[English] 日本語
Yorodumi
- PDB-7peq: Model of the outer rings of the human nuclear pore complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7peq
TitleModel of the outer rings of the human nuclear pore complex
Components
  • (Nuclear pore complex protein ...) x 5
  • Nucleoporin Nup37
  • Nucleoporin Nup43
  • Nucleoporin SEH1
  • Protein SEC13 homolog
KeywordsTRANSPORT PROTEIN / Nuclear Pore Complex / NPC
Function / homology
Function and homology information


GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery ...GATOR2 complex / nephron development / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / COPII-coated vesicle cargo loading / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / nuclear pore organization / somite development / COPII vesicle coat / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / paraxial mesoderm development / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Amino acids regulate mTORC1 / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / attachment of mitotic spindle microtubules to kinetochore / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / protein-containing complex localization / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / nuclear localization sequence binding / positive regulation of mRNA splicing, via spliceosome / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / COPII-mediated vesicle transport / neural tube development / nucleocytoplasmic transport / lamellipodium assembly / Viral Messenger RNA Synthesis / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / SUMOylation of ubiquitinylation proteins / female gonad development / Vpr-mediated nuclear import of PICs / macrophage chemotaxis / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / mRNA transport / Regulation of HSF1-mediated heat shock response / cellular response to nutrient levels / mRNA export from nucleus / nuclear pore / SUMOylation of DNA damage response and repair proteins / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of TORC1 signaling / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / positive regulation of TORC1 signaling / serine-type peptidase activity / nuclear periphery / cellular response to amino acid starvation / SUMOylation of chromatin organization proteins / HCMV Late Events / neurogenesis / chromosome segregation / promoter-specific chromatin binding / RHO GTPases Activate Formins / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / Transcriptional regulation by small RNAs / ER to Golgi transport vesicle membrane / molecular condensate scaffold activity / kinetochore / ISG15 antiviral mechanism / spindle / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / protein transport / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / defense response to Gram-positive bacterium / nuclear speck / ribonucleoprotein complex / lysosomal membrane / cell division / intracellular membrane-bounded organelle
Similarity search - Function
Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nup98, Gle2-binding sequence / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, C-terminal ...Nucleoporin Nup120/160, beta-propeller domain / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nup98, Gle2-binding sequence / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, C-terminal / Non-repetitive/WGA-negative nucleoporin C-terminal / Sec13/Seh1 family / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nup98-96 autopeptidase S59 / NUP C-terminal domain profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96 / Protein SEC13 homolog / Nuclear pore complex protein Nup107 / Nuclear pore complex protein Nup160 / Nucleoporin Nup43 / Nucleoporin Nup37 / Nuclear pore complex protein Nup133 / Nucleoporin SEH1 / Nuclear pore complex protein Nup85
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 35 Å
AuthorsSchuller, A.P. / Wojtynek, M. / Mankus, D. / Tatli, M. / Kronenberg-Tenga, R. / Regmi, S.G. / Dasso, M. / Weis, K. / Medalia, O. / Schwartz, T.U.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM77537 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141834 Switzerland
Swiss National Science FoundationSNSF 31003A_179418 Switzerland
CitationJournal: Nature / Year: 2021
Title: The cellular environment shapes the nuclear pore complex architecture.
Authors: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / ...Authors: Anthony P Schuller / Matthias Wojtynek / David Mankus / Meltem Tatli / Rafael Kronenberg-Tenga / Saroj G Regmi / Phat V Dip / Abigail K R Lytton-Jean / Edward J Brignole / Mary Dasso / Karsten Weis / Ohad Medalia / Thomas U Schwartz /
Abstract: Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about ...Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE). These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.
History
DepositionAug 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 10, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 17, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Nov 24, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.5Jul 17, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Movie
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-12814
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-12814
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AC: Nuclear pore complex protein Nup133
AD: Nuclear pore complex protein Nup107
AE: Nuclear pore complex protein Nup96
AF: Protein SEC13 homolog
AG: Nucleoporin SEH1
AH: Nuclear pore complex protein Nup85
AI: Nucleoporin Nup43
AJ: Nuclear pore complex protein Nup160
AK: Nucleoporin Nup37
BC: Nuclear pore complex protein Nup133
BD: Nuclear pore complex protein Nup107
BE: Nuclear pore complex protein Nup96
BF: Protein SEC13 homolog
BG: Nucleoporin SEH1
BH: Nuclear pore complex protein Nup85
BI: Nucleoporin Nup43
BJ: Nuclear pore complex protein Nup160
BK: Nucleoporin Nup37
CC: Nuclear pore complex protein Nup133
CD: Nuclear pore complex protein Nup107
CE: Nuclear pore complex protein Nup96
CF: Protein SEC13 homolog
CG: Nucleoporin SEH1
CH: Nuclear pore complex protein Nup85
CI: Nucleoporin Nup43
CJ: Nuclear pore complex protein Nup160
CK: Nucleoporin Nup37
DC: Nuclear pore complex protein Nup133
DD: Nuclear pore complex protein Nup107
DE: Nuclear pore complex protein Nup96
DF: Protein SEC13 homolog
DG: Nucleoporin SEH1
DH: Nuclear pore complex protein Nup85
DI: Nucleoporin Nup43
DJ: Nuclear pore complex protein Nup160
DK: Nucleoporin Nup37


