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- PDB-1ugo: Solution structure of the first Murine BAG domain of Bcl2-associa... -

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Basic information

Entry
Database: PDB / ID: 1ugo
TitleSolution structure of the first Murine BAG domain of Bcl2-associated athanogene 5
ComponentsBcl2-associated athanogene 5
KeywordsCHAPERONE / TRIPLE HELIX BUNDLE / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


regulation of inclusion body assembly / Regulation of HSF1-mediated heat shock response / junctional membrane complex / negative regulation of protein refolding / Golgi organization / ubiquitin ligase inhibitor activity / 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 ...regulation of inclusion body assembly / Regulation of HSF1-mediated heat shock response / junctional membrane complex / negative regulation of protein refolding / Golgi organization / ubiquitin ligase inhibitor activity / 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 / 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 / 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 speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsEndoh, H. / Hayashi, F. / Seimiya, K. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. ...Endoh, H. / Hayashi, F. / Seimiya, K. / Shirouzu, M. / Terada, T. / Kigawa, T. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Hirota, H. / Yoshida, M. / Tanaka, A. / Osanai, T. / Arakawa, T. / Carninci, P. / Kawai, J. / Hayashizaki, Y. / 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
DepositionJun 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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 1.4Dec 27, 2023Group: 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: Bcl2-associated athanogene 5


Theoretical massNumber of molelcules
Total (without water)10,9041
Polymers10,9041
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Bcl2-associated athanogene 5


Mass: 10904.047 Da / Num. of mol.: 1 / Fragment: BAG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: FANTOM 2 cDNA 4930405J06 / Plasmid: P020122-13 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q8CI32

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 0.7mM 13C, 15N-labeled protein; 20mM phosphate buffer; 200mM NaCl; 4mM DTT; 0.4mM NaN3; 8% D2O
Solvent system: 92% H2O, 8% D2O
Sample conditionsIonic strength: 220mM / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.811Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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