only, .i.e. excluding the middle domain of nup205. the structure with that domain can be obtained from authors. protein-protein interfaces shall ...Details: this pdb structure includes unambiguous fits only, .i.e. excluding the middle domain of nup205. the structure with that domain can be obtained from authors. protein-protein interfaces shall not be interpreted at residue-level resolution. this pdb structure contains eight models. the model 1 corresponds to the composite structure reported in the journal article associated with this entry. models 2-8 corresponds to the seven best scoring models automatically generated as described in the article. |