Theoretical massNumber of molelcules
Total (without water)2,933,04736
Polymers2,933,04736
Non-polymers00
Water00
1
AC: Nuclear pore complex protein Nup133
AD: Nuclear pore complex protein Nup107
AE: Nuclear pore complex protein Nup96
AF: Protein SEC13 homolog
AG: Nucleoporin SEH1
AH: Nuclear pore complex protein Nup85
AI: Nucleoporin Nup43
AJ: Nuclear pore complex protein Nup160
AK: Nucleoporin Nup37
BC: Nuclear pore complex protein Nup133
BD: Nuclear pore complex protein Nup107
BE: Nuclear pore complex protein Nup96
BF: Protein SEC13 homolog
BG: Nucleoporin SEH1
BH: Nuclear pore complex protein Nup85
BI: Nucleoporin Nup43
BJ: Nuclear pore complex protein Nup160
BK: Nucleoporin Nup37
CC: Nuclear pore complex protein Nup133
CD: Nuclear pore complex protein Nup107
CE: Nuclear pore complex protein Nup96
CF: Protein SEC13 homolog
CG: Nucleoporin SEH1
CH: Nuclear pore complex protein Nup85
CI: Nucleoporin Nup43
CJ: Nuclear pore complex protein Nup160
CK: Nucleoporin Nup37
DC: Nuclear pore complex protein Nup133
DD: Nuclear pore complex protein Nup107
DE: Nuclear pore complex protein Nup96
DF: Protein SEC13 homolog
DG: Nucleoporin SEH1
DH: Nuclear pore complex protein Nup85
DI: Nucleoporin Nup43
DJ: Nuclear pore complex protein Nup160
DK: Nucleoporin Nup37
x 8


Theoretical massNumber of molelcules
Total (without water)23,464,375288
Polymers23,464,375288
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation7

-
Components

-
Nuclear pore complex protein ... , 5 types, 20 molecules ACBCCCDCADBDCDDDAEBECEDEAHBHCHDHAJBJCJDJ

#1: Protein
Nuclear pore complex protein Nup133 / 133 kDa nucleoporin / Nucleoporin Nup133


Mass: 129108.461 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WUM0
#2: Protein
Nuclear pore complex protein Nup107 / 107 kDa nucleoporin / Nucleoporin Nup107


Mass: 106504.969 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P57740
#3: Protein
Nuclear pore complex protein Nup96 / 96 kDa nucleoporin / Nucleoporin Nup96 / Nup96


Mass: 106039.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52948
#6: Protein
Nuclear pore complex protein Nup85 / 85 kDa nucleoporin / FROUNT / Nucleoporin Nup75 / Nucleoporin Nup85 / Pericentrin-1


Mass: 75105.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BW27
#8: Protein
Nuclear pore complex protein Nup160 / 160 kDa nucleoporin / Nucleoporin Nup160


Mass: 162280.203 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q12769

-
Protein , 4 types, 16 molecules AFBFCFDFAGBGCGDGAIBICIDIAKBKCKDK

#4: Protein
Protein SEC13 homolog / GATOR complex protein SEC13 / SEC13-like protein 1 / SEC13-related protein


Mass: 35578.438 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55735
#5: Protein
Nucleoporin SEH1 / GATOR complex protein SEH1 / Nup107-160 subcomplex subunit SEH1 / SEC13-like protein


Mass: 39700.566 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EE3
#7: Protein
Nucleoporin Nup43 / Nup107-160 subcomplex subunit Nup43 / p42


Mass: 42195.652 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NFH3
#9: Protein
Nucleoporin Nup37 / p37 / Nup107-160 subcomplex subunit Nup37


Mass: 36748.512 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NFH4

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Nup96::Neon-AID DLD-1 / Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: cryo-FIB milled sections of DLD1 cells
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: Cells were grown on holey carbon, Au-mesh supports. Grids were rinsed briefly with PBS and manually blotted before plunging into liquid ethane.

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 2.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1IMOD4.11.6volume selection
7UCSF Chimera1.14model fitting
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C8 (8 fold cyclic)
3D reconstructionResolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1252 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionNum. of tomograms: 54 / Num. of volumes extracted: 1552
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 5A9Q

5a9q


Accession code: 5A9Q / Source name: PDB / Type: experimental model
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 78.15 Å2 / Biso mean: 0.9902 Å2 / Biso min: 0 Å2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more