+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32991 | |||||||||
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Title | Cryo-EM structure of RAC in the State C2 RNC-RAC complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RAC / co-translational folding / TRANSLATION | |||||||||
Function / homology | Function and homology information : / translational frameshifting / 'de novo' cotranslational protein folding / Regulation of HSF1-mediated heat shock response / misfolded protein binding / protein folding chaperone complex / regulation of translational fidelity / ribosomal subunit export from nucleus / chaperone-mediated protein folding / protein folding chaperone ...: / translational frameshifting / 'de novo' cotranslational protein folding / Regulation of HSF1-mediated heat shock response / misfolded protein binding / protein folding chaperone complex / regulation of translational fidelity / ribosomal subunit export from nucleus / chaperone-mediated protein folding / protein folding chaperone / heat shock protein binding / Hsp70 protein binding / rRNA processing / unfolded protein binding / protein folding / ribosome binding / protein refolding / transcription coactivator activity / cytoplasmic translation / ribosome / intracellular signal transduction / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 6.0 Å | |||||||||
Authors | Chen Y / Gao N | |||||||||
Funding support | China, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32991.map.gz | 8.1 MB | EMDB map data format | |
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Header (meta data) | emd-32991-v30.xml emd-32991.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_32991.png | 27.7 KB | ||
Filedesc metadata | emd-32991.cif.gz | 5.6 KB | ||
Others | emd_32991_half_map_1.map.gz emd_32991_half_map_2.map.gz | 256 MB 254.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32991 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32991 | HTTPS FTP |
-Validation report
Summary document | emd_32991_validation.pdf.gz | 609.4 KB | Display | EMDB validaton report |
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Full document | emd_32991_full_validation.pdf.gz | 609 KB | Display | |
Data in XML | emd_32991_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_32991_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32991 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32991 | HTTPS FTP |
-Related structure data
Related structure data | 7x3kMC 7x34C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32991.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_32991_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32991_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RAC in the State C2 RNC-RAC complex
Entire | Name: RAC in the State C2 RNC-RAC complex |
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Components |
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-Supramolecule #1: RAC in the State C2 RNC-RAC complex
Supramolecule | Name: RAC in the State C2 RNC-RAC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Zuotin
Macromolecule | Name: Zuotin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 49.109066 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 UniProtKB: Zuotin |
-Macromolecule #2: Ribosome-associated complex subunit SSZ1
Macromolecule | Name: Ribosome-associated complex subunit SSZ1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 58.301453 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: 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 UniProtKB: Ribosome-associated complex subunit SSZ1 |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Staining | Type: NEGATIVE / Material: Uranyl Acetate |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29800 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |