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- PDB-3bl2: Crystal Structure of M11, the BCL-2 Homolog of Murine Gamma-herpe... -

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Basic information

Entry
Database: PDB / ID: 3bl2
TitleCrystal Structure of M11, the BCL-2 Homolog of Murine Gamma-herpesvirus 68, Complexed with Mouse Beclin1 (residues 106-124)
Components
  • Beclin-1
  • V-bcl-2
KeywordsVIRAL PROTEIN/APOPTOSIS / protein-protein complex / viral BCL-2 / Beclin1 / apoptosis / M11 / autophagy / Antiviral defense / Coiled coil / Cytoplasm / Golgi apparatus / Membrane / VIRAL PROTEIN-APOPTOSIS COMPLEX
Function / homology
Function and homology information


Macroautophagy / cellular response to aluminum ion / ISG15 antiviral mechanism / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / engulfment of apoptotic cell ...Macroautophagy / cellular response to aluminum ion / ISG15 antiviral mechanism / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / engulfment of apoptotic cell / positive regulation of autophagosome assembly / symbiont-mediated suppression of host autophagy / early endosome to late endosome transport / cytoplasmic side of mitochondrial outer membrane / negative regulation of autophagosome assembly / symbiont-mediated suppression of host apoptosis / receptor catabolic process / protein targeting to lysosome / SMAD protein signal transduction / Ub-specific processing proteases / response to other organism / phosphatidylinositol-3-phosphate biosynthetic process / negative regulation of programmed cell death / lysosome organization / response to vitamin E / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / p38MAPK cascade / autophagosome assembly / autophagosome maturation / amyloid-beta metabolic process / regulation of macroautophagy / neuron development / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / positive regulation of intrinsic apoptotic signaling pathway / phagocytic vesicle / JNK cascade / positive regulation of autophagy / negative regulation of autophagy / autophagosome / cellular response to epidermal growth factor stimulus / cellular response to amino acid starvation / cellular response to copper ion / regulation of cytokinesis / macroautophagy / trans-Golgi network / circadian rhythm / response to lead ion / autophagy / cellular response to hydrogen peroxide / GTPase binding / protein-containing complex assembly / cytoplasmic vesicle / angiogenesis / regulation of apoptotic process / protein-macromolecule adaptor activity / defense response to virus / host cell cytoplasm / cytoskeleton / response to hypoxia / endosome membrane / regulation of autophagy / nuclear body / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / apoptotic process / dendrite / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein kinase binding / negative regulation of apoptotic process / protein-containing complex / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Apoptosis regulator M11 / Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region ...Apoptosis regulator M11 / Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like / Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Beclin-1 / Apoptosis regulator Bcl-2 homolog
Similarity search - Component
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsOh, B.-H. / Woo, J.-S. / Ku, B.
CitationJournal: Plos Pathog. / Year: 2008
Title: Structural and Biochemical Bases for the Inhibition of Autophagy and Apoptosis by Viral BCL-2 of Murine gamma-Herpesvirus 68
Authors: Ku, B. / Woo, J.-S. / Liang, C. / Lee, K.-H. / Hong, H.-S. / E, X. / Kim, K.-S. / Jung, J.U. / Oh, B.-H.
History
DepositionDec 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-bcl-2
B: V-bcl-2
C: Beclin-1
D: Beclin-1


Theoretical massNumber of molelcules
Total (without water)34,7904
Polymers34,7904
Non-polymers00
Water1,06359
1
A: V-bcl-2
C: Beclin-1


Theoretical massNumber of molelcules
Total (without water)17,3952
Polymers17,3952
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
MethodPISA
2
B: V-bcl-2
D: Beclin-1


Theoretical massNumber of molelcules
Total (without water)17,3952
Polymers17,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
MethodPISA
3
A: V-bcl-2
C: Beclin-1

B: V-bcl-2
D: Beclin-1


Theoretical massNumber of molelcules
Total (without water)34,7904
Polymers34,7904
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area5130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.863, 53.601, 73.586
Angle α, β, γ (deg.)90.000, 107.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein V-bcl-2 / Bcl-2 homolog / Gene 16? / M11


Mass: 15152.237 Da / Num. of mol.: 2 / Fragment: UNP residues 5-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Genus: Rhadinovirus / Gene: v-bcl-2, GAMMAHV.M11, M11 / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P89884
#2: Protein/peptide Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein


Mass: 2242.639 Da / Num. of mol.: 2
Fragment: BCL-2 binding region, BH3-like domain, UNP residues 106-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Becn1 / Plasmid: pPROEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O88597
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 3350, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 13513 / % possible obs: 94 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.582 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.383.30.16211501.46380.5
2.38-2.483.50.14212101.44586.1
2.48-2.593.70.13912911.45690.2
2.59-2.7340.1313431.63593.3
2.73-2.94.30.10613651.52495.1
2.9-3.124.70.0913971.54597.5
3.12-3.435.80.07214071.51598.7
3.43-3.935.90.0614311.75699.4
3.93-4.956.40.04614451.59799.2
4.95-306.20.04414741.64899.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.05 Å29.33 Å
Translation3.05 Å29.33 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABO

2abo


Resolution: 2.3→20 Å / FOM work R set: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 684 4.8 %RANDOM
Rwork0.204 ---
obs-13447 94.1 %-
Solvent computationBsol: 32.021 Å2
Displacement parametersBiso mean: 29.914 Å2
Baniso -1Baniso -2Baniso -3
1--7.076 Å20 Å211.09 Å2
2--3.283 Å20 Å2
3---3.793 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2444 0 0 59 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.0627
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5531.5
X-RAY DIFFRACTIONc_mcangle_it2.6572
X-RAY DIFFRACTIONc_scbond_it2.2672
X-RAY DIFFRACTIONc_scangle_it3.3662.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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