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- PDB-7p0s: ORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 ... -

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Basic information

Entry
Database: PDB / ID: 7p0s
TitleORF virus encoded Bcl-2 homolog ORFV125 in complex with Puma BH3 peptide
Components
  • Apoptosis inhibitor
  • Bcl-2-binding component 3, isoforms 1/2
KeywordsAPOPTOSIS / ORF virus / Bcl-2
Function / homology
Function and homology information


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 ...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 / 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 / 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
Similarity search - Domain/homology
Apoptosis inhibitor / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesOrf virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50315873146 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Viruses / Year: 2021
Title: Structural Investigation of Orf Virus Bcl-2 Homolog ORFV125 Interactions with BH3-Motifs from BH3-Only Proteins Puma and Hrk.
Authors: Suraweera, C.D. / Hinds, M.G. / Kvansakul, M.
History
DepositionJun 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 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 inhibitor
U: Bcl-2-binding component 3, isoforms 1/2
B: Apoptosis inhibitor
C: Bcl-2-binding component 3, isoforms 1/2


Theoretical massNumber of molelcules
Total (without water)38,7424
Polymers38,7424
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.033, 69.564, 92.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Apoptosis inhibitor


Mass: 16160.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Conserved Bcl-2 fold with 7 alpha helices / Source: (gene. exp.) Orf virus / Gene: ORFV125, ORF125 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A0R8HV90
#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.: 2 / Source method: obtained synthetically / Details: Puma BH3 peptide 26-mer / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.03 Å3/Da / Density % sol: 39.32 % / Description: Single rod shaped crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Magnesium acetate, 25% PEG 3350

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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: Mar 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.503→43.283140319 Å / Num. obs: 11059 / % possible obs: 96.97 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.9564032227 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.91
Reflection shellResolution: 2.503→2.6 Å / Rmerge(I) obs: 1.35 / Num. unique obs: 1219 / CC1/2: 0.296 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575_000refinement
DIALSdata reduction
Aimless7.0.078data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ADT

7adt


Resolution: 2.50315873146→43.283140319 Å / SU ML: 0.43090510967 / Cross valid method: FREE R-VALUE / σ(F): 1.33792022765 / Phase error: 36.1923713478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.285825212659 554 5.02859217573 %
Rwork0.24470197337 10463 -
obs0.246848326679 11017 97.006251651 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.50315873146→43.283140319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 0 25 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002480888648862515
X-RAY DIFFRACTIONf_angle_d0.4781441000663405
X-RAY DIFFRACTIONf_chiral_restr0.0323549060059382
X-RAY DIFFRACTIONf_plane_restr0.00245625512657452
X-RAY DIFFRACTIONf_dihedral_angle_d19.80450618651549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5032-2.7550.3945645791071340.3440588927942580X-RAY DIFFRACTION97.9429808733
2.755-3.15360.3448961266551420.3104734924042602X-RAY DIFFRACTION98
3.1536-3.97270.2782308666441230.2557030978212608X-RAY DIFFRACTION96.8096419709
Refinement TLS params.Method: refined / Origin x: 21.6252816749 Å / Origin y: 3.28902382585 Å / Origin z: 5.78428629941 Å
111213212223313233
T0.384150884547 Å20.0418705975045 Å20.00917638843092 Å2-0.340823825349 Å20.0922458285023 Å2--0.423804439475 Å2
L3.1304321334 °22.45069757962 °21.25655432084 °2-4.27144885739 °21.73004796896 °2--2.68811815494 °2
S0.200765695933 Å °-0.115111940674 Å °-0.236455725659 Å °0.134727830671 Å °-0.182628943809 Å °-0.267761010704 Å °-0.154118180905 Å °-0.0700399995837 Å °0.00839016393343 Å °
Refinement TLS groupSelection details: all

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