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- PDB-1m7k: Solution Structure of the SODD BAG Domain -

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Basic information

Entry
Database: PDB / ID: 1m7k
TitleSolution Structure of the SODD BAG Domain
ComponentsSilencer of Death Domains
KeywordsCHAPERONE / THREE HELIX BUNDLE
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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / RNA binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 simulated annealing
AuthorsBrockmann, C. / Leitner, D. / Labudde, D. / Diehl, A. / Sievert, V. / Buessow, K. / Oschkinat, H.
CitationJournal: Febs Lett. / Year: 2004
Title: The solution structure of the SODD BAG domain reveals additional electrostatic interactions in the HSP70 complexes of SODD subfamily BAG domains
Authors: Brockmann, C. / Leitner, D. / Labudde, D. / Diehl, A. / Sievert, V. / Buessow, K. / Kuhne, R. / Oschkinat, H.
History
DepositionJul 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Silencer of Death Domains


Theoretical massNumber of molelcules
Total (without water)11,2761
Polymers11,2761
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 / 400structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Silencer of Death Domains / BAG-family molecular chaperone regulator-4


Mass: 11275.769 Da / Num. of mol.: 1 / Fragment: residues 358-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O95429

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1313D 13C-methyl selective NOESY
1422D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4mM SODD U-15N,13C; 20mM phosphate buffer, pH6.0; 50mM NaCl;94% H20 6%, D2O
21.4mM SODD U-15N,13C; 20mM phosphate buffer, NA; 50mM NaCl;100% D2O
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 300 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
Sparky3.1Goddard, T.D.; Kneller, D.G.data analysis
CNS1.1Brunger, Adams, Clore, Delano, Gros, Grosse-Kunstleve, Jiang, Kuszewski, Nilges, Pannu, Read, Rice, Simonson, Warrenrefinement
RefinementMethod: torsion angle simulated annealing / Software ordinal: 1
Details: Calculated from 723 NOE restraints, 52 from hydrogen bonds and 140 dihedral restraints
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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