[English] 日本語
Yorodumi
- PDB-2qld: human Hsp40 Hdj1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qld
Titlehuman Hsp40 Hdj1
ComponentsDnaJ homolog subfamily B member 1
KeywordsCHAPERONE / primarily beta sheets
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 / protein-folding chaperone binding / ATPase 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 / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHu, J. / Wu, Y. / Li, J. / Fu, Z. / Sha, B.
CitationJournal: Bmc Struct.Biol. / Year: 2008
Title: The crystal structure of the putative peptide-binding fragment from the human Hsp40 protein Hdj1.
Authors: Hu, J. / Wu, Y. / Li, J. / Qian, X. / Fu, Z. / Sha, B.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DnaJ homolog subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)20,7371
Polymers20,7371
Non-polymers00
Water00
1
A: DnaJ homolog subfamily B member 1

A: DnaJ homolog subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)41,4742
Polymers41,4742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area1690 Å2
ΔGint-19 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.010, 191.130, 40.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assemly is generated by the two fold axis: 1-x,y,1/2-z

-
Components

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


Mass: 20737.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB1, DNAJ1, HDJ1, HSPF1 / Plasmid: Pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25685

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM Citric buffer, PEG400 25%, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 20, 2005
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 11070 / Num. obs: 9943 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 18.1
Reflection shellResolution: 2.7→2.82 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.1 / Num. unique all: 882 / Rsym value: 0.382 / % possible all: 65.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
EPMRphasing
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Yeast Hsp40 Sis1

Resolution: 2.7→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.336 681 -random
Rwork0.283 ---
all0.283 11070 --
obs0.283 9943 89.8 %-
Displacement parametersBiso mean: 63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.52 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 0 0 1359
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.7-2.910.423460.388X-RAY DIFFRACTION7215
2.91-3.20.36811350.331X-RAY DIFFRACTION16955
3.2-3.660.37721430.3209X-RAY DIFFRACTION19925
3.66-4.610.34111780.2719X-RAY DIFFRACTION20135
4.61-300.29341790.2518X-RAY DIFFRACTION21145

+
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://pdbjlvh1.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