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- PDB-3agz: Crystal structure of human Hsp40 Hdj1 peptide-binding domain comp... -

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Basic information

Entry
Database: PDB / ID: 3agz
TitleCrystal structure of human Hsp40 Hdj1 peptide-binding domain complexed with a C-terminal peptide of Hsp70
Components
  • DnaJ homolog subfamily B member 1
  • peptide of Heat shock cognate 71 kDa protein
KeywordsCHAPERONE
Function / homology
Function and homology information


lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / sperm head / Lipophagy / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / sperm head / Lipophagy / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / negative regulation of inclusion body assembly / C3HC4-type RING finger domain binding / clathrin coat disassembly / negative regulation of NLRP3 inflammasome complex assembly / CHL1 interactions / ATP-dependent protein disaggregase activity / regulation of protein complex stability / membrane organization / Prp19 complex / presynaptic cytosol / positive regulation of ATP-dependent activity / protein folding chaperone complex / transcription regulator inhibitor activity / postsynaptic cytosol / Lysosome Vesicle Biogenesis / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / non-chaperonin molecular chaperone ATPase / ATPase activator activity / chaperone cofactor-dependent protein refolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / response to unfolded protein / autophagosome / Regulation of HSF1-mediated heat shock response / Attenuation phase / Protein methylation / ATP metabolic process / 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 / heat shock protein binding / cellular response to starvation / mRNA Splicing - Major Pathway / lysosomal lumen / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / ATP-dependent protein folding chaperone / spliceosomal complex / Late endosomal microautophagy / MAPK6/MAPK4 signaling / regulation of protein stability / PKR-mediated signaling / terminal bouton / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / transcription corepressor activity / melanosome / unfolded protein binding / protein-macromolecule adaptor activity / protein folding / Clathrin-mediated endocytosis / cellular response to heat / MHC class II protein complex binding / ATPase binding / protein-folding chaperone binding / protein refolding / blood microparticle / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / ficolin-1-rich granule lumen / dendritic spine / postsynaptic density / lysosome / cadherin binding / ribonucleoprotein complex / lysosomal membrane / focal adhesion / negative regulation of DNA-templated transcription / dendrite / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / negative regulation of transcription by RNA polymerase II / enzyme binding / ATP hydrolysis activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding
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 / 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 cognate 71 kDa protein / DnaJ homolog subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: peptide of Heat shock cognate 71 kDa protein
D: peptide of Heat shock cognate 71 kDa protein
E: peptide of Heat shock cognate 71 kDa protein
F: peptide of Heat shock cognate 71 kDa protein


Theoretical massNumber of molelcules
Total (without water)46,3926
Polymers46,3926
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-40 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.057, 50.904, 90.148
Angle α, β, γ (deg.)90.000, 114.760, 90.000
Int Tables number5
Space group name H-MC121

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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: 21477.994 Da / Num. of mol.: 2 / Fragment: UNP residues 151-340
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: Protein/peptide
peptide of Heat shock cognate 71 kDa protein / Hsp70 / HSPA1A / Heat shock 70 kDa protein 8


Mass: 858.890 Da / Num. of mol.: 4 / Fragment: UNP residues 639-646 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P11142
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.49 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 18% PEG 3350, 0.1M CHES, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.51→81.9 Å / Num. obs: 15642 / % possible obs: 98.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.4
Reflection shellResolution: 2.51→2.59 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.3 / % possible all: 87.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0089refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→29.94 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.882 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.586 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.753 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.269 794 5.1 %RANDOM
Rwork0.22 ---
obs0.222 14847 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.74 Å2 / Biso mean: 34.984 Å2 / Biso min: 7.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.45 Å2
2--1.88 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.51→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 0 96 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223217
X-RAY DIFFRACTIONr_angle_refined_deg1.6972.0084352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.035393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9724.135133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.74515613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0041527
X-RAY DIFFRACTIONr_chiral_restr0.1020.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222383
X-RAY DIFFRACTIONr_mcbond_it0.7411.52005
X-RAY DIFFRACTIONr_mcangle_it1.37823311
X-RAY DIFFRACTIONr_scbond_it2.01431212
X-RAY DIFFRACTIONr_scangle_it3.4824.51041
LS refinement shellResolution: 2.508→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.597 38 -
Rwork0.354 989 -
all-1027 -
obs--87.11 %

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