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- PDB-7wb4: Cryo-EM structure of the NR subunit from X. laevis NPC -

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Entry
Database: PDB / ID: 7wb4
TitleCryo-EM structure of the NR subunit from X. laevis NPC
Components
  • (Nuclear pore complex protein ...) x 3
  • GATOR complex protein SEC13
  • MGC154553 protein
  • MGC83295 protein
  • MGC83926 protein
  • Nuclear pore complex protein
  • Nucleoporin SEH1-B
  • Nup155-prov protein
  • Protein ELYS
  • outer Nup133
  • outer Nup160
KeywordsSTRUCTURAL PROTEIN / nuclear pore complex / nuclear ring / Nup205 / Nup93 / Y complex / Elys
Function / homology
Function and homology information


macromolecule localization / GATOR2 complex / nephron development / macromolecule metabolic process / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nitrogen compound transport / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...macromolecule localization / GATOR2 complex / nephron development / macromolecule metabolic process / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nitrogen compound transport / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / COPII vesicle coat / : / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / RNA export from nucleus / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / mitotic metaphase chromosome alignment / cellular response to nutrient levels / positive regulation of TOR signaling / mRNA transport / mRNA export from nucleus / nuclear pore / positive regulation of TORC1 signaling / cellular response to amino acid starvation / nuclear periphery / kinetochore / protein import into nucleus / protein transport / nuclear membrane / cell division / lysosomal membrane / structural molecule activity / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
ELYS-like domain / ELYS, beta-propeller domain / Nuclear pore complex assembly / beta-propeller of ELYS nucleoporin / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin ...ELYS-like domain / ELYS, beta-propeller domain / Nuclear pore complex assembly / beta-propeller of ELYS nucleoporin / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup37 / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / 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 / Nucleoporin, Nup133/Nup155-like, C-terminal / Nucleoporin FG repeat / Nucleoporin FG repeat region / Non-repetitive/WGA-negative nucleoporin C-terminal / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / 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 autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like / Quinoprotein alcohol dehydrogenase-like superfamily / 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
Uncharacterized protein / Nuclear pore complex protein Nup133 / Nuclear pore complex protein Nup98-Nup96 / Nuclear pore complex protein / MGC154553 protein / Protein ELYS / MGC83295 protein / MGC83926 protein / Nuclear pore complex protein Nup85 / Nucleoporin SEH1-B ...Uncharacterized protein / Nuclear pore complex protein Nup133 / Nuclear pore complex protein Nup98-Nup96 / Nuclear pore complex protein / MGC154553 protein / Protein ELYS / MGC83295 protein / MGC83926 protein / Nuclear pore complex protein Nup85 / Nucleoporin SEH1-B / Nucleoporin 155kDa L homeolog / Nuclear pore complex protein Nup93 / Protein SEC13 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.6 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 nuclear ring from Xenopus laevis nuclear pore complex.
Authors: Gaoxingyu Huang / Xiechao Zhan / Chao Zeng / Xuechen Zhu / Ke Liang / Yanyu Zhao / Pan Wang / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi /
Abstract: Nuclear pore complex (NPC) shuttles cargo across the nuclear envelope. Here we present single-particle cryo-EM structure of the nuclear ring (NR) subunit from Xenopus laevis NPC at an average ...Nuclear pore complex (NPC) shuttles cargo across the nuclear envelope. Here we present single-particle cryo-EM structure of the nuclear ring (NR) subunit from Xenopus laevis NPC at an average resolution of 5.6 Å. The NR subunit comprises two 10-membered Y complexes, each with the nucleoporin ELYS closely associating with Nup160 and Nup37 of the long arm. Unlike the cytoplasmic ring (CR) or inner ring (IR), the NR subunit contains only one molecule each of Nup205 and Nup93. Nup205 binds both arms of the Y complexes and interacts with the stem of inner Y complex from the neighboring subunit. Nup93 connects the stems of inner and outer Y complexes within the same NR subunit, and places its N-terminal extended helix into the axial groove of Nup205 from the neighboring subunit. Together with other structural information, we have generated a composite atomic model of the central ring scaffold that includes the NR, IR, and CR. The IR is connected to the two outer rings mainly through Nup155. This model facilitates functional understanding of vertebrate NPC.
History
DepositionDec 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 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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Assembly

Deposited unit
J: outer Nup133
B: Nuclear pore complex protein Nup85
C: MGC154553 protein
F: MGC83926 protein
d: Nucleoporin SEH1-B
b: Nuclear pore complex protein Nup85
c: MGC154553 protein
E: outer Nup160
e: outer Nup160
f: MGC83926 protein
K: Nup155-prov protein
H: GATOR complex protein SEC13
G: Nuclear pore complex protein Nup96
h: GATOR complex protein SEC13
g: Nuclear pore complex protein Nup96
I: Nuclear pore complex protein
i: Nuclear pore complex protein
L: Nuclear pore complex protein Nup93
A: MGC83295 protein
D: Nucleoporin SEH1-B
O: Nuclear pore complex protein Nup93
M: Nuclear pore complex protein
p: outer Nup133
j: outer Nup133
P: outer Nup133
n: Protein ELYS
N: Protein ELYS


Theoretical massNumber of molelcules
Total (without water)2,926,53927
Polymers2,926,53927
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 , 10 types, 21 molecules JpjPCcFfdDEeKHhIiMAnN

#1: Protein
outer Nup133


Mass: 127551.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8H1I9
#3: Protein MGC154553 protein / outer Nup43


Mass: 41744.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q05AW3
#4: Protein MGC83926 protein


Mass: 36588.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q66IZ6
#5: Protein Nucleoporin SEH1-B / GATOR complex protein SEH1-B / Nup107-160 subcomplex subunit seh1-B


Mass: 39798.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q6GNF1
#6: Protein outer Nup160


Mass: 162658.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8GIX3
#7: Protein Nup155-prov protein


Mass: 154922.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZWL0
#8: Protein GATOR complex protein SEC13 / Protein SEC13 homolog


Mass: 35315.285 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZYJ8
#10: Protein Nuclear pore complex protein


Mass: 105398.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A2RV69
#12: Protein MGC83295 protein


Mass: 227854.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642R6
#13: Protein Protein ELYS / Protein MEL-28 / xELYS


Mass: 268771.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q5U249

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Nuclear pore complex protein ... , 3 types, 6 molecules BbGgLO

#2: Protein Nuclear pore complex protein Nup85 / 85 kDa nucleoporin / Nucleoporin Nup85


Mass: 75160.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q68FJ0
#9: Protein Nuclear pore complex protein Nup96 / Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / ...Nuclear pore complex protein Nup98 / Nuclear pore complex protein Nup98-Nup96 / Nucleoporin Nup96 / Nucleoporin Nup98


Mass: 105079.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HBE3
#11: Protein Nuclear pore complex protein Nup93 / 93 kDa nucleoporin / An4a / Nucleoporin Nup93


Mass: 93565.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZX96

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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 NR 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

CTF correctionType: NONE
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 813020 / Symmetry type: POINT
RefinementHighest resolution: 5.6 Å

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