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- PDB-2d9d: Solution structure of the BAG domain (275-350) of BAG-family mole... -

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Basic information

Entry
Database: PDB / ID: 2d9d
TitleSolution structure of the BAG domain (275-350) of BAG-family molecular chaperone regulator-5
ComponentsBAG family molecular chaperone regulator 5
KeywordsCHAPERONE / triple helix bundle / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of inclusion body assembly / junctional membrane complex / negative regulation of protein refolding / regulation of ubiquitin-protein transferase activity / adenyl-nucleotide exchange factor activity / Golgi organization / ubiquitin ligase inhibitor activity / Regulation of HSF1-mediated heat shock response / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / inclusion body ...regulation of inclusion body assembly / junctional membrane complex / negative regulation of protein refolding / regulation of ubiquitin-protein transferase activity / adenyl-nucleotide exchange factor activity / Golgi organization / ubiquitin ligase inhibitor activity / Regulation of HSF1-mediated heat shock response / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / inclusion body / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / protein folding / negative regulation of neuron projection development / protein-folding chaperone binding / protein stabilization / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / mitochondrion / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
BAG domain / Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BAG family molecular chaperone regulator 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHatta, R. / Hayashi, F. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2010
Title: The C-terminal BAG domain of BAG5 induces conformational changes of the Hsp70 nucleotide-binding domain for ADP-ATP exchange
Authors: Arakawa, A. / Handa, N. / Ohsawa, N. / Shida, M. / Kigawa, T. / Hayashi, F. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 9, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: BAG family molecular chaperone regulator 5


Theoretical massNumber of molelcules
Total (without water)9,8421
Polymers9,8421
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein BAG family molecular chaperone regulator 5 / BCL2-associated athanogene 5 / BAG-5


Mass: 9842.250 Da / Num. of mol.: 1 / Fragment: BAG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG5 / Plasmid: P04070-E03 / Production host: cell free protein synthesis (others) / References: UniProt: Q9UL15

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.96mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 75mM GuOx; 90% H2O; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 345mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.932Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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