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- PDB-1wxv: Solution structure of the ubiquitin domain of BCL-2 binding athan... -

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Basic information

Entry
Database: PDB / ID: 1wxv
TitleSolution structure of the ubiquitin domain of BCL-2 binding athanogene-1
ComponentsBAG-family molecular chaperone regulator-1
KeywordsAPOPTOSIS / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


adenyl-nucleotide exchange factor activity / positive regulation of smooth muscle cell apoptotic process / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / protein-folding chaperone binding / protein stabilization / cell surface receptor signaling pathway / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process ...adenyl-nucleotide exchange factor activity / positive regulation of smooth muscle cell apoptotic process / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / protein-folding chaperone binding / protein stabilization / cell surface receptor signaling pathway / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNiraula, T.N. / Muto, Y. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the ubiquitin domain of BCL-2 binding athanogene-1
Authors: Niraula, T.N. / Muto, Y. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _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-1


Theoretical massNumber of molelcules
Total (without water)9,6311
Polymers9,6311
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)20 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein BAG-family molecular chaperone regulator-1 / BCL-2 binding athanogene- 1 / BAG-1 / Glucocorticoid receptor-associated protein RAP46


Mass: 9630.836 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: BAG1 / Plasmid: P040223-36 / References: UniProt: Q99933

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.04mM ubiquitin domain U-13C, 15N; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02 % NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe200311221Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.913Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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