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- PDB-2b26: The crystal structure of the protein complex of yeast Hsp40 Sis1 ... -

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Basic information

Entry
Database: PDB / ID: 2b26
TitleThe crystal structure of the protein complex of yeast Hsp40 Sis1 and Hsp70 Ssa1
Components
  • Heat shock 70 kDa protein cognate 2
  • SIS1 protein
KeywordsCHAPERONE/PROTEIN TRANSPORT / Hsp40 Sis1 Hsp70 Ssa1 / CHAPERONE-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


detection of misfolded protein / tRNA import into nucleus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / misfolded protein transport / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / : / heat shock protein binding / protein folding chaperone ...detection of misfolded protein / tRNA import into nucleus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / misfolded protein transport / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / : / heat shock protein binding / protein folding chaperone / cellular response to starvation / translational initiation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / protein-folding chaperone binding / cellular response to heat / protein refolding / cytosolic small ribosomal subunit / nucleolus / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Urease metallochaperone UreE, N-terminal domain / : / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / HSP40/DNAj peptide-binding domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain ...Urease metallochaperone UreE, N-terminal domain / : / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / HSP40/DNAj peptide-binding 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 hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Heat shock 70 kDa protein cognate 2 / Protein SIS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsLi, J. / Wu, Y. / Qian, X. / Sha, B.
CitationJournal: Biochem.J. / Year: 2006
Title: Crystal structure of yeast Sis1 peptide-binding fragment and Hsp70 Ssa1 C-terminal complex.
Authors: Li, J. / Wu, Y. / Qian, X. / Sha, B.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIS1 protein
B: SIS1 protein
C: SIS1 protein
D: Heat shock 70 kDa protein cognate 2


Theoretical massNumber of molelcules
Total (without water)59,2524
Polymers59,2524
Non-polymers00
Water00
1
A: SIS1 protein
B: SIS1 protein
D: Heat shock 70 kDa protein cognate 2


Theoretical massNumber of molelcules
Total (without water)39,7643
Polymers39,7643
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: SIS1 protein

C: SIS1 protein


Theoretical massNumber of molelcules
Total (without water)38,9762
Polymers38,9762
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)113.867, 113.867, 173.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SIS1 protein


Mass: 19488.189 Da / Num. of mol.: 3 / Fragment: Yeast Hsp40 Sis1 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SIS1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P25294
#2: Protein/peptide Heat shock 70 kDa protein cognate 2 / Heat shock 70 kDa protein 87D


Mass: 787.811 Da / Num. of mol.: 1 / Fragment: yeast Hsp70 Ssa1 C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Hsc70-2, Hsc2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P11146

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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: 4.75 Å3/Da / Density % sol: 74.12 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9790 0.9793 0.9700
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.971
ReflectionResolution: 3.2→30 Å / Num. obs: 17558

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.339 1754 Random
Rwork0.276 --
all0.276 17558 -
obs0.276 17558 -
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 0 0 3428

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