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- EMDB-32991: Cryo-EM structure of RAC in the State C2 RNC-RAC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32991
TitleCryo-EM structure of RAC in the State C2 RNC-RAC complex
Map data
Sample
  • Complex: RAC in the State C2 RNC-RAC complex
    • Protein or peptide: Zuotin
    • Protein or peptide: Ribosome-associated complex subunit SSZ1
Function / homology
Function and homology information


translational frameshifting / 'de novo' cotranslational protein folding / : / misfolded protein binding / protein folding chaperone complex / ribosomal subunit export from nucleus / regulation of translational fidelity / chaperone-mediated protein folding / protein folding chaperone / Hsp70 protein binding ...translational frameshifting / 'de novo' cotranslational protein folding / : / misfolded protein binding / protein folding chaperone complex / ribosomal subunit export from nucleus / regulation of translational fidelity / chaperone-mediated protein folding / protein folding chaperone / Hsp70 protein binding / heat shock protein binding / rRNA processing / unfolded protein binding / ribosome binding / protein folding / cytoplasmic translation / protein refolding / transcription coactivator activity / ribosome / intracellular signal transduction / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily ...Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head 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 / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Zuotin / Ribosome-associated complex subunit SSZ1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 6.0 Å
AuthorsChen Y / Gao N
Funding support China, 1 items
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
DepositionMar 1, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJun 29, 2022-
Current statusJun 29, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32991.png

Downloads & links

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Map

FileDownload / File: emd_32991.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.032420993 - 0.08148137
Average (Standard dev.)1.2700848e-05 (±0.00060607225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 470.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_32991_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_32991_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RAC in the State C2 RNC-RAC complex

EntireName: RAC in the State C2 RNC-RAC complex
Components
  • Complex: RAC in the State C2 RNC-RAC complex
    • Protein or peptide: Zuotin
    • Protein or peptide: Ribosome-associated complex subunit SSZ1

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Supramolecule #1: RAC in the State C2 RNC-RAC complex

SupramoleculeName: RAC in the State C2 RNC-RAC complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Zuotin

MacromoleculeName: Zuotin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 49.109066 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MFSLPTLTSD ITVEVNSSAT KTPFVRRPVE PVGKFFLQHA QRTLRNHTWS EFERIEAEKN VKTVDESNVD PDELLFDTEL ADEDLLTHD ARDWKTADLY AAMGLSKLRF RATESQIIKA HRKQVVKYHP DKQSAAGGSL DQDGFFKIIQ KAFETLTDSN K RAQYDSCD ...String:
MFSLPTLTSD ITVEVNSSAT KTPFVRRPVE PVGKFFLQHA QRTLRNHTWS EFERIEAEKN VKTVDESNVD PDELLFDTEL ADEDLLTHD ARDWKTADLY AAMGLSKLRF RATESQIIKA HRKQVVKYHP DKQSAAGGSL DQDGFFKIIQ KAFETLTDSN K RAQYDSCD FVADVPPPKK GTDYDFYEAW GPVFEAEARF SKKTPIPSLG NKDSSKKEVE QFYAFWHRFD SWRTFEFLDE DV PDDSSNR DHKRYIERKN KAARDKKKTA DNARLVKLVE RAVSEDPRIK MFKEEEKKEK ERRKWEREAG ARAEAEAKAK AEA EAKAKA ESEAKANASA KADKKKAKEA AKAAKKKNKR AIRNSAKEAD YFGDADKATT IDEQVGLIVD SLNDEELVST ADKI KANAA GAKEVLKESA KTIVDSGKLP SSLLSYFV

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Macromolecule #2: Ribosome-associated complex subunit SSZ1

MacromoleculeName: Ribosome-associated complex subunit SSZ1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 58.301453 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSPVIGITF GNTSSSIAYI NPKNDVDVIA NPDGERAIPS ALSYVGEDEY HGGQALQQLI RNPKNTIINF RDFIGLPFDK CDVSKCANG APAVEVDGKV GFVISRGEGK EEKLTVDEVV SRHLNRLKLA AEDYIGSAVK EAVLTVPTNF SEEQKTALKA S AAKIGLQI ...String:
MSSPVIGITF GNTSSSIAYI NPKNDVDVIA NPDGERAIPS ALSYVGEDEY HGGQALQQLI RNPKNTIINF RDFIGLPFDK CDVSKCANG APAVEVDGKV GFVISRGEGK EEKLTVDEVV SRHLNRLKLA AEDYIGSAVK EAVLTVPTNF SEEQKTALKA S AAKIGLQI VQFINEPSAA LLAHAEQFPF EKDVNVVVAD FGGIRSDAAV IAVRNGIFTI LATAHDLSLG GDNLDTELVE YF ASEFQKK YQANPRKNAR SLAKLKANSS ITKKTLSNAT SATISIDSLA DGFDYHASIN RMRYELVANK VFAQFSSFVD SVI AKAELD PLDIDAVLLT GGVSFTPKLT TNLEYTLPES VEILGPQNKN ASNNPNELAA SGAALQARLI SDYDADELAE ALQP VIVNT PHLKKPIGLI GAKGEFHPVL LAETSFPVQK KLTLKQAKGD FLIGVYEGDH HIEEKTLEPI PKEENAEEDD ESEWS DDEP EVVREKLYTL GTKLMELGIK NANGVEIIFN INKDGALRVT ARDLKTGNAV KGEL

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29800

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