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- EMDB-32061: Cryo-EM structure of Xenopus laevis nuclear pore complex cytoplas... -

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Basic information

Entry
Database: EMDB / ID: EMD-32061
TitleCryo-EM structure of Xenopus laevis nuclear pore complex cytoplasmic ring Nup358 region
Map data
Sample
  • Complex: nuclear pore complex cytoplasmic ring
Keywordscytoplasmic ring / cryo-EM / nuclear pore complex / Xenopus laevis / NUCLEAR PROTEIN
Function / homology
Function and homology information


GATOR2 complex / nephron development / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly ...GATOR2 complex / nephron development / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore inner ring / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / nuclear pore complex assembly / nuclear pore organization / COPII vesicle coat / nuclear pore cytoplasmic filaments / 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 / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / mitotic metaphase chromosome alignment / NLS-bearing protein import into nucleus / cellular response to nutrient levels / ribosomal large subunit export from nucleus / positive regulation of TOR signaling / mRNA transport / ribosomal small subunit export from nucleus / mRNA export from nucleus / nuclear pore / positive regulation of TORC1 signaling / cellular response to amino acid starvation / nuclear periphery / GTPase activator activity / phospholipid binding / kinetochore / protein import into nucleus / protein transport / nuclear membrane / lysosomal membrane / cell division / structural molecule activity / positive regulation of DNA-templated transcription / RNA binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Nucleoporin Nup88 / Nuclear pore component / Nucleoporin NUP88/NUP82 / Nucleoporin Nup37 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nup98, Gle2-binding sequence / Nucleoporin Nup85-like / Nucleoporin Nup120/160 ...Nucleoporin Nup88 / Nuclear pore component / Nucleoporin NUP88/NUP82 / Nucleoporin Nup37 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nup98, Gle2-binding sequence / 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. / 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 / 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 / Nucleoporin 88kDa L homeolog / 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 / Nucleoporin 88kDa L homeolog / MGC83295 protein / MGC83926 protein / Nuclear pore complex protein Nup85 / Nuclear pore complex protein Nup93 / Protein SEC13 homolog / IL4I1 protein / Nucleoporin 214 L homeolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsTai L / Zhu Y / Sun F
Funding support1 items
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, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32061.png

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Map

FileDownload / File: emd_32061.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.24 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-1.1682956 - 2.463604
Average (Standard dev.)0.00991502 (±0.09946171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 716.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.242.242.24
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z716.800716.800716.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.1682.4640.010

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Supplemental data

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Mask #1

Fileemd_32061_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_32061_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_32061_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : nuclear pore complex cytoplasmic ring

EntireName: nuclear pore complex cytoplasmic ring
Components
  • Complex: nuclear pore complex cytoplasmic ring

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Supramolecule #1: nuclear pore complex cytoplasmic ring

SupramoleculeName: nuclear pore complex cytoplasmic ring / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3103

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67886
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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