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Yorodumi- PDB-5ijn: Composite structure of the inner ring of the human nuclear pore c... -
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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) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Nuclear pore complex / Nucleocytoplasmic transport | ||||||
Function / homology | Function and homology information centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / nuclear envelope organization / nuclear pore inner ring / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / regulation of Ras protein signal transduction / positive regulation of mitotic cytokinetic process / protein localization to nuclear inner membrane / nuclear envelope organization / nuclear pore inner ring / 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 / negative regulation of epidermal growth factor receptor signaling pathway / 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 / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / negative regulation of Ras protein signal transduction / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Flemming body / Nuclear import of Rev protein / negative regulation of programmed cell death / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / mitotic centrosome separation / centrosome cycle / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / positive regulation of epidermal growth factor receptor signaling pathway / SUMOylation of chromatin organization proteins / PTB domain binding / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / positive regulation of SMAD protein signal transduction / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / regulation of signal transduction / mRNA transport / protein targeting / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / regulation of mitotic spindle organization / Hsp70 protein binding / positive regulation of mitotic nuclear division / SH2 domain binding / HCMV Late Events / nuclear periphery / ubiquitin binding / Transcriptional regulation by small RNAs / HCMV Early Events / Hsp90 protein binding / cellular senescence / phospholipid binding / mitotic spindle / ISG15 antiviral mechanism / spindle pole / protein import into nucleus / nuclear envelope / signaling receptor complex adaptor activity / protein transport / positive regulation of canonical NF-kappaB signal transduction / snRNP Assembly / nuclear membrane / cell surface receptor signaling pathway / ribonucleoprotein complex / negative regulation of cell population proliferation / chromatin binding / centrosome / positive regulation of DNA-templated transcription / negative regulation of apoptotic process / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 21.4 Å | ||||||
Authors | Kosinski, J. / Mosalaganti, S. / von Appen, A. / Beck, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Science / Year: 2016 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ijn.cif.gz | 15.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ijn.ent.gz | 10.4 MB | Display | PDB format |
PDBx/mmJSON format | 5ijn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ijn_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 5ijn_full_validation.pdf.gz | 6.9 MB | Display | |
Data in XML | 5ijn_validation.xml.gz | 2.2 MB | Display | |
Data in CIF | 5ijn_validation.cif.gz | 3.4 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/5ijn ftp://data.pdbj.org/pub/pdb/validation_reports/ij/5ijn | HTTPS FTP |
-Related structure data
-Links
-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)) |
-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.) Homo sapiens (human) / Cell line: HELA / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: O75694 #2: Protein | Mass: 93599.102 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q8N1F7 #3: Protein | Mass: 228172.875 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q92621 #4: Protein | Mass: 55491.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q7Z3B4 #5: Protein | Mass: 60941.480 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q9BVL2 |
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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.) Homo sapiens (human) / Cell line: HELA / Gene: NUP62 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: P37198 |
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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 |
-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 |
-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: OTHER |
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) |
-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. |