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Yorodumi- PDB-5ijo: Alternative composite structure of the inner ring of the human nu... -
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-Basic information
Entry | Database: PDB / ID: 5ijo | ||||||
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Title | Alternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Nuclear pore complex / Nucleocytoplasmic transport | ||||||
Function / homology | Function and homology information 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 / nuclear envelope organization / nuclear pore inner ring / protein localization to nuclear inner membrane / 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 / nuclear envelope organization / nuclear pore inner ring / protein localization to nuclear inner membrane / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / atrial cardiac muscle cell action potential / 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 / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / negative regulation of programmed cell death / Transport of Mature mRNA Derived from an Intronless Transcript / negative regulation of Ras protein signal transduction / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / SUMOylation of RNA binding proteins / Flemming body / Nuclear import of Rev protein / mitotic centrosome separation / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / centrosome cycle / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / positive regulation of epidermal growth factor receptor signaling pathway / PTB domain binding / mitotic metaphase chromosome alignment / nuclear localization sequence binding / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / negative regulation of epidermal growth factor receptor signaling pathway / 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 / mRNA transport / regulation of signal transduction / protein targeting / mRNA export from nucleus / nuclear pore / SUMOylation of DNA damage response and repair proteins / regulation of mitotic spindle organization / Hsp70 protein binding / SH2 domain binding / positive regulation of mitotic nuclear division / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / ubiquitin binding / Transcriptional regulation by small RNAs / Hsp90 protein binding / phospholipid binding / mitotic spindle / ISG15 antiviral mechanism / spindle pole / HCMV Early Events / protein import into nucleus / cellular senescence / protein transport / signaling receptor complex adaptor activity / nuclear envelope / snRNP Assembly / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / ribonucleoprotein complex / negative regulation of cell population proliferation / centrosome / chromatin binding / protein-containing complex binding / negative regulation of apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / nucleoplasm / identical protein binding / membrane / cytosol / cytoplasm 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 | 5ijo.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ijo.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 5ijo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ijo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5ijo_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5ijo_validation.xml.gz | 349.7 KB | Display | |
Data in CIF | 5ijo_validation.cif.gz | 561.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/5ijo ftp://data.pdbj.org/pub/pdb/validation_reports/ij/5ijo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Symmetry | Point symmetry: (Schoenflies symbol: C8 (8 fold cyclic)) |
-Components
-Nuclear pore complex protein ... , 3 types, 12 molecules ABEKQWCIOUDP
#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 / Gene: NUP155, KIAA0791 / 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 / Gene: NUP93, KIAA0095 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q8N1F7 #3: Protein | Mass: 228172.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA / Gene: NUP205, C7orf14, KIAA0225 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q92621 |
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-Protein , 4 types, 14 molecules FLRXGMSYHNTZJV
#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 / Gene: NUP54 / 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 / Gene: NUP58, KIAA0410, NUPL1 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q9BVL2 #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 #7: Protein | Mass: 196256.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA / Gene: NUP188, KIAA0169 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q5SRE5 |
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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-#8 / Source: MULTIPLE SOURCES |
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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 | ||||||||||||
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 domains of nup188 and nup205. the structure with that domains can be obtained from authors. protein-protein ...Details: this pdb structure includes unambiguous fits only, .i.e. excluding the middle domains of nup188 and nup205. the structure with that domains can be obtained from authors. protein-protein interfaces shall not be interpreted at residue-level resolution. |