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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 / BAX complex / protein insertion into mitochondrial membrane / 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 / BAX complex / protein insertion into mitochondrial membrane / 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 / glycosphingolipid metabolic process / B cell homeostatic proliferation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / mitochondrial fragmentation involved in apoptotic process / apoptotic process involved in blood vessel morphogenesis / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / symbiont-mediated suppression of host apoptosis / post-embryonic camera-type eye morphogenesis / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / B cell apoptotic process / regulation of nitrogen utilization / endoplasmic reticulum calcium ion homeostasis / positive regulation of epithelial cell apoptotic process / fertilization / calcium ion transport into cytosol / motor neuron apoptotic process / mitochondrial fusion / epithelial cell apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / execution phase of apoptosis / apoptotic mitochondrial changes / hypothalamus development / thymocyte apoptotic process / positive regulation of calcium ion transport into cytosol / pore complex / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / odontogenesis of dentin-containing tooth / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / BH3 domain binding / B cell homeostasis / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of mitochondrial membrane potential / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / host cell membrane / blood vessel remodeling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / host cell mitochondrion / Pyroptosis / cellular response to unfolded protein / ectopic germ cell programmed cell death / negative regulation of fibroblast proliferation / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / supramolecular fiber organization / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway / homeostasis of number of cells within a tissue / release of sequestered calcium ion into cytosol / response to salt stress / negative regulation of protein binding / Hsp70 protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of release of sequestered calcium ion into cytosol / regulation of mitochondrial membrane potential / kidney development / response to gamma radiation / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / cerebral cortex development / cellular response to virus / response to toxic substance / intrinsic apoptotic signaling pathway in response to DNA damage / neuron migration / cellular response to UV / positive regulation of neuron apoptotic process / nuclear envelope
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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / 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 / 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 D Biol Crystallogr / Year: 2015
Title: Structural basis of Deerpox virus-mediated inhibition of apoptosis.
Authors: Denis R Burton / Sofia Caria / Bevan Marshall / Michele Barry / Marc Kvansakul /
Abstract: Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use ...Apoptosis is a key innate defence mechanism to eliminate virally infected cells. To counteract premature host-cell apoptosis, poxviruses have evolved numerous molecular strategies, including the use of Bcl-2 proteins, to ensure their own survival. Here, it is reported that the Deerpox virus inhibitor of apoptosis, DPV022, only engages a highly restricted set of death-inducing Bcl-2 proteins, including Bim, Bax and Bak, with modest affinities. Structural analysis reveals that DPV022 adopts a Bcl-2 fold with a dimeric domain-swapped topology and binds pro-death Bcl-2 proteins via two conserved ligand-binding grooves found on opposite sides of the dimer. Structures of DPV022 bound to Bim, Bak and Bax BH3 domains reveal that a partial obstruction of the binding groove is likely to be responsible for the modest affinities of DPV022 for BH3 domains. These findings reveal that domain-swapped dimeric Bcl-2 folds are not unusual and may be found more widely in viruses. Furthermore, the modest affinities of DPV022 for pro-death Bcl-2 proteins suggest that two distinct classes of anti-apoptotic viral Bcl-2 proteins exist: those that are monomeric and tightly bind a range of death-inducing Bcl-2 proteins, and others such as DPV022 that are dimeric and only bind a very limited number of death-inducing Bcl-2 proteins with modest affinities.
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
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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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