[English] 日本語
Yorodumi- PDB-7x34: Cryo-EM structure of RNC-RAC complex in presence of Ssb from S. c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7x34 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of RNC-RAC complex in presence of Ssb from S. cerevisiae 2 | ||||||
Components |
| ||||||
Keywords | TRANSLATION/RNA / RAC / co-translational folding / TRANSLATION / TRANSLATION-RNA complex | ||||||
Function / homology | Function and homology information translational frameshifting / 'de novo' cotranslational protein folding / Regulation of HSF1-mediated heat shock response / protein folding chaperone complex / regulation of translational fidelity / ribosomal subunit export from nucleus / Hsp70 protein binding / rRNA processing / protein folding / ribosome binding ...translational frameshifting / 'de novo' cotranslational protein folding / Regulation of HSF1-mediated heat shock response / protein folding chaperone complex / regulation of translational fidelity / ribosomal subunit export from nucleus / Hsp70 protein binding / rRNA processing / protein folding / ribosome binding / transcription coactivator activity / ribosome / intracellular signal transduction / nucleolus / mitochondrion / DNA binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Chen, Y. / Gao, N. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2022 Title: Structural remodeling of ribosome associated Hsp40-Hsp70 chaperones during co-translational folding. Authors: Yan Chen / Bin Tsai / Ningning Li / Ning Gao / Abstract: Ribosome associated complex (RAC), an obligate heterodimer of HSP40 and HSP70 (Zuo1 and Ssz1 in yeast), is conserved in eukaryotes and functions as co-chaperone for another HSP70 (Ssb1/2 in yeast) to ...Ribosome associated complex (RAC), an obligate heterodimer of HSP40 and HSP70 (Zuo1 and Ssz1 in yeast), is conserved in eukaryotes and functions as co-chaperone for another HSP70 (Ssb1/2 in yeast) to facilitate co-translational folding of nascent polypeptides. Many mechanistic details, such as the coordination of one HSP40 with two HSP70s and the dynamic interplay between RAC-Ssb and growing nascent chains, remain unclear. Here, we report three sets of structures of RAC-containing ribosomal complexes isolated from Saccharomyces cerevisiae. Structural analyses indicate that RAC on the nascent-chain-free ribosome is in an autoinhibited conformation, and in the presence of a nascent chain at the peptide tunnel exit (PTE), RAC undergoes large-scale structural remodeling to make Zuo1 J-Domain more accessible to Ssb. Our data also suggest a role of Zuo1 in orienting Ssb-SBD proximal to the PTE for easy capture of the substrate. Altogether, in accordance with previous data, our work suggests a sequence of structural remodeling events for RAC-Ssb during co-translational folding, triggered by the binding and passage of growing nascent chain from one to another. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7x34.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7x34.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 7x34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7x34_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7x34_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7x34_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 7x34_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/7x34 ftp://data.pdbj.org/pub/pdb/validation_reports/x3/7x34 | HTTPS FTP |
-Related structure data
Related structure data | 32978MC 7x3kC 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
#1: Protein | Mass: 10619.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: ZUO1, YGR285C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32527 |
---|---|
#2: RNA chain | Mass: 42010.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 834774822 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RNC-RAC complex in presence of Ssb from S. cerevisiae 2 Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES |
EM staining | Type: NEGATIVE / Material: Uranyl Acetate |
Vitrification | Cryogen name: NITROGEN |
-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: SPOT SCAN |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65816 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refine LS restraints |
|