[English] 日本語
Yorodumi
- PDB-3agz: Crystal structure of human Hsp40 Hdj1 peptide-binding domain comp... -

+
Open data


ID or keywords:

Loading...

-
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


regulation of protein import / lumenal side of lysosomal membrane / sperm head / negative regulation of supramolecular fiber organization / protein carrier chaperone / negative regulation of transcription from RNA polymerase II promoter in response to stress / positive regulation by host of viral genome replication / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / postsynaptic specialization membrane / Lipophagy ...regulation of protein import / lumenal side of lysosomal membrane / sperm head / negative regulation of supramolecular fiber organization / protein carrier chaperone / negative regulation of transcription from RNA polymerase II promoter in response to stress / positive regulation by host of viral genome replication / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / postsynaptic specialization membrane / Lipophagy / GABA synthesis, release, reuptake and degradation / chaperone-mediated autophagy translocation complex disassembly / clathrin-uncoating ATPase activity / slow axonal transport / protein targeting to lysosome involved in chaperone-mediated autophagy / glycinergic synapse / negative regulation of inclusion body assembly / late endosomal microautophagy / regulation of postsynapse organization / CHL1 interactions / C3HC4-type RING finger domain binding / regulation of protein complex stability / ATP-dependent protein disaggregase activity / photoreceptor ribbon synapse / membrane organization / presynaptic cytosol / chaperone complex / Prp19 complex / positive regulation of mRNA splicing, via spliceosome / positive regulation of ATP-dependent activity / Lysosome Vesicle Biogenesis / misfolded protein binding / postsynaptic cytosol / Golgi Associated Vesicle Biogenesis / ATPase activator activity / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / phosphatidylserine binding / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / Protein methylation / HSF1-dependent transactivation / response to unfolded protein / ATP metabolic process / regulation of cellular response to heat / Regulation of HSF1-mediated heat shock response / Attenuation phase / regulation of protein-containing complex assembly / forebrain development / cellular response to unfolded protein / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Hsp70 protein binding / protein folding chaperone / mRNA Splicing - Major Pathway / lysosomal lumen / cellular response to starvation / vesicle-mediated transport / spliceosomal complex / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / Late endosomal microautophagy / mRNA splicing, via spliceosome / terminal bouton / transcription corepressor activity / protein-macromolecule adaptor activity / regulation of protein stability / Chaperone Mediated Autophagy / melanosome / unfolded protein binding / Clathrin-mediated endocytosis / protein folding / ribonucleoprotein complex / late endosome / MHC class II protein complex binding / protein refolding / ATPase binding / lysosomal membrane / chaperone binding / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / blood microparticle / ficolin-1-rich granule lumen / dendritic spine / lysosome / postsynaptic density / regulation of cell cycle / cadherin binding / glutamatergic synapse / focal adhesion / neuronal cell body / dendrite / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / Neutrophil degranulation / ATP hydrolysis activity / perinuclear region of cytoplasm
Similarity search - Function
Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / HSP40/DnaJ peptide-binding / DnaJ C terminal domain / Chaperone DnaJ, C-terminal / 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 / DnaJ C terminal domain / Chaperone DnaJ, C-terminal / 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 1. / Heat shock hsp70 proteins family signature 2. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more