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Basic information

Entry
Database: PDB / ID: 5ijn
TitleComposite structure of the inner ring of the human nuclear pore complex (32 copies of Nup205)
Components
  • (NUCLEAR PORE COMPLEX PROTEIN ...) x 5
  • Nuclear pore glycoprotein p62
KeywordsTRANSPORT 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 / 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 / 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 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 / nuclear pore organization / atrial cardiac muscle cell action potential / positive regulation of protein localization to centrosome / Nuclear Pore Complex (NPC) Disassembly / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of Ribonucleoproteins into the Host Nucleus / miRNA processing / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / negative regulation of Ras protein signal transduction / NLS-bearing protein import into nucleus / SUMOylation of SUMOylation proteins / nuclear localization sequence binding / structural constituent of nuclear pore / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / Flemming body / SUMOylation of RNA binding proteins / mitotic centrosome separation / NEP/NS2 Interacts with the Cellular Export Machinery / 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 / centrosome cycle / negative regulation of programmed cell death / nucleocytoplasmic transport / positive regulation of epidermal growth factor receptor signaling pathway / Viral Messenger RNA Synthesis / PTB domain binding / poly(A)+ mRNA export from nucleus / 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 / regulation of signal transduction / mRNA transport / 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 / ubiquitin binding / HCMV Late Events / Hsp90 protein binding / Transcriptional regulation by small RNAs / phospholipid binding / ISG15 antiviral mechanism / protein import into nucleus / HCMV Early Events / spindle pole / 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 / cytoplasm / cytosol
Similarity search - Function
Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin p58/p45 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 ...Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin p58/p45 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin complex subunit 54 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin, Nup155-like / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like
Similarity search - Domain/homology
Nuclear pore complex protein Nup155 / Nuclear pore glycoprotein p62 / Nucleoporin p54 / Nuclear pore complex protein Nup93 / Nuclear pore complex protein Nup205 / Nucleoporin p58/p45
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 21.4 Å
AuthorsKosinski, J. / Mosalaganti, S. / von Appen, A. / Beck, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council30921 Germany
CitationJournal: 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
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name
Revision 1.2Sep 20, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.3Oct 3, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: NUCLEAR PORE COMPLEX PROTEIN NUP155
B: NUCLEAR PORE COMPLEX PROTEIN NUP155
C: NUCLEAR PORE COMPLEX PROTEIN NUP93
D: NUCLEAR PORE COMPLEX PROTEIN NUP205
E: NUCLEAR PORE COMPLEX PROTEIN NUP155
F: NUCLEAR PORE COMPLEX PROTEIN NUP54
G: NUCLEAR PORE COMPLEX PROTEIN NUP58
H: Nuclear pore glycoprotein p62
I: NUCLEAR PORE COMPLEX PROTEIN NUP93
J: NUCLEAR PORE COMPLEX PROTEIN NUP205
K: NUCLEAR PORE COMPLEX PROTEIN NUP155
L: NUCLEAR PORE COMPLEX PROTEIN NUP54
M: NUCLEAR PORE COMPLEX PROTEIN NUP58
N: Nuclear pore glycoprotein p62
O: NUCLEAR PORE COMPLEX PROTEIN NUP93
P: NUCLEAR PORE COMPLEX PROTEIN NUP205
Q: NUCLEAR PORE COMPLEX PROTEIN NUP155
R: NUCLEAR PORE COMPLEX PROTEIN NUP54
S: NUCLEAR PORE COMPLEX PROTEIN NUP58
T: Nuclear pore glycoprotein p62
U: NUCLEAR PORE COMPLEX PROTEIN NUP93
V: NUCLEAR PORE COMPLEX PROTEIN NUP205
W: NUCLEAR PORE COMPLEX PROTEIN NUP155
X: NUCLEAR PORE COMPLEX PROTEIN NUP54
Y: NUCLEAR PORE COMPLEX PROTEIN NUP58
Z: Nuclear pore glycoprotein p62


Theoretical massNumber of molelcules
Total (without water)2,898,12026
Polymers2,898,12026
Non-polymers00
Water00
1
A: NUCLEAR PORE COMPLEX PROTEIN NUP155
B: NUCLEAR PORE COMPLEX PROTEIN NUP155
C: NUCLEAR PORE COMPLEX PROTEIN NUP93
D: NUCLEAR PORE COMPLEX PROTEIN NUP205
E: NUCLEAR PORE COMPLEX PROTEIN NUP155
F: NUCLEAR PORE COMPLEX PROTEIN NUP54
G: NUCLEAR PORE COMPLEX PROTEIN NUP58
H: Nuclear pore glycoprotein p62
I: NUCLEAR PORE COMPLEX PROTEIN NUP93
J: NUCLEAR PORE COMPLEX PROTEIN NUP205
K: NUCLEAR PORE COMPLEX PROTEIN NUP155
L: NUCLEAR PORE COMPLEX PROTEIN NUP54
M: NUCLEAR PORE COMPLEX PROTEIN NUP58
N: Nuclear pore glycoprotein p62
O: NUCLEAR PORE COMPLEX PROTEIN NUP93
P: NUCLEAR PORE COMPLEX PROTEIN NUP205
Q: NUCLEAR PORE COMPLEX PROTEIN NUP155
R: NUCLEAR PORE COMPLEX PROTEIN NUP54
S: NUCLEAR PORE COMPLEX PROTEIN NUP58
T: Nuclear pore glycoprotein p62
U: NUCLEAR PORE COMPLEX PROTEIN NUP93
V: NUCLEAR PORE COMPLEX PROTEIN NUP205
W: NUCLEAR PORE COMPLEX PROTEIN NUP155
X: NUCLEAR PORE COMPLEX PROTEIN NUP54
Y: NUCLEAR PORE COMPLEX PROTEIN NUP58
Z: Nuclear pore glycoprotein p62
x 8


Theoretical massNumber of molelcules
Total (without water)23,184,963208
Polymers23,184,963208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation7
Number of models8
SymmetryPoint symmetry: (Schoenflies symbol: C8 (8 fold cyclic))

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Components

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NUCLEAR PORE COMPLEX PROTEIN ... , 5 types, 22 molecules ABEKQWCIOUDJPVFLRXGMSY

#1: Protein
NUCLEAR PORE COMPLEX PROTEIN NUP155


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
NUCLEAR PORE COMPLEX PROTEIN NUP93


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
NUCLEAR PORE COMPLEX PROTEIN NUP205


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
NUCLEAR PORE COMPLEX PROTEIN NUP54


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
NUCLEAR PORE COMPLEX PROTEIN NUP58


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
Nuclear pore glycoprotein p62 / 62 kDa nucleoporin / Nucleoporin Nup62


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Nuclear envelope / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Molecular weightValue: 23 MDa / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron 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
IDNameVersionCategory
2SerialEMimage acquisition
7UCSF Chimera1.9model fitting
8IMPg0552c9cmodel fitting
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 correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 21.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8400 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 101 / Num. of volumes extracted: 1112
Atomic model buildingProtocol: 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.

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