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- PDB-7adt: Orf virus Apoptosis inhibitor ORFV125 -

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Basic information

Entry
Database: PDB / ID: 7adt
TitleOrf virus Apoptosis inhibitor ORFV125
Components
  • Apoptosis inhibitor
  • Apoptosis regulator BAX
KeywordsAPOPTOSIS / Orf virus / Bcl-2 / ITC
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in embryonic digit morphogenesis / Release of apoptotic factors from the mitochondria / mitochondrial permeability transition pore complex / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / fertilization / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / motor neuron apoptotic process / channel activity / mitochondrial fusion / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / BH domain binding / execution phase of apoptosis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / odontogenesis of dentin-containing tooth / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / germ cell development / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of mitochondrial membrane potential / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / blood vessel remodeling / ectopic germ cell programmed cell death / cellular response to unfolded protein / Pyroptosis / supramolecular fiber organization / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / homeostasis of number of cells within a tissue / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / response to gamma radiation / apoptotic signaling pathway / neuron migration / positive regulation of protein-containing complex assembly / response to toxic substance / cellular response to virus / cerebral cortex development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / positive regulation of neuron apoptotic process
Similarity search - Function
Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like ...Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / 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
Apoptosis inhibitor / Apoptosis regulator BAX
Similarity search - Component
Biological speciesOrf virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21003693835 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1007918 Australia
CitationJournal: Biochem.J. / Year: 2020
Title: Crystal structures of ORFV125 provide insight into orf virus-mediated inhibition of apoptosis.
Authors: Suraweera, C.D. / Hinds, M.G. / Kvansakul, M.
History
DepositionSep 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis inhibitor
U: Apoptosis regulator BAX
B: Apoptosis inhibitor
C: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,24154
Polymers38,6264
Non-polymers1,61550
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-351 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.511, 45.564, 105.965
Angle α, β, γ (deg.)90.000, 106.057, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11U-204-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABUC

#1: Protein Apoptosis inhibitor


Mass: 16160.256 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 3152.553 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07812

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Non-polymers , 4 types, 91 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.09 Å3/Da / Density % sol: 41.05 % / Description: long thick rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 5.5, 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: 0.99587 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99587 Å / Relative weight: 1
ReflectionResolution: 2.21→37.64 Å / Num. obs: 16213 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.9705645972 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.098 / Net I/σ(I): 4.8
Reflection shellResolution: 2.21→2.28 Å / Rmerge(I) obs: 0.594 / Num. unique obs: 1395 / CC1/2: 0.452

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DIALSdata reduction
Aimlessdata scaling
AutoSolphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.21003693835→34.3388921084 Å / SU ML: 0.326509203053 / Cross valid method: FREE R-VALUE / σ(F): 1.40018282824 / Phase error: 33.6646935192
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259255962966 785 4.84897152387 %
Rwork0.23314951234 15404 -
obs0.234552303192 16189 99.7904210072 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.1745541771 Å2
Refinement stepCycle: LAST / Resolution: 2.21003693835→34.3388921084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 81 41 2510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002003043461582443
X-RAY DIFFRACTIONf_angle_d0.4565570891613284
X-RAY DIFFRACTIONf_chiral_restr0.0308190750274382
X-RAY DIFFRACTIONf_plane_restr0.0024018608047428
X-RAY DIFFRACTIONf_dihedral_angle_d18.59246131931511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21003693835-2.34850.3749846831251410.3355991283442531X-RAY DIFFRACTION99.7387084733
2.3485-2.52970.3684683256551240.2931998945772552X-RAY DIFFRACTION99.8135024245
2.5297-2.78420.2920236046731160.2694569482922558X-RAY DIFFRACTION99.9252615845
2.7842-3.18690.2668103147531350.2477395615882558X-RAY DIFFRACTION99.7776954428
3.1869-4.01410.2461138384661320.2108441041892561X-RAY DIFFRACTION99.8887240356
4.0141-100.2237899658241370.2064577012232644X-RAY DIFFRACTION99.606017192
Refinement TLS params.Method: refined / Origin x: 23.1755398604 Å / Origin y: 14.7633245811 Å / Origin z: 17.6191133355 Å
111213212223313233
T0.24112611467 Å20.0611240250515 Å20.0317344124274 Å2-0.202202943876 Å20.00555848030749 Å2--0.219434847803 Å2
L3.97411286247 °22.2295353712 °21.64613706505 °2-2.61923098448 °20.807899671911 °2--2.10257204004 °2
S-0.110463461204 Å °-0.0591388058151 Å °-0.026554274037 Å °-0.135227393935 Å °0.071535787855 Å °-0.257862517918 Å °-0.0274082210934 Å °0.00515799631788 Å °0.0409371876225 Å °
Refinement TLS groupSelection details: all

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