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- PDB-7wkk: Cryo-EM structure of the IR subunit from X. laevis NPC -

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Basic information

Entry
Database: PDB / ID: 7wkk
TitleCryo-EM structure of the IR subunit from X. laevis NPC
Components
  • Aaas-prov protein
  • IL4I1 protein
  • MGC83295 protein
  • MGC84997 protein
  • Nuclear pore complex protein Nup93
  • Nucleoporin NDC1
  • Nup155-prov protein
  • Nup188 domain-containing protein
  • Nup54
KeywordsSTRUCTURAL PROTEIN / nuclear pore complex / inner ring / Nup205 / Nup93 / Nup188 / Nup155 / NDC1 / Aladin
Function / homology
Function and homology information


nuclear pore transmembrane ring / protein localization to nuclear inner membrane / 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 / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore ...nuclear pore transmembrane ring / protein localization to nuclear inner membrane / 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 / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / mRNA transport / nuclear pore / nuclear periphery / phospholipid binding / protein import into nucleus / spindle pole / protein transport / nuclear membrane / protein-macromolecule adaptor activity / centrosome / cytosol
Similarity search - Function
: / Nucleoporin protein Ndc1-Nup / Nucleoporin protein Ndc1-Nup / Aladin seven-bladed propeller / Aladin / Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal ...: / Nucleoporin protein Ndc1-Nup / Nucleoporin protein Ndc1-Nup / Aladin seven-bladed propeller / Aladin / Nup188 SH3-like domain / Nucleoporin FG repeated region / Nup54, C-terminal interacting domain / Nup54 C-terminal interacting domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / Nucleoporin p58/p45 / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup188 / 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 / Armadillo-type fold / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nucleoporin NUP188 / 54 kDa nucleoporin / MGC84997 protein / MGC83295 protein / Nucleoporin NDC1 / Aaas-prov protein / Nuclear pore complex protein Nup155 / Nuclear pore complex protein Nup93 / Nuclear pore glycoprotein p62
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHuang, G. / Zhan, X. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2022
Title: Cryo-EM structure of the inner ring from the Xenopus laevis nuclear pore complex.
Authors: Gaoxingyu Huang / Xiechao Zhan / Chao Zeng / Ke Liang / Xuechen Zhu / Yanyu Zhao / Pan Wang / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi /
Abstract: Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an ...Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an average resolution of 4.2 Å. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin hetero-trimer of Nup62/58/54 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure reveals the molecular basis for the IR subunit assembly of a vertebrate NPC.
History
DepositionJan 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MGC83295 protein
B: Nup188 domain-containing protein
C: Nuclear pore complex protein Nup93
D: Nup155-prov protein
E: Nuclear pore complex protein Nup93
F: Nup155-prov protein
G: Nup54
H: IL4I1 protein
I: MGC84997 protein
J: Nup54
L: IL4I1 protein
K: MGC84997 protein
M: Nup155-prov protein
a: MGC83295 protein
b: Nup188 domain-containing protein
c: Nuclear pore complex protein Nup93
d: Nup155-prov protein
e: Nuclear pore complex protein Nup93
f: Nup155-prov protein
g: Nup54
h: IL4I1 protein
i: MGC84997 protein
j: Nup54
l: IL4I1 protein
k: MGC84997 protein
m: Nup155-prov protein
O: Aaas-prov protein
N: Nucleoporin NDC1
o: Aaas-prov protein
n: Nucleoporin NDC1


Theoretical massNumber of molelcules
Total (without water)3,117,50330
Polymers3,117,50330
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 9 types, 30 molecules AaBbCEceDFMdfmGJgjHLhlIKikOoNn

#1: Protein MGC83295 protein / Nup205


Mass: 227854.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642R6
#2: Protein Nup188 domain-containing protein


Mass: 195848.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8F1N1
#3: Protein
Nuclear pore complex protein Nup93 / 93 kDa nucleoporin / An4a / Nucleoporin Nup93


Mass: 93565.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZX96
#4: Protein
Nup155-prov protein


Mass: 154922.422 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZWL0
#5: Protein
Nup54


Mass: 58618.617 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: K9ZTJ6
#6: Protein
IL4I1 protein / Nup62 / Nuclear pore complex glycoprotein p62


Mass: 55969.496 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q91349
#7: Protein
MGC84997 protein / Nup58


Mass: 61216.863 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q5EAX5
#8: Protein Aaas-prov protein / ALADIN


Mass: 57120.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q6DCM0
#9: Protein Nucleoporin NDC1 / xNDC1 / Transmembrane protein 48


Mass: 74420.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q6AX31

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The IR subunit / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Xenopus laevis (African clawed frog)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: 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: 4000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2093631 / Symmetry type: POINT
RefinementHighest resolution: 4.2 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00392625
ELECTRON MICROSCOPYf_angle_d0.485128758
ELECTRON MICROSCOPYf_dihedral_angle_d4.94418476
ELECTRON MICROSCOPYf_chiral_restr0.03917923
ELECTRON MICROSCOPYf_plane_restr0.00318476

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