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- PDB-1m62: Solution structure of the BAG domain from BAG4/SODD -

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Basic information

Entry
Database: PDB / ID: 1m62
TitleSolution structure of the BAG domain from BAG4/SODD
ComponentsBAG-family molecular chaperone regulator-4
KeywordsCHAPERONE / BAG domain / BAG4 / SODD / Silencer of Death Domains / Hsp70/Hsc70 co-chaperone
Function / homology
Function and homology information


negative regulation of mRNA modification / Signaling by plasma membrane FGFR1 fusions / negative regulation of protein targeting to mitochondrion / adenyl-nucleotide exchange factor activity / TNF signaling / ruffle assembly / positive regulation of fibroblast migration / positive regulation of actin filament polymerization / positive regulation of cell adhesion / Regulation of HSF1-mediated heat shock response ...negative regulation of mRNA modification / Signaling by plasma membrane FGFR1 fusions / negative regulation of protein targeting to mitochondrion / adenyl-nucleotide exchange factor activity / TNF signaling / ruffle assembly / positive regulation of fibroblast migration / positive regulation of actin filament polymerization / positive regulation of cell adhesion / Regulation of HSF1-mediated heat shock response / positive regulation of stress fiber assembly / cellular response to epidermal growth factor stimulus / Signaling by FGFR1 in disease / protein localization to plasma membrane / protein folding / positive regulation of peptidyl-serine phosphorylation / cellular response to tumor necrosis factor / protein-folding chaperone binding / protein stabilization / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / RNA binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBriknarova, K. / Takayama, S. / Homma, S. / Baker, K. / Cabezas, E. / Hoyt, D.W. / Li, Z. / Satterthwait, A.C. / Ely, K.R.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: BAG4/SODD protein contains a short BAG domain.
Authors: Briknarova, K. / Takayama, S. / Homma, S. / Baker, K. / Cabezas, E. / Hoyt, D.W. / Li, Z. / Satterthwait, A.C. / Ely, K.R.
History
DepositionJul 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BAG-family molecular chaperone regulator-4


Theoretical massNumber of molelcules
Total (without water)9,9741
Polymers9,9741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 28structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein BAG-family molecular chaperone regulator-4 / Silencer of death domains


Mass: 9973.530 Da / Num. of mol.: 1 / Fragment: BAG domain (Residues 371-457)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG4/SODD / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95429

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C/15N-separated NOESY
1223D 15N-separated NOESY
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D H(CCO)NH
1613D C(CO)NH
1713D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM BAG4 BD U-15N 13C, 10 mM potassium phosphate buffer pH 7.2, 100 mM KCl, 1 mM DTT, 1 mM EDTA90% H2O/10% D2O
21.5 mM BAG4 BD U-15N, 10 mM potassium phosphate buffer pH 7.2, 100 mM KCl, 1 mM DTT, 1 mM EDTA90% H2O/10% D2O
Sample conditionsIonic strength: 0.12 / pH: 7.2 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian Inc.collection
Felix2000MSI/Accelrys Inc.processing
Felix2000MSI/Accelrys Inc.data analysis
CNS1Brunger et al.structure solution
CNS1Brunger et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 28 / Conformers submitted total number: 25

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