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- PDB-4uf2: Deerpox virus DPV022 in complex with Bax BH3 -

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Basic information

Entry
Database: PDB / ID: 4uf2
TitleDeerpox virus DPV022 in complex with Bax BH3
Components
  • Antiapoptotic membrane protein
  • Apoptosis regulator BAX
KeywordsVIRAL PROTEIN / DEERPOX VIRUS / APOPTOSIS / BCL-2 / BAX BH3
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 / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / : / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c / 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 / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / Transcriptional regulation by RUNX2 / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / calcium ion transport into cytosol / channel activity / motor neuron apoptotic process / mitochondrial fusion / positive regulation of epithelial cell apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / epithelial cell apoptotic process / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / BH3 domain binding / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / germ cell development / negative regulation of mitochondrial membrane potential / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / host cell mitochondrion / negative regulation of apoptotic signaling pathway / B cell homeostasis / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / host cell membrane / 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 peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to gamma radiation / neuron migration / : / cerebral cortex development / response to toxic substance / cellular response to virus
Similarity search - Function
Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / 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. ...Poxvirus F1/C10 / Apoptosis regulator M11L like / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Apoptosis regulator BAX / Antiapoptotic membrane protein / Apoptosis regulator DPV022
Similarity search - Component
Biological speciesDeerpox virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBurton, D.R. / Kvansakul, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural Basis of Deerpox Virus-Mediated Inhibition of Apoptosis.
Authors: Burton, D.R. / Caria, S. / Marshall, B. / Barry, M. / Kvansakul, M.
History
DepositionDec 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Jun 30, 2021Group: Database references / Other ...Database references / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / struct_ref / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _entity_src_gen.plasmid_name / _pdbx_database_status.status_code_sf / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Antiapoptotic membrane protein
B: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)22,7862
Polymers22,7862
Non-polymers00
Water0
1
A: Antiapoptotic membrane protein
B: Apoptosis regulator BAX

A: Antiapoptotic membrane protein
B: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)45,5724
Polymers45,5724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area8610 Å2
ΔGint-62.7 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.481, 92.481, 45.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Antiapoptotic membrane protein / DPV022


Mass: 19633.271 Da / Num. of mol.: 1 / Fragment: BCL-2, UNP RESIDUES 1-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deerpox virus (strain W-1170-84) / Strain: W-1170-84 / Gene: DpV84gp022 / Plasmid: pDUET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q08FF8, UniProt: Q08FX8*PLUS
#2: Protein/peptide Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 3152.553 Da / Num. of mol.: 1 / Fragment: BH3, UNP RESIDUES 50-77 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07812
Sequence detailsSTRUCTURE FROM CONSTRUCT RESIDUES 1-155

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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: 1.99 Å3/Da / Density % sol: 81.6 %
Description: RESIDUES FROM 1 AND 2 AND FROM 138 TO 155 ARE DISORDERED IN DPV022 AND IN BAX BH3 THE RESIDUES FROM 51 TO 56 AND 76 TO 78 ARE MISSING.
Crystal growpH: 6
Details: 20% PEG 6000, 0.2M MES PH 6.0, 0,2M AMMONIUM SULPHATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.93537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2013 / Details: SILICON MIRRORS (ADAPTIVE AND U-BENT)
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93537 Å / Relative weight: 1
ReflectionResolution: 3→92.48 Å / Num. obs: 4297 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 76.19 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2
Reflection shellResolution: 3→3.18 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DPV022_BIM

Resolution: 3→46.24 Å / SU ML: 0.03 / σ(F): 1.35 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2743 194 4.6 %
Rwork0.2142 --
obs0.2167 4265 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.6 Å2
Refinement stepCycle: LAST / Resolution: 3→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 0 0 1260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021272
X-RAY DIFFRACTIONf_angle_d0.4031704
X-RAY DIFFRACTIONf_dihedral_angle_d9.348497
X-RAY DIFFRACTIONf_chiral_restr0.017199
X-RAY DIFFRACTIONf_plane_restr0.001213
LS refinement shellResolution: 3.0005→46.246 Å
RfactorNum. reflection% reflection
Rfree0.2743 194 -
Rwork0.2142 4071 -
obs--100 %

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