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- PDB-2abo: NMR structure of gamma herpesvirus 68 a viral Bcl-2 homolog -

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Basic information

Entry
Database: PDB / ID: 2abo
TitleNMR structure of gamma herpesvirus 68 a viral Bcl-2 homolog
Componentsbcl-2 homolog
KeywordsVIRAL PROTEIN / viral bcl-2 homolog / murine gamma herpes virus
Function / homology
Function and homology information


: / suppression by virus of host autophagy / : / regulation of apoptotic process / host cell cytoplasm
Similarity search - Function
Apoptosis regulator M11 / Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator Bcl-2 homolog
Similarity search - Component
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsLoh, J. / Huang, Q. / Petros, A.M. / Nettesheim, D. / van Dyk, L.F. / Labrada, L. / Speck, S.H. / Levine, B. / Olejniczak, E.T. / Virgin, H.W.
CitationJournal: Plos Pathog. / Year: 2005
Title: A surface groove essential for viral Bcl-2 function during chronic infection in vivo.
Authors: Loh, J. / Huang, Q. / Petros, A.M. / Nettesheim, D. / van Dyk, L.F. / Labrada, L. / Speck, S.H. / Levine, B. / Olejniczak, E.T. / Virgin, H.W.
History
DepositionJul 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bcl-2 homolog


Theoretical massNumber of molelcules
Total (without water)15,7531
Polymers15,7531
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)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein bcl-2 homolog


Mass: 15752.925 Da / Num. of mol.: 1 / Fragment: truncated Bcl-2 homolog
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus / Gene: gamma HV68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P89884

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
1.1 mM HV68-viral BCL2 U-15N, 13C, 20mM Tris; 90% H2O, 10% D2O100% D2O
2.5 mM HV68-viral BCL2 U-15N, 13C, 75% 2H ; 20mM Tris; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 20mM Tris / pH: 7.8 / Pressure: ambient / Temperature: 303 K

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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
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX5002

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Processing

NMR softwareName: CNS / Developer: brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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