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Entry
Database: PDB / ID: 7tdz
TitleCryo-EM model of protomer of the cytoplasmic ring of the nuclear pore complex from Xenopus laevis
Components
  • (Nuclear pore complex protein ...Nuclear pore) x 2
  • Nuclear pore complex proteinNuclear pore
  • Nucleoporin SEH1-A
  • Nup133Nuclear pore complex protein Nup133
  • Nup155-prov protein
  • Nup160Nucleoporin 160
  • Nup205Nucleoporin 205
  • Nup214
  • Nup358RANBP2
  • Nup37Nucleoporin 37
  • Nup42
  • Nup62Nuclear pore glycoprotein p62
  • Nup88A protein
  • Protein SEC13 homolog
KeywordsNUCLEAR PROTEIN / Nuclear pore complex
Function / homology
Function and homology information


macromolecule localization / GATOR2 complex / nephron development / macromolecule metabolic process / nuclear pore inner ring / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nitrogen compound transport / nuclear pore central transport channel ...macromolecule localization / GATOR2 complex / nephron development / macromolecule metabolic process / nuclear pore inner ring / protein localization to nuclear inner membrane / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nitrogen compound transport / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / : / nuclear pore organization / nuclear pore outer ring / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / COPII vesicle coat / 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 / 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 / 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 / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Nucleoporin Nup88 / Nuclear pore component / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / Nucleoporin Nup37 / Nucleoporin, NSP1-like, C-terminal / Nucleoporin NSP1/NUP62 / Nsp1-like C-terminal region / Nucleoporin Nup85-like ...Nucleoporin Nup88 / Nuclear pore component / Nucleoporin NUP88/NUP82 / Nuclear pore complex protein NUP98-NUP96 / Nucleoporin, Nup155-like, C-terminal, subdomain 3 / 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, Nup155-like / Nucleoporin, Nup155-like, C-terminal, subdomain 1 / Nucleoporin, Nup155-like, C-terminal, subdomain 2 / Nucleoporin Nup186/Nup192/Nup205 / Nuclear pore complex protein / Nuclear pore complex scaffold, nucleoporins 186/192/205 / 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
Uncharacterized protein / Nuclear pore complex protein Nup133 / Nuclear pore complex protein Nup98-Nup96 / RANBP2-like and GRIP domain-containing protein 3 isoform X2 / Nuclear pore complex protein / MGC154553 protein / Nucleoporin SEH1-A / Nup88A protein / MGC83295 protein / MGC83926 protein ...Uncharacterized protein / Nuclear pore complex protein Nup133 / Nuclear pore complex protein Nup98-Nup96 / RANBP2-like and GRIP domain-containing protein 3 isoform X2 / Nuclear pore complex protein / MGC154553 protein / Nucleoporin SEH1-A / Nup88A protein / MGC83295 protein / MGC83926 protein / Nuclear pore complex protein Nup85 / Nucleoporin 155kDa L homeolog / Protein SEC13 homolog / IL4I1 protein / Nucleoporin CAN
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsFontana, P. / Wu, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Science / Year: 2022
Title: Structure of cytoplasmic ring of nuclear pore complex by integrative cryo-EM and AlphaFold.
Authors: Pietro Fontana / Ying Dong / Xiong Pi / Alexander B Tong / Corey W Hecksel / Longfei Wang / Tian-Min Fu / Carlos Bustamante / Hao Wu /
Abstract: INTRODUCTION The nuclear pore complex (NPC) is the molecular conduit in the nuclear membrane of eukaryotic cells that regulates import and export of biomolecules between the nucleus and the cytosol, ...INTRODUCTION The nuclear pore complex (NPC) is the molecular conduit in the nuclear membrane of eukaryotic cells that regulates import and export of biomolecules between the nucleus and the cytosol, with vertebrate NPCs ~110 to 125 MDa in molecular mass and ~120 nm in diameter. NPCs are organized into four main rings: the cytoplasmic ring (CR) at the cytosolic side, the inner ring and the luminal ring on the plane of the nuclear membrane, and the nuclear ring facing the nucleus. Each ring possesses an approximate eightfold symmetry and is composed of multiple copies of different nucleoporins. NPCs have been implicated in numerous biological processes, and their dysfunctions are associated with a growing number of serious human diseases. However, despite pioneering studies from many groups over the past two decades, we still lack a full understanding of NPCs' organization, dynamics, and complexity. RATIONALE We used the oocyte as a model system for the structural characterization because each oocyte possesses a large number of NPC particles that can be visualized on native nuclear membranes without the aid of detergent extraction. We used single-particle cryo-electron microscopy (cryo-EM) analysis on data collected at different stage tilt angles for three-dimensional reconstruction and structure prediction with AlphaFold for model building. RESULTS We reconstructed the CR map of NPC at 6.9 and 6.7 Å resolutions for the full CR protomer and a core region, respectively, and predicted the structures of the individual nucleoporins using AlphaFold because no high-resolution models of Nups were available. For any ambiguous subunit interactions, we also predicted complex structures, which further guided model fitting of the CR protomer. We placed the nucleoporin or complex structures into the CR density to obtain an almost full CR atomic model, composed of the inner and outer Y-complexes, two copies of Nup205, two copies of the Nup214-Nup88-Nup62 complex, one Nup155, and five copies of Nup358. In particular, we predicted the largest protein in the NPC, Nup358, as having an S-shaped globular domain, a coiled-coil domain, and a largely disordered C-terminal region containing phenylalanine-glycine (FG) repeats previously shown to form a gel-like condensate phase for selective cargo passage. Four of the Nup358 copies clamp around the inner and outer Y-complexes to stabilize the CR, and the fifth Nup358 situates in the center of the cluster of clamps. AlphaFold also predicted a homo-oligomeric, likely specifically pentameric, coiled-coil structure of Nup358 that may provide the avidity for Nup358 recruitment to the NPC and for lowering the threshold for Nup358 condensation in NPC biogenesis. CONCLUSION Our studies offer an example of integrative cryo-EM and structure prediction as a general approach for attaining more precise models of megadalton protein complexes from medium-resolution density maps. The more accurate and almost complete model of the CR presented here expands our understanding of the molecular interactions in the NPC and represents a substantial step forward toward the molecular architecture of a full NPC, with implications for NPC function, biogenesis, and regulation. [Figure: see text].
History
DepositionJan 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Nuclear pore complex protein
h: Nuclear pore complex protein
t: Nup62
s: Nup214
r: Nup88A protein
g: Protein SEC13 homolog
G: Protein SEC13 homolog
L: Nup205
l: Nup205
E: Nucleoporin SEH1-A
e: Nucleoporin SEH1-A
D: Nup42
d: Nup42
C: Nuclear pore complex protein Nup85
c: Nuclear pore complex protein Nup85
U: Nup155-prov protein
P: Nup358
O: Nup358
Q: Nup358
N: Nup358
M: Nup358
B: Nup37
b: Nup37
A: Nup160
a: Nup160
I: Nup133
F: Nuclear pore complex protein Nup96
f: Nuclear pore complex protein Nup96
R: Nup88A protein
S: Nup214
i: Nup133
T: Nup62


