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- PDB-6sr6: Crystal structure of the RAC core with a pseudo substrate bound t... -

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Basic information

Entry
Database: PDB / ID: 6sr6
TitleCrystal structure of the RAC core with a pseudo substrate bound to Ssz1 SBD
Components
  • Putative heat shock protein
  • Putative ribosome associated protein
KeywordsCHAPERONE / Hsp70
Function / homology
Function and homology information


'de novo' cotranslational protein folding / regulation of translational fidelity / Hsp70 protein binding / ATP-dependent protein folding chaperone / ribosome binding / ATP binding / cytoplasm
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Heat shock protein 70 family ...Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Putative ribosome associated protein / Putative heat shock protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsValentin Gese, G. / Lapouge, K. / Kopp, J. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB 1036-TP22 Germany
German Research FoundationSI 586/6-1 Germany
CitationJournal: Nat Commun / Year: 2020
Title: The ribosome-associated complex RAC serves in a relay that directs nascent chains to Ssb.
Authors: Zhang, Y. / Valentin Gese, G. / Conz, C. / Lapouge, K. / Kopp, J. / Wolfle, T. / Rospert, S. / Sinning, I.
History
DepositionSep 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative heat shock protein
B: Putative ribosome associated protein
C: Putative heat shock protein
D: Putative ribosome associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,2918
Polymers141,2284
Non-polymers1,0634
Water1,63991
1
A: Putative heat shock protein
B: Putative ribosome associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1454
Polymers70,6142
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-52 kcal/mol
Surface area25190 Å2
MethodPISA
2
C: Putative heat shock protein
D: Putative ribosome associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1454
Polymers70,6142
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-52 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.977, 258.454, 53.017
Angle α, β, γ (deg.)90.000, 100.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Putative heat shock protein /


Mass: 63706.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0008010 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0RZX9
#2: Protein Putative ribosome associated protein


Mass: 6906.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0006310 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0RYD6
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20.5% (v/v) PEG 3350, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→48.4 Å / Num. obs: 46860 / % possible obs: 98.9 % / Redundancy: 6 % / Biso Wilson estimate: 38.97 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4516 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
XDS20180126data reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MB9

5mb9


Resolution: 2.5→33.71 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 --Random selection
Rwork0.1889 ---
obs-46801 98.85 %-
Refinement stepCycle: LAST / Resolution: 2.5→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8732 0 64 91 8887

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