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- PDB-3agx: Crystal structure of human Hsp40 Hdj1 peptide-binding domain -

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Basic information

Entry
Database: PDB / ID: 3agx
TitleCrystal structure of human Hsp40 Hdj1 peptide-binding domain
ComponentsDnaJ homolog subfamily B member 1
KeywordsCHAPERONE
Function / homology
Function and homology information


sperm head / negative regulation of inclusion body assembly / positive regulation of ATP-dependent activity / transcription regulator inhibitor activity / ATPase activator activity / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase ...sperm head / negative regulation of inclusion body assembly / positive regulation of ATP-dependent activity / transcription regulator inhibitor activity / ATPase activator activity / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / Regulation of HSF1-mediated heat shock response / Attenuation phase / regulation of cellular response to heat / protein folding chaperone / forebrain development / Hsp70 protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MAPK6/MAPK4 signaling / transcription corepressor activity / unfolded protein binding / cellular response to heat / ATPase binding / protein-folding chaperone binding / dendritic spine / postsynaptic density / cadherin binding / neuronal cell body / glutamatergic synapse / nucleolus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
DnaJ homolog subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.85 Å
AuthorsSuzuki, H. / Noguchi, S. / Satow, Y.
CitationJournal: Biochemistry / Year: 2010
Title: Peptide-binding sites as revealed by the crystal structures of the human Hsp40 Hdj1 C-terminal domain in complex with the octapeptide from human Hsp70
Authors: Suzuki, H. / Noguchi, S. / Arakawa, H. / Tokida, T. / Hashimoto, M. / Satow, Y.
History
DepositionApr 12, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily B member 1
B: DnaJ homolog subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)40,9642
Polymers40,9642
Non-polymers00
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-26 kcal/mol
Surface area18580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.252, 40.921, 62.650
Angle α, β, γ (deg.)90.000, 96.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DnaJ homolog subfamily B member 1 / Heat shock 40 kDa protein 1 / Heat shock protein 40 / HSP40 / DnaJ protein homolog 1 / Human DnaJ ...Heat shock 40 kDa protein 1 / Heat shock protein 40 / HSP40 / DnaJ protein homolog 1 / Human DnaJ protein 1 / hDj-1


Mass: 20481.914 Da / Num. of mol.: 2 / Fragment: UNP residues 161-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB1, DNAJ1, HDJ1, HSPF1 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P25685
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% PEG 3350, 0.1M Na citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: May 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→102.6 Å / Num. obs: 42368 / % possible obs: 94.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.101
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 1.3 / % possible all: 64.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0089refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.85→42.03 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.785 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2145 5.1 %RANDOM
Rwork0.228 ---
obs0.229 40223 94.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.74 Å2 / Biso mean: 43.581 Å2 / Biso min: 15.42 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å2-0.67 Å2
2---1.16 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 0 215 2794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222665
X-RAY DIFFRACTIONr_angle_refined_deg1.5322.0063590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4185320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46922.991107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71815537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4691526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221928
X-RAY DIFFRACTIONr_mcbond_it0.9881.51624
X-RAY DIFFRACTIONr_mcangle_it1.71722687
X-RAY DIFFRACTIONr_scbond_it2.09231041
X-RAY DIFFRACTIONr_scangle_it3.5514.5903
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 108 -
Rwork0.332 2006 -
all-2114 -
obs--64.77 %

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