Theoretical massNumber of molelcules
Total (without water)4,313,68132
Polymers4,313,68132
Non-polymers00
Water0
1


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

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Components

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Protein , 13 types, 28 molecules HhtTsSrRgGLlEeDdUPOQNMBbAaIi

#1: 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
#2: Protein Nup62 / Nuclear pore glycoprotein p62 / 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
#3: Protein Nup214 / 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
#4: 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
#5: Protein Protein SEC13 homolog / GATOR complex protein SEC13


Mass: 33914.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZYJ8
#6: Protein Nup205 / Nucleoporin 205 / 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
#7: Protein Nucleoporin SEH1-A / GATOR complex protein SEH1-A / Nup107-160 subcomplex subunit seh1-A


Mass: 36037.664 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q4FZW5
#8: Protein Nup42 / MGC154553 protein


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
#10: 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
#11: Protein
Nup358 / RANBP2


Mass: 322784.344 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HGL2
#12: Protein Nup37 / Nucleoporin 37 / 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
#13: Protein Nup160 / Nucleoporin 160


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
#14: Protein Nup133 / Nuclear pore complex protein 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

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Nuclear pore complex protein ... , 2 types, 4 molecules CcFf

#9: 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
#15: 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: 77887.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HBE3

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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: Cytoplasmic ring of nuclear pore complex / 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333214 / Symmetry type: POINT

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