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- PDB-7x89: Tid1 -

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Basic information

Entry
Database: PDB / ID: 7x89
TitleTid1
ComponentsDnaJ homolog subfamily A member 3, mitochondrial
KeywordsCHAPERONE / Heat shock protein
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 programmed cell death / activation-induced cell death of T cells / small GTPase-mediated signal transduction / neuromuscular junction development / 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 programmed cell death / activation-induced cell death of T cells / small GTPase-mediated signal transduction / neuromuscular junction development / negative regulation of type II interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / mitochondrial nucleoid / response to type II interferon / NF-kappaB binding / positive regulation of T cell proliferation / negative regulation of canonical NF-kappaB signal transduction / Hsp70 protein binding / positive regulation of protein ubiquitination / negative regulation of protein kinase activity / mitochondrion organization / neuromuscular junction / cytoplasmic side of plasma membrane / cellular senescence / unfolded protein binding / protein folding / T cell differentiation in thymus / response to heat / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / postsynaptic membrane / 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 / zinc ion binding / ATP binding / nucleus / 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
AuthorsJang, J. / Lee, S.H. / Kang, D.H. / Sim, D.W. / Jo, K.S. / Ryu, H. / Kim, E.H. / Ryu, K.S. / Lee, J.H. / Kim, J.H. / Won, H.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural studies on the J-domain and GF-motif of the mitochondrial Hsp40, Tid1
Authors: Jang, J. / Lee, S.H. / Kang, D.H. / Kim, J.H. / Sim, D.W. / Jo, K.S. / Won, H.S. / Ryu, K.S. / Kim, E.H. / Ryu, H. / Lee, J.H.
History
DepositionMar 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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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 / Production host: Escherichia coli (E. coli) / 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
112isotropic13D 1H-15N NOESY
122isotropic13D 1H-13C NOESY
132isotropic23D (H)CCH-TOCSY
142isotropic23D CCH-TOCSY
152isotropic13D HN(CA)CB
162isotropic13D HN(CA)CO
172isotropic13D CBCA(CO)NH
182isotropic13D HNCO

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Sample preparation

DetailsType: solution
Contents: 200 uM [U-13C; U-15N] DnaJ homolog subfamily A member 3, mitochondrial, 200 uM [U-15N] DnaJ homolog subfamily A member 3, mitochondrial, 90% H2O/10% D2O
Label: Tid1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 200 uM / Component: DnaJ homolog subfamily A member 3, mitochondrial / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CHARMMB. R. Brooksrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 5
Details: 1365 NOE distances were used and 62 dihedral angles were used
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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