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- PDB-6u3s: Solution NMR structure of the DNAJB6b deltaST variant (Aligned on... -

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Basic information

Entry
Database: PDB / ID: 6u3s
TitleSolution NMR structure of the DNAJB6b deltaST variant (Aligned on the CTD domain)
ComponentsDnaJ homolog subfamily B member 6
KeywordsCHAPERONE / Hsp40 / Antiaggregation / amyloid
Function / homology
Function and homology information


chorion development / chorio-allantoic fusion / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / negative regulation of inclusion body assembly / intermediate filament organization / ATPase activator activity / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein folding / regulation of cellular response to heat ...chorion development / chorio-allantoic fusion / syncytiotrophoblast cell differentiation involved in labyrinthine layer development / negative regulation of inclusion body assembly / intermediate filament organization / ATPase activator activity / protein localization to nucleus / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein folding / regulation of cellular response to heat / protein folding chaperone / heat shock protein binding / Hsp70 protein binding / extracellular matrix organization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Z disc / regulation of protein localization / unfolded protein binding / protein folding / protein-folding chaperone binding / actin cytoskeleton organization / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / DNA binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
DnaJ homolog subfamily B member 2 / 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 B member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKaramanos, T.K. / Clore, G.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK-029023 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis.
Authors: Karamanos, T.K. / Tugarinov, V. / Clore, G.M.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 14, 2023Group: Advisory / Database references / Other
Category: database_2 / pdbx_database_remark / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog subfamily B member 6


Theoretical massNumber of molelcules
Total (without water)21,8311
Polymers21,8311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Apart frm analytical SEC, NMR calculated relaxation and hydrodynamic parameters confirm monomeric state
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DnaJ homolog subfamily B member 6 / HHDJ1 / Heat shock protein J2 / HSJ-2 / MRJ / MSJ-1


Mass: 21831.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNAJB6, HSJ2, MRJ, MSJ1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75190

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N TROSY
121isotropic23D HN(CA)CB
131isotropic23D HNCA
141isotropic13D HNCO
1164isotropic23D HNCO
153isotropic22D 1H-13C HMQC
162isotropic22D 1H-13C HMQC constant time
172isotropic23D HMCMCBCA
182isotropic23D HMCM(CBCA)CO
195isotropic33D HHN NOESY-TROSY
1103isotropic43D HHC NOESY-HMQC
1113isotropic23D HHC HMQC-NOESY
1123isotropic43D HCC HMQC-NOESY-HMQC
1135isotropic12D HN PRE
2146anisotropic32D HN ARTSY PF1
1177anisotropic32D HN ARTSY PegHex

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution12e-04 M [U-13C; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2ODCN_sample90% H2O/10% D2O
solution22e-04 M [ILV-CH3; U-13C; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 100% D2OILV_U13C_sample100% D2OSpecifically protonated at CH3-ILV positions, uniformly 13C, 15N, 2H
solution32e-04 M [ILV-CH3; U-15N; U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 100% D2OILV_sample100% D2OSpecifically protonated at CH3-ILV positions, uniformly 15N, 2H
solution42e-04 M [U-13C; U-15N] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2OCN_sample90% H2O/10% D2O
solution52e-04 M [U-15N;U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2ODN_sample90% H2O/10% D2O
filamentous virus62e-04 M [U-15N;U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.1 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2OPF1_sample90% H2O/10% D2O
gel solution70.0002 M [U-15N;U-2H] DNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b, 0.05 M sodium chloride, 0.02 % w/v sodium azide, 0.02 M sodium phosphate, 90% H2O/10% D2OPeg/Hex_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.0002 MDNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b[U-13C; U-15N; U-2H]1
0.05 Msodium chloridenatural abundance1
0.02 % w/vsodium azidenatural abundance1
0.02 Msodium phosphatenatural abundance1
0.0002 MDNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b[ILV-CH3; U-13C; U-15N; U-2H]2
0.05 Msodium chloridenatural abundance2
0.02 % w/vsodium azidenatural abundance2
0.02 Msodium phosphatenatural abundance2
0.0002 MDNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b[ILV-CH3; U-15N; U-2H]3
0.05 Msodium chloridenatural abundance3
0.02 % w/vsodium azidenatural abundance3
0.02 Msodium phosphatenatural abundance3
0.0002 MDNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b[U-13C; U-15N]4
0.05 Msodium chloridenatural abundance4
0.02 % w/vsodium azidenatural abundance4
0.02 Msodium phosphatenatural abundance4
0.0002 MDNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b[U-15N;U-2H]5
0.05 Msodium chloridenatural abundance5
0.02 % w/vsodium azidenatural abundance5
0.02 Msodium phosphatenatural abundance5
0.0002 MDNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b[U-15N;U-2H]6
0.1 Msodium chloridenatural abundance6
0.02 % w/vsodium azidenatural abundance6
0.02 Msodium phosphatenatural abundance6
0.0002 MDNAJB6b deltaST variant. This variant is missing residues 132-183 in comparison to the full-length DNAJB6b[U-15N;U-2H]7
0.05 Msodium chloridenatural abundance7
0.02 % w/vsodium azidenatural abundance7
0.02 Msodium phosphatenatural abundance7
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)PH err
187 mMcondition_16.7 1 atm298 K
2145 mMPF1_condition7 1 atm298 K0.1

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III8003
Bruker AVANCE IIIBrukerAVANCE III9004

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Processing

NMR software
NameDeveloperClassification
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CcpNmr AnalysisCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10

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