[English] 日本語
Yorodumi- PDB-7woo: Cryo-EM structure of the inner ring protomer of the Saccharomyces... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7woo | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN / nuclear pore complex / inner ring / protomer / Saccharomyces cerevisiae | ||||||
Function / homology | Function and homology information nuclear pore linkers / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / nuclear pore inner ring / regulation of nucleocytoplasmic transport / chromosome, subtelomeric region / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore complex assembly ...nuclear pore linkers / mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / nuclear pore inner ring / regulation of nucleocytoplasmic transport / chromosome, subtelomeric region / nuclear pore central transport channel / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / Transport of Mature mRNA derived from an Intron-Containing Transcript / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Regulation of HSF1-mediated heat shock response / nuclear pore nuclear basket / SUMOylation of SUMOylation proteins / tRNA export from nucleus / SUMOylation of RNA binding proteins / structural constituent of nuclear pore / SUMOylation of chromatin organization proteins / RNA export from nucleus / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear localization sequence binding / NLS-bearing protein import into nucleus / ribosomal large subunit export from nucleus / mRNA transport / nuclear pore / ribosomal small subunit export from nucleus / nuclear periphery / molecular condensate scaffold activity / chromosome segregation / promoter-specific chromatin binding / heterochromatin formation / phospholipid binding / protein import into nucleus / nuclear envelope / protein transport / nuclear membrane / amyloid fibril formation / chromatin binding / protein-containing complex binding / DNA binding / RNA binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.71 Å | ||||||
Authors | Li, Z.Q. / Chen, S.J.B. / Zhao, L. / Sui, S.F. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Cell Res / Year: 2022 Title: Near-atomic structure of the inner ring of the Saccharomyces cerevisiae nuclear pore complex. Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Xiong Pi / Shan Sun / Peiyi Wang / Sen-Fang Sui / Abstract: Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their ...Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their huge size and highly dynamic nature. Here we determined the structure of the asymmetric unit of the inner ring (IR monomer) at 3.73 Å resolution by single-particle cryo-electron microscopy, and created an atomic model of the intact IR consisting of 192 molecules of 8 nucleoporins. In each IR monomer, the Z-shaped Nup188-Nup192 complex in the middle layer is sandwiched by two approximately parallel rhomboidal structures in the inner and outer layers, while Nup188, Nup192 and Nic96 link all subunits to constitute a relatively stable IR monomer. In contrast, the intact IR is assembled by loose and instable interactions between IR monomers. These structures, together with previously reported structural information of IR, reveal two distinct interaction modes between IR monomers and extensive flexible connections in IR assembly, providing a structural basis for the stability and malleability of IR. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7woo.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7woo.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 7woo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7woo_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7woo_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7woo_validation.xml.gz | 238.6 KB | Display | |
Data in CIF | 7woo_validation.cif.gz | 360.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/7woo ftp://data.pdbj.org/pub/pdb/validation_reports/wo/7woo | HTTPS FTP |
-Related structure data
Related structure data | 32653MC 7wo9C 7wotC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 8 types, 12 molecules AZCDEFGJHKIL
#1: Protein | Mass: 96291.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P34077 #2: Protein | | Mass: 156827.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40064 #3: Protein | | Mass: 169651.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38181 #4: Protein | | Mass: 188753.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P52593 #5: Protein | | Mass: 191718.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P47054 #6: Protein | Mass: 49174.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q02199 #7: Protein | Mass: 57547.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P48837 #8: Protein | Mass: 86611.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P14907 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Cryo-EM structure of the inner ring protomer of the Saccharomyces cerevisiae nuclear pore complex Type: COMPLEX / Entity ID: #4 / Source: NATURAL |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE |
---|---|
3D reconstruction | Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1266268 / Symmetry type: POINT |