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Yorodumi- EMDB-14480: Cryo-EM structure of the ribosome-associated RAC complex on the 8... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14480 | |||||||||
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Title | Cryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-2 conformation | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information RNA polymerase I core factor complex / 'de novo' cotranslational protein folding / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / RNA polymerase I core promoter sequence-specific DNA binding / protein glycosylation / 90S preribosome / regulation of translational fidelity / translation regulator activity / maturation of LSU-rRNA ...RNA polymerase I core factor complex / 'de novo' cotranslational protein folding / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / RNA polymerase I core promoter sequence-specific DNA binding / protein glycosylation / 90S preribosome / regulation of translational fidelity / translation regulator activity / maturation of LSU-rRNA / Hsp70 protein binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / maturation of SSU-rRNA / methyltransferase activity / small-subunit processome / protein kinase C binding / ATP-dependent protein folding chaperone / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / cytosolic large ribosomal subunit / methylation / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / ATP binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Thermochaetoides thermophila DSM 1495 (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Kisonaite M / Wild K / Sinning I | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structural inventory of cotranslational protein folding by the eukaryotic RAC complex. Authors: Miglė Kišonaitė / Klemens Wild / Karine Lapouge / Genís Valentín Gesé / Nikola Kellner / Ed Hurt / Irmgard Sinning / Abstract: The challenge of nascent chain folding at the ribosome is met by the conserved ribosome-associated complex (RAC), which forms a chaperone triad with the Hsp70 protein Ssb in fungi, and consists of ...The challenge of nascent chain folding at the ribosome is met by the conserved ribosome-associated complex (RAC), which forms a chaperone triad with the Hsp70 protein Ssb in fungi, and consists of the non-canonical Hsp70 Ssz1 and the J domain protein Zuotin (Zuo1). Here we determine cryo-EM structures of Chaetomium thermophilum RAC bound to 80S ribosomes. RAC adopts two distinct conformations accommodating continuous ribosomal rotation by a flexible lever arm. It is held together by a tight interaction between the Ssz1 substrate-binding domain and the Zuo1 N terminus, and additional contacts between the Ssz1 nucleotide-binding domain and Zuo1 J- and Zuo1 homology domains, which form a rigid unit. The Zuo1 HPD motif conserved in J-proteins is masked in a non-canonical interaction by the Ssz1 nucleotide-binding domain, and allows the positioning of Ssb for activation by Zuo1. Overall, we provide the basis for understanding how RAC cooperates with Ssb in a dynamic nascent chain interaction and protein folding. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14480.map.gz | 404.1 MB | EMDB map data format | |
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Header (meta data) | emd-14480-v30.xml emd-14480.xml | 101.2 KB 101.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14480_fsc.xml | 22.2 KB | Display | FSC data file |
Images | emd_14480.png | 153.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14480 | HTTPS FTP |
-Validation report
Summary document | emd_14480_validation.pdf.gz | 608 KB | Display | EMDB validaton report |
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Full document | emd_14480_full_validation.pdf.gz | 607.6 KB | Display | |
Data in XML | emd_14480_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_14480_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14480 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14480 | HTTPS FTP |
-Related structure data
Related structure data | 7z3oMC 7z3nC M: atomic model generated by this map C: citing same article (ref.) |
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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_14480.map.gz / Format: CCP4 / Size: 437.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : Chaetomium thermophilum RAC on 80S ribosome
+Supramolecule #1: Chaetomium thermophilum RAC on 80S ribosome
