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- PDB-6cgh: Solution structure of the four-helix bundle region of human J-pro... -

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Basic information

Entry
Database: PDB / ID: 6cgh
TitleSolution structure of the four-helix bundle region of human J-protein Zuotin, a component of ribosome-associated complex (RAC)
ComponentsDnaJ homolog subfamily C member 2
KeywordsCHAPERONE / Zuotin / J-protein / Hsp70 / molecular chaperone / DNAJC2 / Hsp40 / Ribosome-Associated Complex (RAC) / Mpp11
Function / homology
Function and homology information


'de novo' cotranslational protein folding / ubiquitin-modified histone reader activity / negative regulation of DNA biosynthetic process / ATPase activator activity / Regulation of HSF1-mediated heat shock response / regulation of translational fidelity / regulation of cellular response to heat / Hsp70 protein binding / ribosome binding / chromatin organization ...'de novo' cotranslational protein folding / ubiquitin-modified histone reader activity / negative regulation of DNA biosynthetic process / ATPase activator activity / Regulation of HSF1-mediated heat shock response / regulation of translational fidelity / regulation of cellular response to heat / Hsp70 protein binding / ribosome binding / chromatin organization / histone binding / nuclear membrane / DNA replication / chromatin binding / nucleolus / positive regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / SANT domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / SANT domain profile. / DnaJ molecular chaperone homology domain / dnaJ domain profile. / SANT domain / Chaperone J-domain superfamily / DnaJ domain / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DnaJ homolog subfamily C member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsShrestha, O.K. / Lee, W. / Tonelli, M. / Cornilescu, G. / Markley, J.L. / Ciesielski, S.J. / Craig, E.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM31107 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM27870 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM103399 United States
CitationJournal: Plos One / Year: 2019
Title: Structure and evolution of the 4-helix bundle domain of Zuotin, a J-domain protein co-chaperone of Hsp70.
Authors: Shrestha, O.K. / Sharma, R. / Tomiczek, B. / Lee, W. / Tonelli, M. / Cornilescu, G. / Stolarska, M. / Nierzwicki, L. / Czub, J. / Markley, J.L. / Marszalek, J. / Ciesielski, S.J. / Craig, E.A.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
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 C member 2


Theoretical massNumber of molelcules
Total (without water)10,4021
Polymers10,4021
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 area6440 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DnaJ homolog subfamily C member 2 / M-phase phosphoprotein 11 / Zuotin-related factor 1


Mass: 10401.884 Da / Num. of mol.: 1 / Fragment: UNP residues 346-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJC2, MPHOSPH11, MPP11, ZRF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99543

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HBHA(CO)NH
181isotropic13D H(CCO)NH
191isotropic13D C(CO)NH
151isotropic12D 1H-13C HSQC aliphatic
161isotropic13D 1H-15N NOESY
171isotropic13D 1H-13C NOESY
1101isotropic21H-15N IPAP HSQC
1113anisotropic21H-15N IPAP HSQC
1124anisotropic31H-15N IPAP HSQC
1132isotropic12D 1H-15N HSQC
1141isotropic43D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1300 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O20 mM sodium phosphate buffer, pH 7.5 containing 250 mM NaCl and 5 mM dithiothreitol with 7% 2H2O and 0.02% NaN315N_13C_sample93% H2O/7% D2O
bicelle3200 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O20 mM sodium phosphate buffer, pH 7.5 containing 250 mM NaCl and 5 mM dithiothreitol with 7% 2H2O and 0.02% NaN3, 5% w/v bicelles 30:10:1 DMPC/DHPC/CTAB15N_13C_sample_bic_ctab93% H2O/7% D2O
bicelle4150 uM [U-100% 13C; U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O20 mM sodium phosphate buffer, pH 7.5 containing 250 mM NaCl and 5 mM dithiothreitol with 7% 2H2O and 0.02% NaN3, 5% w/v C12E5/hexanol/CTAB 0.96/1/0.1 doped with CTAB (PEG/CTAB=27:1)15N_13C_sample_peg_ctab93% H2O/7% D2O
solution2300 uM [U-100% 15N] Mpp11 (346-432), 93% H2O/7% D2O20 mM sodium phosphate buffer, pH 7.5 containing 250 mM NaCl and 5 mM dithiothreitol with 7% 2H2O and 0.02% NaN315N_sample93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMMpp11 (346-432)[U-100% 13C; U-100% 15N]1
200 uMMpp11 (346-432)[U-100% 13C; U-100% 15N]3
150 uMMpp11 (346-432)[U-100% 13C; U-100% 15N]4
300 uMMpp11 (346-432)[U-100% 15N]2
Sample conditionsDetails: 20 mM sodium phosphate buffer, pH 7.5 containing 250 mM NaCl and 5 mM dithiothreitol with 7% 2H2O and 0.02% NaN3
Ionic strength: 250 mM NaCl and 20 mM sodium phosphate mM / Label: Mpp11_NMR / pH: 7.5 / Pressure: Ambient Pa / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNSVarianVNS6001
Bruker AVANCEBrukerAVANCE7502
Bruker AVANCEBrukerAVANCE6003
Varian VNSVarianVNS9004

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
APESShin, Lee and Leepeak picking
NMRFAM-SPARKYLee, Tonelli and Markleypeak picking
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
PINE-SPARKYLee, Westler, Bahrami, Eghbalnia and Markleychemical shift assignment
PONDEROSA-C/SLee, Stark and Markleystructure calculation
AUDANALee, Petit, Cornilescu, Stark and Markleystructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
PONDEROSA-C/SLee, Stark and Markleyrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
Refinement
MethodSoftware ordinalDetails
molecular dynamics11High temp molecular dynamics, simulated annealing, and torsion angle dynamics by PONDEROSA-C/S coupled with XPLOR-NIH (eefx force field)
molecular dynamics12High temp molecular dynamics, simulated annealing, and torsion angle dynamics by PONDEROSA-C/S coupled with XPLOR-NIH (eefx force field)
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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