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- PDB-4mi8: Crystal structure of the complex of murine gamma-herpesvirus 68 B... -

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Basic information

Entry
Database: PDB / ID: 4mi8
TitleCrystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide
Components
  • Bcl-2 homolog (Gene 16?)
  • Beclin-1
KeywordsVIRAL PROTEIN/APOPTOSIS / BH3D / Bcl-2 family / anti-apoptotic and anti-autophagic activities / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSu, M. / Mei, Y. / Sinha, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Targeting gamma-herpesvirus 68 Bcl-2-mediated down-regulation of autophagy.
Authors: Su, M. / Mei, Y. / Sanishvili, R. / Levine, B. / Colbert, C.L. / Sinha, S.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Feb 17, 2016Group: Structure summary
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2 homolog (Gene 16?)
B: Bcl-2 homolog (Gene 16?)
C: Beclin-1
D: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3808
Polymers38,9964
Non-polymers3844
Water2,396133
1
A: Bcl-2 homolog (Gene 16?)
C: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5943
Polymers19,4982
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-29 kcal/mol
Surface area8140 Å2
MethodPISA
2
B: Bcl-2 homolog (Gene 16?)
D: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7865
Polymers19,4982
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-47 kcal/mol
Surface area8290 Å2
MethodPISA
3
B: Bcl-2 homolog (Gene 16?)
D: Beclin-1
hetero molecules

B: Bcl-2 homolog (Gene 16?)
D: Beclin-1
hetero molecules

A: Bcl-2 homolog (Gene 16?)
C: Beclin-1
hetero molecules

A: Bcl-2 homolog (Gene 16?)
C: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,76116
Polymers77,9928
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area15740 Å2
ΔGint-221 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.598, 140.844, 54.038
Angle α, β, γ (deg.)90.00, 127.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21B-363-

HOH

31B-364-

HOH

41C-206-

HOH

51D-213-

HOH

61D-214-

HOH

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Components

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


Mass: 16652.883 Da / Num. of mol.: 2 / Fragment: UNP residues 2-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Gene: GAMMAHV.M11, M11, v-bcl-2, v-bcl-2 GAMMAHV.M11 / Plasmid: pET21(d+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P89884
#2: Protein/peptide Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 2845.235 Da / Num. of mol.: 2 / Fragment: UNP residues 107-130 / Mutation: G120E, D121A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14457
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 17, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 24220 / Num. obs: 24082 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.14 Å / % possible all: 91.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.16 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.664 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22362 989 5.1 %RANDOM
Rwork0.15637 ---
obs0.15973 24082 99.4 %-
all-24220 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.06 Å2
2---0.04 Å20 Å2
3---0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3566 Å0.2748 Å
Luzzati d res low-5 Å
Luzzati sigma a0.357 Å0.275 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 20 133 2695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022614
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9513539
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8895309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.3223.68125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99515455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9191516
X-RAY DIFFRACTIONr_chiral_restr0.120.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021942
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 21 -
Rwork0.155 458 -
obs--27.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.90620.3261-0.24657.5447-2.03761.3266-0.00640.3130.0936-0.1901-0.0546-0.5255-0.00730.04550.0610.1386-0.02030.08810.11620.00810.0859-5.631341.370613.2718
22.1173-0.47760.44132.40180.69811.42490.09280.1702-0.13380.1979-0.0260.01580.1699-0.0555-0.06680.0959-0.0378-0.05990.0819-0.00760.07378.240670.904412.7799
38.8079-2.1041-2.59728.4085-2.07963.1155-0.09210.4181-0.6039-0.3665-0.1888-0.30240.2909-0.01810.28090.12760.00660.0980.025-0.02770.1315-6.456226.155414.9517
411.052-0.96353.48484.245-0.38413.7665-0.1786-0.08780.6392-0.11780.13110.0338-0.2871-0.02270.04750.1459-0.0121-0.04630.01050.00670.11448.375786.192713.9477
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 136
2X-RAY DIFFRACTION2B2 - 137
3X-RAY DIFFRACTION3C108 - 127
4X-RAY DIFFRACTION4D106 - 127

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