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Basic information

Entry
Database: PDB / ID: 5ijo
TitleAlternative composite structure of the inner ring of the human nuclear pore complex (16 copies of Nup188, 16 copies of Nup205)
Components
  • (Nuclear pore complex protein ...Nuclear pore) x 3
  • Nuclear pore glycoprotein p62
  • Nucleoporin NUP188 homolog
  • Nucleoporin p54
  • Nucleoporin p58/p45
KeywordsTRANSPORT PROTEIN / Nuclear pore complex / Nucleocytoplasmic transport
Function / homology
Function and homology information


positive regulation of mitotic cytokinetic process / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel ...positive regulation of mitotic cytokinetic process / centriole assembly / regulation of protein import into nucleus / positive regulation of centriole replication / nuclear pore inner ring / protein localization to nuclear inner membrane / regulation of Ras protein signal transduction / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel / nuclear pore organization / nuclear pore complex assembly / atrial cardiac muscle cell action potential / Nuclear Pore Complex (NPC) Disassembly / positive regulation of protein localization to centrosome / 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 / negative regulation of Ras protein signal transduction / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / RNA export from nucleus / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Flemming body / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / negative regulation of programmed cell death / mitotic centrosome separation / centrosome cycle / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / nuclear localization sequence binding / positive regulation of epidermal growth factor receptor signaling pathway / PTB domain binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / negative regulation of epidermal growth factor receptor signaling pathway / 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 / protein targeting / mRNA transport / regulation of signal transduction / mRNA export from nucleus / SUMOylation of DNA damage response and repair proteins / nuclear pore / regulation of mitotic spindle organization / Hsp70 protein binding / SH2 domain binding / nuclear periphery / SUMOylation of chromatin organization proteins / positive regulation of mitotic nuclear division / HCMV Late Events / ubiquitin binding / phospholipid binding / Transcriptional regulation by small RNAs / Hsp90 protein binding / mitotic spindle / ISG15 antiviral mechanism / spindle pole / HCMV Early Events / protein import into nucleus / cellular senescence / signaling receptor complex adaptor activity / protein transport / nuclear envelope / snRNP Assembly / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / 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 / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal / Nucleoporin p58/p45 / Nucleoporin Nup188, N-terminal / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin, Nup155-like, C-terminal, subdomain 3 ...Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal / Nucleoporin p58/p45 / Nucleoporin Nup188, N-terminal / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin Nup54, alpha-helical domain / Nucleoporin NSP1/NUP62 / Nucleoporin Nup188 / Nsp1-like C-terminal region / Nucleoporin complex subunit 54 / Nucleoporin, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex scaffold, nucleoporins 186/192/205 / Nucleoporin interacting component Nup93/Nic96 / Nup93/Nic96 / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / Armadillo-type fold
Similarity search - Domain/homology
Nuclear pore complex protein Nup155 / Nuclear pore glycoprotein p62 / Nucleoporin NUP188 / 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 1.1Sep 20, 2017Group: Data collection / Database references / Category: em_image_scans / pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.2Oct 3, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.3Dec 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]

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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: Nucleoporin p54
G: Nucleoporin p58/p45
H: Nuclear pore glycoprotein p62
I: Nuclear pore complex protein Nup93
J: Nucleoporin NUP188 homolog
K: Nuclear pore complex protein Nup155
L: Nucleoporin p54
M: Nucleoporin p58/p45
N: Nuclear pore glycoprotein p62
O: Nuclear pore complex protein Nup93
P: Nuclear pore complex protein Nup205
Q: Nuclear pore complex protein Nup155
R: Nucleoporin p54
S: Nucleoporin p58/p45
T: Nuclear pore glycoprotein p62
U: Nuclear pore complex protein Nup93
V: Nucleoporin NUP188 homolog
W: Nuclear pore complex protein Nup155
X: Nucleoporin p54
Y: Nucleoporin p58/p45
Z: Nuclear pore glycoprotein p62


Theoretical massNumber of molelcules
Total (without water)2,834,28826
Polymers2,834,28826
Non-polymers00
Water0
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: Nucleoporin p54
G: Nucleoporin p58/p45
H: Nuclear pore glycoprotein p62
I: Nuclear pore complex protein Nup93
J: Nucleoporin NUP188 homolog
K: Nuclear pore complex protein Nup155
L: Nucleoporin p54
M: Nucleoporin p58/p45
N: Nuclear pore glycoprotein p62
O: Nuclear pore complex protein Nup93
P: Nuclear pore complex protein Nup205
Q: Nuclear pore complex protein Nup155
R: Nucleoporin p54
S: Nucleoporin p58/p45
T: Nuclear pore glycoprotein p62
U: Nuclear pore complex protein Nup93
V: Nucleoporin NUP188 homolog
W: Nuclear pore complex protein Nup155
X: Nucleoporin p54
Y: Nucleoporin p58/p45
Z: Nuclear pore glycoprotein p62
x 8


Theoretical massNumber of molelcules
Total (without water)22,674,304208
Polymers22,674,304208
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation7
SymmetryPoint symmetry: (Schoenflies symbol: C8 (8 fold cyclic))

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Components

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Nuclear pore complex protein ... , 3 types, 12 molecules ABEKQWCIOUDP

#1: Protein
Nuclear pore complex protein Nup155 / Nuclear pore / 155 kDa nucleoporin / Nucleoporin 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 / Gene: NUP155, KIAA0791 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: O75694
#2: Protein
Nuclear pore complex protein Nup93 / Nuclear pore / 93 kDa nucleoporin / Nucleoporin 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 / Gene: NUP93, KIAA0095 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q8N1F7
#3: Protein Nuclear pore complex protein Nup205 / Nuclear pore / 205 kDa nucleoporin / Nucleoporin Nup205


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
Nucleoporin p54 / 54 kDa nucleoporin / 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 / Gene: NUP54 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q7Z3B4
#5: Protein
Nucleoporin p58/p45 / 58 kDa nucleoporin / Nucleoporin-like protein 1 / 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 / Gene: NUP58, KIAA0410, NUPL1 / Cell line (production host): HELA / Production host: Homo sapiens (human) / References: UniProt: Q9BVL2
#6: Protein
Nuclear pore glycoprotein p62 / / 62 kDa nucleoporin / Nucleoporin Nup62 / NUCLEAR PORE COMPLEX PROTEIN 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
#7: Protein Nucleoporin NUP188 homolog / hNup188 / NUCLEAR PORE COMPLEX PROTEIN NUP188


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

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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-#8 / Source: MULTIPLE SOURCES
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 FIELDBright-field microscopy
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
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
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 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.

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