+Open data
-Basic information
Entry | Database: PDB / ID: 8hbn | ||||||
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Title | Structure of the Mex67-Mtr2-1 heterodimer | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / nuclear export factor | ||||||
Function / homology | Function and homology information nuclear RNA export factor complex / nuclear pore central transport channel / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNA binding / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding ...nuclear RNA export factor complex / nuclear pore central transport channel / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNA binding / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / mRNA export from nucleus / U6 snRNA binding / nuclear pore / U1 snRNA binding / mRNA binding / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å | ||||||
Authors | Li, Z.Q. / Chen, S.J. / Sui, S.F. | ||||||
Funding support | China, 1items
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Citation | Journal: Nature / Year: 2023 Title: Nuclear export of pre-60S particles through the nuclear pore complex. Authors: Zongqiang Li / Shuaijiabin Chen / Liang Zhao / Guoqiang Huang / Huiqin Xu / Xiaoyun Yang / Peiyi Wang / Ning Gao / Sen-Fang Sui / Abstract: The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal ...The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm. The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the export of these gigantic ribonucleoproteins requires numerous export factors. Here we report the cryo-electron microscopy structure of native pre-60S particles trapped in the channel of yeast NPCs. In addition to known assembly factors, multiple factors with export functions are also included in the structure. These factors in general bind to either the flexible regions or subunit interface of the pre-60S particle, and virtually form many anchor sites for NPC binding. Through interactions with phenylalanine-glycine (FG) repeats from various nucleoporins of NPC, these factors collectively facilitate the passage of the pre-60S particle through the central FG repeat network of the NPC. Moreover, in silico analysis of the axial and radial distribution of pre-60S particles within the NPC shows that a single NPC can take up to four pre-60S particles simultaneously, and pre-60S particles are enriched in the inner ring regions close to the wall of the NPC with the solvent-exposed surface facing the centre of the nuclear pore. Our data suggest a translocation model for the export of pre-60S particles through the NPC. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hbn.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hbn.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hbn_validation.pdf.gz | 366.7 KB | Display | wwPDB validaton report |
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Full document | 8hbn_full_validation.pdf.gz | 379.2 KB | Display | |
Data in XML | 8hbn_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 8hbn_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/8hbn ftp://data.pdbj.org/pub/pdb/validation_reports/hb/8hbn | HTTPS FTP |
-Related structure data
Related structure data | 34638MC 8hfrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 67417.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MEX67, YPL169C, P2520 / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q99257 |
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#2: Protein | Mass: 20802.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: MTR2, YKL186C / Production host: Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P34232 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mex67-Mtr2-1 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Buffer solution | pH: 7.4 |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 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: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86343 / Symmetry type: POINT |