+Macromolecule #1: 26S rRNA
+Macromolecule #2: 18S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #5: Putative guanine nucleotide-binding protein
+Macromolecule #6: HABP4_PAI-RBP1 domain-containing protein
+Macromolecule #7: Putative ribosome associated protein
+Macromolecule #8: Putative heat shock protein
+Macromolecule #9: 60S ribosomal protein L2-like protein
+Macromolecule #10: 60S ribosomal protein L3-like protein
+Macromolecule #11: 60S ribosomal protein L4-like protein
+Macromolecule #12: 60S ribosomal protein l5-like protein
+Macromolecule #13: 60S ribosomal protein L6
+Macromolecule #14: 60S ribosomal protein l7-like protein
+Macromolecule #15: 60S ribosomal protein L8
+Macromolecule #16: uL6
+Macromolecule #17: 60S ribosomal protein L10-like protein
+Macromolecule #18: Putative ribosomal protein
+Macromolecule #19: 60S ribosomal protein L12-like protein
+Macromolecule #20: 60S ribosomal protein L13
+Macromolecule #21: 60S ribosomal protein L14-like protein
+Macromolecule #22: Ribosomal protein L15
+Macromolecule #23: 60S ribosomal protein L16-like protein
+Macromolecule #24: 60S ribosomal protein l17-like protein
+Macromolecule #25: Ribosomal protein L18-like protein
+Macromolecule #26: Ribosomal protein L19
+Macromolecule #27: 60S ribosomal protein L20
+Macromolecule #28: 60S ribosomal protein l21-like protein
+Macromolecule #29: 60S ribosomal protein L22-like protein
+Macromolecule #30: 60S ribosomal protein l23-like protein
+Macromolecule #31: eL24
+Macromolecule #32: 60S ribosomal protein L25-like protein
+Macromolecule #33: 60S ribosomal protein L26-like protein
+Macromolecule #34: 60S ribosomal protein L27
+Macromolecule #35: 60S ribosomal protein L28-like protein
+Macromolecule #36: 60S ribosomal protein L29
+Macromolecule #37: 60S ribosomal protein l30-like protein
+Macromolecule #38: Putative 60S ribosomal protein
+Macromolecule #39: 60S ribosomal protein L32-like protein
+Macromolecule #40: 60S ribosomal protein l33-like protein
+Macromolecule #41: Ribosomal protein l34-like protein
+Macromolecule #42: Dolichyl-diphosphooligosaccharide--protein glycotransferase
+Macromolecule #43: 60S ribosomal protein L36
+Macromolecule #44: Ribosomal protein L37
+Macromolecule #45: eL38
+Macromolecule #46: Ribosomal protein eL39
+Macromolecule #47: Putative ribosomal protein
+Macromolecule #48: 60S ribosomal protein L41-A
+Macromolecule #49: 60S ribosomal protein L44-like protein
+Macromolecule #50: 60S ribosomal protein L43-like protein
+Macromolecule #51: Putative 60S ribosomal protein
+Macromolecule #52: 60S acidic ribosomal protein P0
+Macromolecule #53: Nascent chain
+Macromolecule #54: 40S ribosomal protein S0
+Macromolecule #55: 40S ribosomal protein S1
+Macromolecule #56: 40S ribosomal protein S2-like protein
+Macromolecule #57: 40S ribosomal protein S3-like protein
+Macromolecule #58: 40S ribosomal protein S4
+Macromolecule #59: 40S ribosomal protein s5-like protein
+Macromolecule #60: 40S ribosomal protein S6
+Macromolecule #61: 40S ribosomal protein S7
+Macromolecule #62: 40S ribosomal protein S8
+Macromolecule #63: 40S ribosomal protein s9-like protein
+Macromolecule #64: 40S ribosomal protein s10-like protein
+Macromolecule #65: 40S ribosomal protein S11-like protein
+Macromolecule #66: 40S ribosomal protein S12
+Macromolecule #67: 40S ribosomal protein S13-like protein
+Macromolecule #68: 40S ribosomal protein S14-like protein
+Macromolecule #69: 40S ribosomal protein s15-like protein
+Macromolecule #70: 40S ribosomal protein S16-like protein
+Macromolecule #71: 40S ribosomal protein S17-like protein
+Macromolecule #72: Putative ribosomal protein
+Macromolecule #73: 40S ribosomal protein S19-like protein
+Macromolecule #74: 40S ribosomal protein S20-like protein
+Macromolecule #75: 40S ribosomal protein S21-like protein
+Macromolecule #76: 40S ribosomal protein S22-like protein
+Macromolecule #77: 40S ribosomal protein s23-like protein
+Macromolecule #78: 40S ribosomal protein S24
+Macromolecule #79: 40S ribosomal protein S25
+Macromolecule #80: 40S ribosomal protein S26
+Macromolecule #81: Ribosomal protein s27-like protein
+Macromolecule #82: 40S ribosomal protein S28-like protein
+Macromolecule #83: Ribosomal protein uS14
+Macromolecule #84: 40S ribosomal protein S30
+Macromolecule #85: 40S ribosomal protein S27a-like protein
+Macromolecule #86: MAGNESIUM ION
+Macromolecule #87: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #88: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |