[English] 日本語
Yorodumi
- PDB-2lgw: Solution Structure of the J Domain of HSJ1a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lgw
TitleSolution Structure of the J Domain of HSJ1a
ComponentsDnaJ homolog subfamily B member 2
KeywordsCHAPERONE / J domain / HSJ1a / co-chaperon
Function / homology
Function and homology information


: / regulation of chaperone-mediated protein folding / negative regulation of protein deubiquitination / extrinsic component of endoplasmic reticulum membrane / : / negative regulation of inclusion body assembly / positive regulation of ATP-dependent activity / ubiquitin-modified protein reader activity / proteasome binding / cytoplasmic side of endoplasmic reticulum membrane ...: / regulation of chaperone-mediated protein folding / negative regulation of protein deubiquitination / extrinsic component of endoplasmic reticulum membrane / : / negative regulation of inclusion body assembly / positive regulation of ATP-dependent activity / ubiquitin-modified protein reader activity / proteasome binding / cytoplasmic side of endoplasmic reticulum membrane / ATPase activator activity / regulation of protein ubiquitination / polyubiquitin modification-dependent protein binding / response to unfolded protein / chaperone-mediated protein folding / inclusion body / Hsp70 protein binding / ubiquitin binding / positive regulation of protein ubiquitination / negative regulation of protein binding / negative regulation of cell growth / neuron cellular homeostasis / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of protein localization / protein-folding chaperone binding / protein refolding / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of cell population proliferation / ubiquitin protein ligase binding / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
DnaJ homolog subfamily B member 2 / DnaJ domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / Ubiquitin-interacting motif. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain ...DnaJ homolog subfamily B member 2 / DnaJ domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / Ubiquitin-interacting motif. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaJ homolog subfamily B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsZhou, C. / Gao, X. / Cao, C. / Hu, H.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The C-terminal helices of heat shock protein 70 are essential for J-domain binding and ATPase activation.
Authors: Gao, X.C. / Zhou, C.J. / Zhou, Z.R. / Wu, M. / Cao, C.Y. / Hu, H.Y.
History
DepositionAug 2, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DnaJ homolog subfamily B member 2


Theoretical massNumber of molelcules
Total (without water)11,2971
Polymers11,2971
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein DnaJ homolog subfamily B member 2 / DnaJ protein homolog 1 / Heat shock 40 kDa protein 3 / Heat shock protein J1 / HSJ-1


Mass: 11297.479 Da / Num. of mol.: 1 / Fragment: UNP residues 1-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P25686

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HN(CA)CB
1323D CBCA(CO)NH
1423D C(CO)NH
1523D HNCO
1613D HNHA
1723D (H)CCH-TOCSY
1813D 1H-15N NOESY
1923D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] protein-1, 20 mM potassium phosphate-2, 50 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein-4, 20 mM potassium phosphate-5, 50 mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity-1[U-100% 15N]1
20 mMpotassium phosphate-21
50 mMsodium chloride-31
1 mMentity-4[U-100% 13C; U-100% 15N]2
20 mMpotassium phosphate-52
50 mMsodium chloride-62
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardpeak picking
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15 / Representative conformer: 1

+
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