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- PDB-6iws: Solution structure of the J-domain of Tid1, a Mitochondrial Hsp40... -

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Basic information

Entry
Database: PDB / ID: 6iws
TitleSolution structure of the J-domain of Tid1, a Mitochondrial Hsp40/DnaJ Protein
ComponentsDnaJ homolog subfamily A member 3, mitochondrial
KeywordsCHAPERONE / Tid1 / mtHsp40 / DnaJA3 / J-domain / Solution structure / HPD motif
Function / homology
Function and homology information


IkappaB kinase complex binding / type II interferon receptor binding / skeletal muscle acetylcholine-gated channel clustering / GTPase regulator activity / mitochondrial DNA replication / negative regulation of NF-kappaB transcription factor activity / neuromuscular junction development / small GTPase-mediated signal transduction / activation-induced cell death of T cells / negative regulation of type II interferon-mediated signaling pathway ...IkappaB kinase complex binding / type II interferon receptor binding / skeletal muscle acetylcholine-gated channel clustering / GTPase regulator activity / mitochondrial DNA replication / negative regulation of NF-kappaB transcription factor activity / neuromuscular junction development / small GTPase-mediated signal transduction / activation-induced cell death of T cells / negative regulation of type II interferon-mediated signaling pathway / response to type II interferon / mitochondrial nucleoid / NF-kappaB binding / positive regulation of T cell proliferation / negative regulation of canonical NF-kappaB signal transduction / Hsp70 protein binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / mitochondrion organization / positive regulation of protein ubiquitination / negative regulation of protein kinase activity / neuromuscular junction / cytoplasmic side of plasma membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / cellular senescence / unfolded protein binding / protein folding / T cell differentiation in thymus / response to heat / postsynaptic membrane / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein stabilization / mitochondrial matrix / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / 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 / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. ...: / 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 / 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
Similarity search - Domain/homology
DnaJ homolog subfamily A member 3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSim, D.W. / Jo, K.S. / Won, H.S. / Kim, J.H.
CitationJournal: To Be Published
Title: Solution structure of the J-domain of Tid1, a Mitochondrial Hsp40/DnaJ Protein
Authors: Sim, D.W. / Jo, K.S. / Won, H.S. / Kim, J.H.
History
DepositionDec 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily A member 3, mitochondrial


Theoretical massNumber of molelcules
Total (without water)8,5901
Polymers8,5901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5840 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1target function

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Components

#1: Protein DnaJ homolog subfamily A member 3, mitochondrial / DnaJ protein Tid-1 / hTid-1 / Hepatocellular carcinoma-associated antigen 57 / Tumorous imaginal ...DnaJ protein Tid-1 / hTid-1 / Hepatocellular carcinoma-associated antigen 57 / Tumorous imaginal discs protein Tid56 homolog


Mass: 8589.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJA3, HCA57, TID1 / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLyss / References: UniProt: Q96EY1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic23D HN(CA)CB
121anisotropic23D CBCA(CO)NH
131anisotropic23D HNCO
141anisotropic23D HN(CA)CO
151anisotropic23D 1H-15N NOESY
161anisotropic23D 1H-13C NOESY
171anisotropic13D (H)CCH-TOCSY
1101anisotropic13D (H)CCH-COSY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] J_domain, 300 mM sodium chloride, 1 mM Dithiothreitol, 20 mM TRIS, 10 % v/v D2O, 90% H2O/10% D2O
Details: The N-terminally tagged histidines were then cleaved with the protease (factor Xa)
Label: 13/15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMJ_domain[U-13C; U-15N]1
300 mMsodium chloridenatural abundance1
1 mMDithiothreitolnatural abundance1
20 mMTRISnatural abundance1
10 % v/vD2Onatural abundance1
Sample conditionsDetails: 1.0mM J-domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 300mM NaCl; 1mM d-DTT; 10% D2O, 90% H2O
Ionic strength: 300 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker Bruker Biospin Avance 900 spectrometerBrukerBruker Biospin Avance 900 spectrometer9001equipped with a cryoprobe
Bruker Bruker Biospin Avance 800 spectrometerBrukerBruker Biospin Avance 800 spectrometer8002equipped with a cryoprobe

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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