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- PDB-2lo1: NMR structure of the protein BC008182, a DNAJ-like domain from Ho... -

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Basic information

Entry
Database: PDB / ID: 2lo1
TitleNMR structure of the protein BC008182, a DNAJ-like domain from Homo sapiens
ComponentsDnaJ homolog subfamily A member 1
KeywordsCHAPERONE / PSI-Biology / Joint Center for Structural Genomics / JCSG / Partnership for Stem Cell Biology / STEMCELL
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 / molecular dynamics
Model detailsclosest to the average, model 9
AuthorsDutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
CitationJournal: To be Published
Title: NMR structure of the protein BC008182, DNAJ homolog from Homo sapiens
Authors: Dutta, S.K. / Serrano, P. / Geralt, M. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG) / Partnership for Stem Cell Biology (STEMCELL)
History
DepositionJan 9, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references / Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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 1


Theoretical massNumber of molelcules
Total (without water)8,2241
Polymers8,2241
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 / 80target function
RepresentativeModel #1closest to the average

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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: 8224.290 Da / Num. of mol.: 1 / Fragment: J domain residues 1-70
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
1214D HACANH APSY
1315D (HA)CA(CO)NH APSY
1415D CBCA(CO)NH APSY
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1.2 mM [U-98% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 5 mM sodium azide, 50 mM sodium chloride, 95 % H2O, 5 % D2O, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMentity-1[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate-21
5 mMsodium azide-31
50 mMsodium chloride-41
95 %H2O-51
5 %D2O-61
Sample conditionsIonic strength: 0.08 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert P.structure solution
TopSpin2.1Brukercollection
TopSpin2.1Brukerprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1317 / NOE intraresidue total count: 361 / NOE long range total count: 269 / NOE medium range total count: 339 / NOE sequential total count: 348
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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