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- PDB-7per: Model of the inner ring of the human nuclear pore complex -

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Basic information

Entry
Database: PDB / ID: 7per
TitleModel of the inner ring of the human nuclear pore complex
Components
  • (Nuclear pore complex protein ...) x 3
  • Nuclear pore glycoprotein p62
  • Nucleoporin p54
  • Nucleoporin p58/p45
KeywordsTRANSPORT PROTEIN / Nuclear Pore Complex / NPC
Function / homology
Function and homology information


centriole assembly / nuclear pore inner ring / positive regulation of centriole replication / regulation of protein import into nucleus / regulation of Ras protein signal transduction / protein localization to nuclear inner membrane / positive regulation of mitotic cytokinetic process / nuclear envelope organization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore central transport channel ...centriole assembly / nuclear pore inner ring / positive regulation of centriole replication / regulation of protein import into nucleus / regulation of Ras protein signal transduction / protein localization to nuclear inner membrane / positive regulation of mitotic cytokinetic process / 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 / 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 Ras protein signal transduction / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / Flemming body / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / RNA export from nucleus / negative regulation of programmed cell death / NEP/NS2 Interacts with the Cellular Export Machinery / mitotic centrosome separation / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / centrosome cycle / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / Viral Messenger RNA Synthesis / positive regulation of epidermal growth factor receptor signaling pathway / nuclear localization sequence binding / PTB domain binding / mitotic metaphase chromosome alignment / 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 signal transduction / Regulation of HSF1-mediated heat shock response / mRNA transport / protein targeting / mRNA export from nucleus / nuclear pore / SUMOylation of DNA damage response and repair proteins / regulation of mitotic spindle organization / Hsp70 protein binding / positive regulation of mitotic nuclear division / SH2 domain binding / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / ubiquitin binding / Transcriptional regulation by small RNAs / Hsp90 protein binding / mitotic spindle / phospholipid binding / 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
Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin p58/p45 / 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, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup54/Nup57/Nup44 / Nucleoporin p58/p45 / 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 / 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, 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: 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-GM144113 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 1.5Oct 16, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,587,40624
Polymers2,587,40624
Non-polymers00
Water00
1
F: Nucleoporin p54
G: Nucleoporin p58/p45
H: Nuclear pore glycoprotein p62
X: Nucleoporin p54
Y: Nucleoporin p58/p45
Z: Nuclear pore glycoprotein p62
L: Nucleoporin p54
M: Nucleoporin p58/p45
N: Nuclear pore glycoprotein p62
R: Nucleoporin p54
S: Nucleoporin p58/p45
T: Nuclear pore glycoprotein p62
P: Nuclear pore complex protein Nup205
V: Nuclear pore complex protein Nup205
D: Nuclear pore complex protein Nup205
J: Nuclear pore complex protein Nup205
W: Nuclear pore complex protein Nup155
K: Nuclear pore complex protein Nup155
C: Nuclear pore complex protein Nup93
I: Nuclear pore complex protein Nup93
O: Nuclear pore complex protein Nup93
U: Nuclear pore complex protein Nup93
E: Nuclear pore complex protein Nup155
Q: Nuclear pore complex protein Nup155
x 8


Theoretical massNumber of molelcules
Total (without water)20,699,247192
Polymers20,699,247192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation7

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Components

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Protein , 3 types, 12 molecules FXLRGYMSHZNT

#1: Protein
Nucleoporin p54 / 54 kDa nucleoporin / NUCLEAR PORE COMPLEX PROTEIN NUP54


Mass: 55491.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7Z3B4
#2: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BVL2
#3: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37198

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

#4: Protein
Nuclear pore complex protein Nup205 / 205 kDa nucleoporin / Nucleoporin Nup205


Mass: 228172.875 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92621
#5: Protein
Nuclear pore complex protein Nup155 / 155 kDa nucleoporin / Nucleoporin Nup155


Mass: 155357.281 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75694
#6: Protein
Nuclear pore complex protein Nup93 / 93 kDa nucleoporin / Nucleoporin Nup93


Mass: 93599.102 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N1F7

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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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.

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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: 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)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: UCSF Chimera / Version: 1.14 / Category: model 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: 5IJN

5ijn


Accession code: 5IJN / Source name: PDB / Type: experimental model

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