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- PDB-2m6y: The solution structure of the J-domain of human DnaJA1 -

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Basic information

Entry
Database: PDB / ID: 2m6y
TitleThe solution structure of the J-domain of human DnaJA1
ComponentsDnaJ homolog subfamily A member 1
KeywordsCHAPERONE / protein / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


regulation of protein transport / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / C3HC4-type RING finger domain binding / flagellated sperm motility / Tat protein binding / negative regulation of JUN kinase activity / protein localization to mitochondrion / negative regulation of establishment of protein localization to mitochondrion / low-density lipoprotein particle receptor binding / androgen receptor signaling pathway ...regulation of protein transport / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / C3HC4-type RING finger domain binding / flagellated sperm motility / Tat protein binding / negative regulation of JUN kinase activity / protein localization to mitochondrion / negative regulation of establishment of protein localization to mitochondrion / low-density lipoprotein particle receptor binding / androgen receptor signaling pathway / cytoplasmic side of endoplasmic reticulum membrane / ATPase activator activity / response to unfolded protein / negative regulation of protein ubiquitination / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Hsp70 protein binding / G protein-coupled receptor binding / microtubule cytoskeleton / unfolded protein binding / protein folding / protein-folding chaperone binding / response to heat / protein refolding / spermatogenesis / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / mitochondrion / extracellular exosome / ATP binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / DnaJ domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain ...DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Heat shock protein DnaJ, cysteine-rich domain superfamily / DnaJ 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DnaJ homolog subfamily A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, simulated annealing
Model detailslowest energy, model1
AuthorsStark, J.L. / Mehla, K. / Chaika, N. / Acton, T.B. / Xiao, R. / Singh, P.K. / Montelione, G.T. / Powers, R. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Biochemistry / Year: 2014
Title: Structure and function of human DnaJ homologue subfamily a member 1 (DNAJA1) and its relationship to pancreatic cancer.
Authors: Stark, J.L. / Mehla, K. / Chaika, N. / Acton, T.B. / Xiao, R. / Singh, P.K. / Montelione, G.T. / Powers, R.
History
DepositionApr 14, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily A member 1


Theoretical massNumber of molelcules
Total (without water)9,0951
Polymers9,0951
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 / 400structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DnaJ homolog subfamily A member 1 / DnaJ protein homolog 2 / HSDJ / Heat shock 40 kDa protein 4 / Heat shock protein J2 / HSJ-2 / Human ...DnaJ protein homolog 2 / HSDJ / Heat shock 40 kDa protein 4 / Heat shock protein J2 / HSJ-2 / Human DnaJ protein 2 / hDj-2


Mass: 9095.297 Da / Num. of mol.: 1 / Fragment: J-domain (UNP residues 1-67)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJA1, DNAJ2, HDJ2, HSJ2, HSPF4 / Production host: Escherichia coli (E. coli) / References: UniProt: P31689

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HN(CA)CO
1513D HNCA
1613D HN(CO)CA
1713D CBCA(CO)NH
1813D CBCANH
1913D HNHA
11013D HBHA(CO)NH
11113D CC(CO)NH
11213D HCC(CO)NH
11313D (H)CCH-TOCSY
11413D (H)CCH-COSY
11513D 1H-15N NOESY
11613D 1H-13C NOESY

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Sample preparation

DetailsContents: 1.03 mM [U-13C; U-15N] J-domain of DnaJA1, 20 mM MES, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 50 uM DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.03 mMJ-domain of DnaJA1-1[U-13C; U-15N]1
20 mMMES-21
0.02 %sodium azide-31
10 mMDTT-41
5 mMcalcium chloride-51
100 mMsodium chloride-61
50 uMDSS-71
Sample conditionsIonic strength: 125 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2.2CCPNchemical shift assignment
CcpNmr Analysis2.2.2CCPNdata analysis
CcpNmr Analysis2.2.2CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionestructure validation
TopSpinBruker Biospincollection
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
RefinementMethod: distance geometry, torsion angle dynamics, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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