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- PDB-7x34: Cryo-EM structure of RNC-RAC complex in presence of Ssb from S. c... -

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Basic information

Entry
Database: PDB / ID: 7x34
TitleCryo-EM structure of RNC-RAC complex in presence of Ssb from S. cerevisiae 2
Components
  • RNA (130-mer)
  • Zuotin
KeywordsTRANSLATION/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 / ribosomal subunit export from nucleus / regulation of translational fidelity / 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 / ribosomal subunit export from nucleus / regulation of translational fidelity / Hsp70 protein binding / rRNA processing / protein folding / ribosome binding / transcription coactivator activity / intracellular signal transduction / ribosome / nucleolus / mitochondrion / DNA binding / cytoplasm / cytosol
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / : / Ribosome-associated complex head domain / Zuotin-like, zuotin homology domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain ...Ribosome-associated complex head domain / Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / : / Ribosome-associated complex head domain / Zuotin-like, zuotin homology domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / Zuotin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 3.1 Å
AuthorsChen, Y. / Gao, N.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: 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
DepositionFeb 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.0Jun 29, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Jun 29, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 29, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.2Jun 18, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Zuotin
3: RNA (130-mer)


Theoretical massNumber of molelcules
Total (without water)52,6302
Polymers52,6302
Non-polymers00
Water00
1


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

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Components

#1: Protein Zuotin / DnaJ-related protein ZUO1 / J protein ZUO1 / Heat shock protein 40 homolog ZUO1 / Ribosome- ...DnaJ-related protein ZUO1 / J protein ZUO1 / Heat shock protein 40 homolog ZUO1 / Ribosome-associated complex subunit ZUO1


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 RNA (130-mer) / h44 of 18S rRNA


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
Has protein modificationN

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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: 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 solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65816 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0093009
ELECTRON MICROSCOPYf_angle_d1.1554523
ELECTRON MICROSCOPYf_dihedral_angle_d18.8641229
ELECTRON MICROSCOPYf_chiral_restr0.047588
ELECTRON MICROSCOPYf_plane_restr0.007222

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