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- PDB-7vop: Cryo-EM structure of Xenopus laevis nuclear pore complex cytoplas... -

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Basic information

Entry
Database: PDB / ID: 7vop
TitleCryo-EM structure of Xenopus laevis nuclear pore complex cytoplasmic ring subunit
Components
  • (Nuclear pore complex protein ...Nuclear pore) x 3
  • GATOR complex protein SEC13
  • IL4I1 protein
  • MGC154553 protein
  • MGC83295 protein
  • MGC83926 protein
  • Nuclear pore complex proteinNuclear pore
  • Nucleoporin 160kDa
  • Nucleoporin CAN
  • Nucleoporin SEH1-A
  • Nup358RANBP2
  • Nup88A protein
  • outer Nup133
KeywordsNUCLEAR PROTEIN / cytoplasmic ring / cryo-EM / nuclear pore complex / Xenopus laevis
Function / homology
Function and homology information


GATOR2 complex / nephron development / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / mitotic metaphase chromosome alignment / cellular response to nutrient levels / ribosomal small subunit export from nucleus ...GATOR2 complex / nephron development / nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / attachment of mitotic spindle microtubules to kinetochore / structural constituent of nuclear pore / mitotic metaphase chromosome alignment / cellular response to nutrient levels / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / intracellular transport / mRNA transport / nuclear pore / positive regulation of TORC1 signaling / nuclear periphery / kinetochore / protein transport / nuclear membrane / lysosomal membrane / cell division / structural molecule activity / metal ion binding / nucleus / cytosol
Similarity search - Function
Nucleoporin Nup88 / Nuclear pore component / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin Nup37 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin Nup85-like / Nucleoporin Nup120/160 ...Nucleoporin Nup88 / Nuclear pore component / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin Nup37 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin Nup85-like / Nucleoporin Nup120/160 / Nup85 Nucleoporin / Nuclear pore protein 84/107 / Nuclear pore protein 84 / 107 / Nuclear pore complex protein Nup133-like / Nup358/RanBP2 E3 ligase domain / Nup358/RanBP2 E3 ligase domain / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex protein / 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 / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96 / Nuclear pore complex protein Nup133 / RANBP2-like and GRIP domain-containing protein 3 isoform X2 / Nucleoporin 160kDa / Nuclear pore complex protein / MGC154553 protein / Nucleoporin SEH1-A / Nup88A protein / MGC83295 protein / MGC83926 protein ...Nuclear pore complex protein Nup98-Nup96 / Nuclear pore complex protein Nup133 / RANBP2-like and GRIP domain-containing protein 3 isoform X2 / Nucleoporin 160kDa / Nuclear pore complex protein / MGC154553 protein / Nucleoporin SEH1-A / Nup88A protein / MGC83295 protein / MGC83926 protein / Nuclear pore complex protein Nup85 / Nuclear pore complex protein Nup93 / Protein SEC13 homolog / IL4I1 protein / Nucleoporin CAN
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsTai, L. / Zhu, Y. / Sun, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Cell / Year: 2022
Title: 8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI.
Authors: Linhua Tai / Yun Zhu / He Ren / Xiaojun Huang / Chuanmao Zhang / Fei Sun /
Abstract: The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo- ...The nuclear pore complex (NPC), one of the largest protein complexes in eukaryotes, serves as a physical gate to regulate nucleocytoplasmic transport. Here, we determined the 8 Å resolution cryo-electron microscopic (cryo-EM) structure of the outer rings containing nuclear ring (NR) and cytoplasmic ring (CR) from the Xenopus laevis NPC, with local resolutions reaching 4.9 Å. With the aid of AlphaFold2, we managed to build a pseudoatomic model of the outer rings, including the Y complexes and flanking components. In this most comprehensive and accurate model of outer rings to date, the almost complete Y complex structure exhibits much tighter interaction in the hub region. In addition to two copies of Y complexes, each asymmetric subunit in CR contains five copies of Nup358, two copies of the Nup214 complex, two copies of Nup205 and one copy of newly identified Nup93, while that in NR contains one copy of Nup205, one copy of ELYS and one copy of Nup93. These in-depth structural features represent a great advance in understanding the assembly of NPCs.
History
DepositionOct 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 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

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Structure visualization

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Assembly

Deposited unit
A: Nuclear pore complex protein Nup85
B: MGC154553 protein
C: Nucleoporin SEH1-A
D: Nucleoporin 160kDa
E: MGC83926 protein
F: Nuclear pore complex protein Nup96
G: GATOR complex protein SEC13
H: Nuclear pore complex protein
I: outer Nup133
J: Nuclear pore complex protein Nup85
K: MGC154553 protein
L: Nucleoporin SEH1-A
M: Nucleoporin 160kDa
N: MGC83926 protein
O: Nuclear pore complex protein Nup96
P: GATOR complex protein SEC13
Q: Nuclear pore complex protein
R: outer Nup133
S: MGC83295 protein
T: MGC83295 protein
U: Nuclear pore complex protein Nup93
V: Nup358
W: Nup358
X: Nup358
Y: Nup358
Z: Nup358
a: Nucleoporin CAN
b: Nup88A protein
c: IL4I1 protein
d: Nup88A protein
e: Nucleoporin CAN
f: IL4I1 protein


Theoretical massNumber of molelcules
Total (without water)4,326,61532
Polymers4,326,61532
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Nuclear pore complex protein ... , 3 types, 5 molecules AJFOU

#1: Protein Nuclear pore complex protein Nup85 / Nuclear pore / 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
#6: Protein Nuclear pore complex protein Nup96 / Nuclear pore / 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: 104742.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1B8XZT4
#11: Protein Nuclear pore complex protein Nup93 / Nuclear pore / 93 kDa nucleoporin / An4a / Nucleoporin Nup93


Mass: 93565.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZX96

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Protein , 12 types, 27 molecules BKCLDMENGPHQIRSTVWXYZaebdcf

#2: 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
#3: Protein Nucleoporin SEH1-A / GATOR complex protein SEH1-A / Nup107-160 subcomplex subunit seh1-A


Mass: 39777.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q4FZW5
#4: Protein Nucleoporin 160kDa


Mass: 160427.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A6I8QA34
#5: 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
#7: 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
#8: Protein Nuclear pore complex protein / Nuclear pore


Mass: 105398.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A2RV69
#9: Protein outer Nup133


Mass: 127551.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8H1I9
#10: Protein MGC83295 protein


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
#12: Protein
Nup358 / RANBP2


Mass: 325736.625 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HGL2
#13: Protein Nucleoporin CAN


Mass: 209080.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q9PVZ2
#14: Protein Nup88A protein


Mass: 82573.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q4KLQ6
#15: Protein IL4I1 protein / Nuclear pore complex glycoprotein p62


Mass: 55969.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q91349

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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: nuclear pore complex cytoplasmic ring / 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 FIELDBright-field microscopy / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 354460 / Symmetry type: POINT

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