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- PDB-2ctr: Solution structure of J-domain from human DnaJ subfamily B menber 9 -

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Basic information

Entry
Database: PDB / ID: 2ctr
TitleSolution structure of J-domain from human DnaJ subfamily B menber 9
ComponentsDnaJ homolog subfamily B member 9
KeywordsCHAPERONE / DnaJ / J-domain / helix-turn-helix / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of IRE1-mediated unfolded protein response / XBP1(S) activates chaperone genes / misfolded protein binding / positive regulation of immunoglobulin production / response to unfolded protein / ERAD pathway / Hsp70 protein binding / response to endoplasmic reticulum stress / B cell differentiation / protein-folding chaperone binding ...negative regulation of IRE1-mediated unfolded protein response / XBP1(S) activates chaperone genes / misfolded protein binding / positive regulation of immunoglobulin production / response to unfolded protein / ERAD pathway / Hsp70 protein binding / response to endoplasmic reticulum stress / B cell differentiation / protein-folding chaperone binding / endoplasmic reticulum lumen / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / extracellular exosome / cytoplasm
Similarity search - Function
: / DnaJ 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 / Helix Hairpins ...: / DnaJ 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaJ homolog subfamily B member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Tosion angle dynamics
AuthorsKobayashi, N. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of J-domain from human DnaJ subfamily B menber 9
Authors: Kobayashi, N. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 24, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily B member 9


Theoretical massNumber of molelcules
Total (without water)9,5311
Polymers9,5311
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)20 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein DnaJ homolog subfamily B member 9 / Microvascular endothelial differentiation gene-1 protein / Mdg-1 / UNQ743/PRO1471


Mass: 9531.461 Da / Num. of mol.: 1 / Fragment: J-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: DNAJB9 / Plasmid: P040517-03 / References: UniProt: Q9UBS3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.11mM DnaJ domain U-13C,15N; 20mM Phosphate buffer Na (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9297Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: Tosion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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