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Yorodumi- PDB-7z3o: Cryo-EM structure of the ribosome-associated RAC complex on the 8... -
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-Basic information
Entry | Database: PDB / ID: 7z3o | ||||||
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Title | Cryo-EM structure of the ribosome-associated RAC complex on the 80S ribosome - RAC-2 conformation | ||||||
Components |
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Keywords | CHAPERONE / RAC / ribosome-associated complex / thermophilic eukaryotic ribosome / 80S | ||||||
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 transcription factor SL1 complex / protein N-linked glycosylation via asparagine / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / nucleolar large rRNA transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...RNA polymerase I core factor complex / 'de novo' cotranslational protein folding / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / RNA polymerase transcription factor SL1 complex / protein N-linked glycosylation via asparagine / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / nucleolar large rRNA transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation regulator activity / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hsp70 protein binding / 90S preribosome / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-translational protein modification / maturation of LSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / positive regulation of apoptotic signaling pathway / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / ATP-dependent protein folding chaperone / rRNA processing / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / methylation / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / mRNA binding / nucleolus / RNA binding / ATP binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Thermochaetoides thermophila DSM 1495 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Kisonaite, M. / Wild, K. / Sinning, I. | ||||||
Funding support | Germany, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z3o.cif.gz | 4.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7z3o.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7z3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/7z3o ftp://data.pdbj.org/pub/pdb/validation_reports/z3/7z3o | HTTPS FTP |
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-Related structure data
Related structure data | 14480MC 7z3nC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (-0.658442754557, -0.531266819807, 0.533112281929), (-0.583756662667, 0.80759219771, 0.083803347128), (-0.475059257107, -0.256028139802, -0.841883776935)Vector: 451. ...NCS oper: (Code: given Matrix: (-0.658442754557, -0.531266819807, 0.533112281929), Vector: |
-Components
-RNA chain , 4 types, 4 molecules 1234
#1: RNA chain | Mass: 1078730.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
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#2: RNA chain | Mass: 578772.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
#3: RNA chain | Mass: 38596.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
#4: RNA chain | Mass: 50147.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
-Protein , 9 types, 9 molecules ABCDLHLWLhLkLs
#5: Protein | Mass: 35149.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9U0 |
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#6: Protein | Mass: 32667.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S428 |
#7: Protein | Mass: 51048.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RYD6 |
#8: Protein | Mass: 62449.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZX9 |
#16: Protein | Mass: 21582.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
#31: Protein | Mass: 18081.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
#42: Protein | Mass: 14643.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#45: Protein | Mass: 9537.339 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
#52: Protein | Mass: 33853.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SGP3 |
+60S ribosomal protein ... , 29 types, 30 molecules LALBLCLDLELFLGLILKLLLMLOLPLSLTLULVLXLYLZLaLbLcLeLfLiLnLrLoLp
-Putative ribosomal ... , 3 types, 3 molecules LJLmSS
#18: Protein | Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHQ2 |
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#47: Protein | Mass: 14609.222 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S8G4 |
#72: Protein | Mass: 17826.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S6J7 |
-Ribosomal protein ... , 8 types, 8 molecules LNLQLRLgLjLlSbSd
#22: Protein | Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0RZ88 |
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#25: Protein | Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9B5 |
#26: Protein | Mass: 22409.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S9T3 |
#41: Protein | Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SFN0 |
#44: Protein | Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S101 |
#46: Protein | Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
#81: Protein | Mass: 8923.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S1S4 |
#83: Protein | Mass: 6504.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
-Putative 60S ribosomal ... , 2 types, 2 molecules LdLq
#38: Protein | Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SD68 |
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#51: Protein | Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHJ6 |
-Protein/peptide , 1 types, 1 molecules NC
#53: Protein/peptide | Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
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+40S ribosomal protein ... , 29 types, 29 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSTSUSVSWSXSYSZSaScSeSf
-Non-polymers , 3 types, 481 molecules
#86: Chemical | ChemComp-MG / #87: Chemical | ChemComp-ATP / | #88: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Chaetomium thermophilum RAC on 80S ribosome / Type: COMPLEX / Entity ID: #1-#85 / Source: NATURAL |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 39.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 284425 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7OLC | ||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 167.43 Å2 | ||||||||||||||||||||||||||||
Refine LS restraints |
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Refine LS restraints NCS | Type: NCS constraints / Rms dev position: 0.00069612097187 Å |