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- PDB-3dvu: Crystal structure of the complex of murine gamma-herpesvirus 68 B... -

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Basic information

Entry
Database: PDB / ID: 3dvu
TitleCrystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain
Components
  • Beclin-1
  • V-bcl-2
KeywordsViral Protein/apoptosis / AUTOPHAGY / PROTEIN-PROTEIN COMPLEX / VIRAL BCL-2 / BECLIN 1 / APOPTOSIS / M11 / ANTIVIRAL DEFENSE / BH3 DOMAIN / Coiled coil / Cytoplasm / Golgi apparatus / Membrane / Polymorphism / Viral Protein-apoptosis COMPLEX
Function / homology
Function and homology information


cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / engulfment of apoptotic cell / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of stress granule assembly / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization ...cellular response to aluminum ion / phosphatidylinositol 3-kinase complex, class III / engulfment of apoptotic cell / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of stress granule assembly / response to mitochondrial depolarisation / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host autophagy / positive regulation of autophagosome assembly / negative regulation of autophagosome assembly / cytoplasmic side of mitochondrial outer membrane / receptor catabolic process / SMAD protein signal transduction / protein targeting to lysosome / early endosome to late endosome transport / late endosome to vacuole transport / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / negative regulation of programmed cell death / response to iron(II) ion / lysosome organization / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / Macroautophagy / positive regulation of cardiac muscle hypertrophy / RSV-host interactions / p38MAPK cascade / autophagosome assembly / response to vitamin E / autophagosome maturation / amyloid-beta metabolic process / regulation of macroautophagy / neuron development / phosphatidylinositol 3-kinase binding / cellular defense response / cellular response to glucose starvation / mitophagy / positive regulation of intrinsic apoptotic signaling pathway / phagocytic vesicle / JNK cascade / cellular response to copper ion / positive regulation of autophagy / cellular response to epidermal growth factor stimulus / cellular response to amino acid starvation / autophagosome / regulation of cytokinesis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / trans-Golgi network / response to lead ion / ISG15 antiviral mechanism / autophagy / cellular response to hydrogen peroxide / circadian rhythm / GTPase binding / Translation of Replicase and Assembly of the Replication Transcription Complex / protein-containing complex assembly / protein-macromolecule adaptor activity / regulation of apoptotic process / molecular adaptor activity / defense response to virus / host cell cytoplasm / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / regulation of autophagy / endosome membrane / Ub-specific processing proteases / nuclear body / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / apoptotic process / dendrite / ubiquitin protein ligase binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / identical protein binding / cytosol / cytoplasm
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
Apoptosis regulator Bcl-2 homolog / Beclin-1
Similarity search - Component
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSinha, S.
CitationJournal: Autophagy / Year: 2008
Title: Molecular basis of the regulation of Beclin 1-dependent autophagy by the gamma-herpesvirus 68 Bcl-2 homolog M11.
Authors: Sinha, S. / Colbert, C.L. / Becker, N. / Wei, Y. / Levine, B.
History
DepositionJul 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 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 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _struct_ref_seq_dif.details
Revision 1.4Nov 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)38,9964
Polymers38,9964
Non-polymers00
Water1,69394
1
A: V-bcl-2
C: Beclin-1


Theoretical massNumber of molelcules
Total (without water)19,4982
Polymers19,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-17 kcal/mol
Surface area7940 Å2
MethodPISA
2
B: V-bcl-2
D: Beclin-1


Theoretical massNumber of molelcules
Total (without water)19,4982
Polymers19,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-15 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.424, 53.134, 64.059
Angle α, β, γ (deg.)90.00, 96.67, 90.00
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: 16652.883 Da / Num. of mol.: 2 / Fragment: residues 2-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Gene: v-bcl-2, GAMMAHV.M11, M11 / Plasmid: pET21(d+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P89884
#2: Protein/peptide Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 2845.193 Da / Num. of mol.: 2 / Fragment: BH3 domain, residues 105-130 / Source method: obtained synthetically
Details: Peptide synthesis; The peptide corresponding to human Beclin 1 residues 105-130 was chemically synthesized.
References: UniProt: Q14457
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 3350, 0.1M sodium acetate, pH 4.5, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97874 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22424 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.156 / Rsym value: 0.156 / Net I/σ(I): 6.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1394 / Rsym value: 0.42

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ABO with residues 52-73 removed.

2abo


Resolution: 2.5→19.7 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1493683.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 551 5.5 %RANDOM
Rwork0.226 ---
obs0.226 9936 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2445 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 66.5 Å2
Baniso -1Baniso -2Baniso -3
1-17.35 Å20 Å2-24.67 Å2
2---4.67 Å20 Å2
3----12.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 94 2578
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it2.362.5
X-RAY DIFFRACTIONc_mcangle_it4.023
X-RAY DIFFRACTIONc_scbond_it3.613
X-RAY DIFFRACTIONc_scangle_it5.494.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 96 6.7 %
Rwork0.33 1335 -
obs-1911 82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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