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- PDB-7p33: Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with B... -

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Basic information

Entry
Database: PDB / ID: 7p33
TitleEpstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide
Components
  • Apoptosis regulator BHRF1
  • BH3-interacting domain death agonist p15
KeywordsAPOPTOSIS / Gamma herpes virus / Epstein-Barr virus / BHRF-1 / Bcl-2
Function / homology
Function and homology information


cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of fibroblast apoptotic process / symbiont-mediated suppression of host autophagy / symbiont-mediated suppression of host apoptosis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...cysteine-type endopeptidase regulator activity involved in apoptotic process / mitochondrial outer membrane permeabilization / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of fibroblast apoptotic process / symbiont-mediated suppression of host autophagy / symbiont-mediated suppression of host apoptosis / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / regulation of epithelial cell proliferation / establishment of protein localization to membrane / death receptor binding / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / protein targeting to mitochondrion / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / apoptotic mitochondrial changes / mitochondrial ATP synthesis coupled electron transport / regulation of T cell proliferation / regulation of G1/S transition of mitotic cell cycle / signal transduction in response to DNA damage / extrinsic apoptotic signaling pathway via death domain receptors / host cell membrane / host cell mitochondrion / Activation of BAD and translocation to mitochondria / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / protein-containing complex assembly / neuron apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding / mitochondrion / membrane / cytosol
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Apoptosis regulator BHRF1 / BH3-interacting domain death agonist
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78542723478 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Viruses / Year: 2022
Title: Crystal Structures of Epstein-Barr Virus Bcl-2 Homolog BHRF1 Bound to Bid and Puma BH3 Motif Peptides.
Authors: Suraweera, C.D. / Hinds, M.G. / Kvansakul, M.
History
DepositionJul 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator BHRF1
B: Apoptosis regulator BHRF1
C: Apoptosis regulator BHRF1
D: Apoptosis regulator BHRF1
E: Apoptosis regulator BHRF1
G: BH3-interacting domain death agonist p15
H: BH3-interacting domain death agonist p15
F: BH3-interacting domain death agonist p15
I: BH3-interacting domain death agonist p15
J: BH3-interacting domain death agonist p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,86412
Polymers117,70710
Non-polymers1572
Water1,11762
1
A: Apoptosis regulator BHRF1
G: BH3-interacting domain death agonist p15


Theoretical massNumber of molelcules
Total (without water)23,5412
Polymers23,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-16 kcal/mol
Surface area10090 Å2
MethodPISA
2
B: Apoptosis regulator BHRF1
F: BH3-interacting domain death agonist p15


Theoretical massNumber of molelcules
Total (without water)23,5412
Polymers23,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area8960 Å2
MethodPISA
3
C: Apoptosis regulator BHRF1
H: BH3-interacting domain death agonist p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6043
Polymers23,5412
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-13 kcal/mol
Surface area10190 Å2
MethodPISA
4
D: Apoptosis regulator BHRF1
I: BH3-interacting domain death agonist p15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6363
Polymers23,5412
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-17 kcal/mol
Surface area9550 Å2
MethodPISA
5
E: Apoptosis regulator BHRF1
J: BH3-interacting domain death agonist p15


Theoretical massNumber of molelcules
Total (without water)23,5412
Polymers23,5412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-14 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.208, 94.208, 455.582
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein
Apoptosis regulator BHRF1 / Early antigen protein R / EA-R / Nuclear antigen


Mass: 19848.367 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Strain: B95-8 / Gene: BHRF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03182
#2: Protein/peptide
BH3-interacting domain death agonist p15 / p15 BID


Mass: 3693.111 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P55957
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.68 % / Description: thick hexagonal prism
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4M Ammonium phosphate mono basic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.785→46.8542271629 Å / Num. obs: 28893 / % possible obs: 92.17 % / Redundancy: 11.9 % / Biso Wilson estimate: 59.5883072532 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.4
Reflection shellResolution: 2.785→2.94 Å / Rmerge(I) obs: 1.207 / Num. unique obs: 4267 / CC1/2: 0.586

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless7.1.007data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XPX

2xpx


Resolution: 2.78542723478→46.8542271629 Å / SU ML: 0.437300470854 / Cross valid method: FREE R-VALUE / σ(F): 1.3497953026 / Phase error: 28.0524443425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.274075422541 1396 4.83563684229 %
Rwork0.22970835287 27473 -
obs0.231906605748 28869 92.1978794073 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.4775184542 Å2
Refinement stepCycle: LAST / Resolution: 2.78542723478→46.8542271629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7192 0 9 62 7263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002014675076697353
X-RAY DIFFRACTIONf_angle_d0.3966130372769978
X-RAY DIFFRACTIONf_chiral_restr0.03181316873081123
X-RAY DIFFRACTIONf_plane_restr0.002118132500411277
X-RAY DIFFRACTIONf_dihedral_angle_d18.35679578434339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78542723478-2.8850.3795809090031410.3105538823822731X-RAY DIFFRACTION94.8794185662
2.885-3.00050.3302331044051430.2947792526842854X-RAY DIFFRACTION98.1335952849
3.0005-3.1370.3723836307291520.2666284189862851X-RAY DIFFRACTION98.0091383812
3.137-3.30230.3092669774251240.2470719983442841X-RAY DIFFRACTION97.8225008248
3.3023-3.50920.2716833110111110.2531873211692292X-RAY DIFFRACTION77.5161290323
3.5092-3.780.2766520255151120.2355467408452443X-RAY DIFFRACTION82.4725629438
3.78-4.16020.2806255163871320.2022041435272510X-RAY DIFFRACTION85.2533075186
4.1602-4.76170.2119344768981710.1791278731842886X-RAY DIFFRACTION96.8324358568
4.7617-5.99720.2440642991791560.2116721792162937X-RAY DIFFRACTION96.2651727358

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