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- PDB-7p9w: Epstein-Barr virus encoded apoptosis regulator BHRF1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 7p9w
TitleEpstein-Barr virus encoded apoptosis regulator BHRF1 in complex with Puma BH3
Components
  • Apoptosis regulator BHRF1
  • Bcl-2-binding component 3, isoforms 1/2
KeywordsAPOPTOSIS / BHRF-1 / Bcl-2 / Epstein-Barr virus
Function / homology
Function and homology information


symbiont-mediated suppression of host apoptosis / positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of cysteine-type endopeptidase activity / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process ...symbiont-mediated suppression of host apoptosis / positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of cysteine-type endopeptidase activity / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / Activation of PUMA and translocation to mitochondria / FOXO-mediated transcription of cell death genes / negative regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / host cell mitochondrion / host cell membrane / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / cellular response to ionizing radiation / determination of adult lifespan / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to hypoxia / mitochondrial outer membrane / DNA damage response / mitochondrion / membrane / cytosol
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
AMMONIUM ION / 1,3-PROPANDIOL / PHOSPHATE ION / Apoptosis regulator BHRF1 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00010064633 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 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 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: Bcl-2-binding component 3, isoforms 1/2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,22125
Polymers23,0592
Non-polymers1,16223
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-106 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.772, 62.772, 92.592
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 19848.367 Da / Num. of mol.: 1
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 Bcl-2-binding component 3, isoforms 1/2 / JFY-1 / p53 up-regulated modulator of apoptosis


Mass: 3210.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1

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Non-polymers , 7 types, 79 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Chemical ChemComp-PDO / 1,3-PROPANDIOL / 1,3-Propanediol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#8: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M Ammonium phosphate monobasic

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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: Feb 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→46.88 Å / Num. obs: 14768 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 32.9318121567 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.4
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.992 / Num. unique obs: 1053 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XPX

2xpx


Resolution: 2.00010064633→35.2465186007 Å / SU ML: 0.219989114422 / Cross valid method: FREE R-VALUE / σ(F): 1.33751952487 / Phase error: 25.9130784494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.256882827465 722 4.90156143924 %
Rwork0.219650371857 14008 -
obs0.221447812589 14730 99.8035097229 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.9736061707 Å2
Refinement stepCycle: LAST / Resolution: 2.00010064633→35.2465186007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 61 56 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001767620800321487
X-RAY DIFFRACTIONf_angle_d0.4119930816442003
X-RAY DIFFRACTIONf_chiral_restr0.0290843368927219
X-RAY DIFFRACTIONf_plane_restr0.00283527050189252
X-RAY DIFFRACTIONf_dihedral_angle_d16.1402002144863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.00010064633-2.15450.3190591575941180.2873843968792763X-RAY DIFFRACTION99.7921718046
2.1545-2.37130.266044573371340.2468370294472757X-RAY DIFFRACTION99.7928891957
2.3713-2.71430.2672107758831550.2264076977462784X-RAY DIFFRACTION99.898028552
2.7143-3.41930.2592176723251670.2198497429642764X-RAY DIFFRACTION99.8977505112
Refinement TLS params.Method: refined / Origin x: 93.5433610824 Å / Origin y: -12.3516755543 Å / Origin z: 5.31897999283 Å
111213212223313233
T0.261595120868 Å2-0.0190761920424 Å2-0.0100438664959 Å2-0.228245283867 Å2-0.0131631405913 Å2--0.252150201733 Å2
L1.13265784223 °2-0.109242677499 °20.456039225959 °2-1.78138854189 °20.701418788726 °2--2.31813948912 °2
S0.0543283108051 Å °0.0624198297159 Å °0.0173431514983 Å °-0.00560847646872 Å °0.0395941807937 Å °-0.11296135727 Å °0.20160559493 Å °0.0973999547206 Å °7.55001853869E-5 Å °
Refinement TLS groupSelection details: all

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