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- PDB-4uf3: Deerpox virus DPV022 in complex with Bim BH3 -

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Basic information

Entry
Database: PDB / ID: 4uf3
TitleDeerpox virus DPV022 in complex with Bim BH3
Components
  • Antiapoptotic membrane protein
  • Bcl-2-like protein 11
KeywordsVIRAL PROTEIN / DPV022 / DEERPOX VIRUS / APOPTOSIS / BCL-2 / BIM BH3
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / symbiont-mediated perturbation of host apoptosis / symbiont-mediated suppression of host apoptosis / ear development / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / tube formation / positive regulation of T cell apoptotic process / regulation of organ growth / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / positive regulation of IRE1-mediated unfolded protein response / B cell homeostasis / host cell membrane / host cell mitochondrion / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / cell-matrix adhesion / post-embryonic development / thymus development / kidney development / positive regulation of protein-containing complex assembly / : / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by BRAF and RAF1 fusions / spermatogenesis / microtubule binding / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / protein kinase binding / apoptotic process / mitochondrion / membrane / cytosol
Similarity search - Function
Poxvirus F1/C10 / Apoptosis regulator M11L like / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x ...Poxvirus F1/C10 / Apoptosis regulator M11L like / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 11 / Antiapoptotic membrane protein / Apoptosis regulator DPV022
Similarity search - Component
Biological speciesDeerpox virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.7 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_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 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)22,9082
Polymers22,9082
Non-polymers00
Water1267
1
A: Antiapoptotic membrane protein
B: Bcl-2-like protein 11

A: Antiapoptotic membrane protein
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)45,8164
Polymers45,8164
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area9110 Å2
ΔGint-69.7 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.389, 94.389, 45.541
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 Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3274.691 Da / Num. of mol.: 1 / Fragment: BH3, UNP RESIDUES 141-166 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.7 % / Description: IODINE DERIVATIVE
Crystal growpH: 5.5
Details: 17% PEG 8000, 0.2M MES PH 5.5, 0.2M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95370, 1.5498
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 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 wavelength
IDWavelength (Å)Relative weight
10.95371
21.54981
ReflectionResolution: 2.7→94.39 Å / Num. obs: 6039 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Biso Wilson estimate: 65.25 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.5
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.7→19.99 Å / SU ML: 0.39 / σ(F): 2 / Phase error: 29.54 / Stereochemistry target values: ML
Details: RESIDUES FROM 1 AND 2 AND FROM 138 TO 155 ARE MISSING IN DPV022. IN BIM,THE RESIDUES 50 AND 55 AS WELL AS 74-76
RfactorNum. reflection% reflection
Rfree0.2206 273 4.6 %
Rwork0.2051 --
obs0.2059 5980 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 0 7 1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031288
X-RAY DIFFRACTIONf_angle_d0.5671731
X-RAY DIFFRACTIONf_dihedral_angle_d14.347493
X-RAY DIFFRACTIONf_chiral_restr0.023197
X-RAY DIFFRACTIONf_plane_restr0.002217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7004-3.39950.34991280.25322780X-RAY DIFFRACTION100
3.3995-19.99040.19381450.19052927X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.19420.6479-0.18525.26443.21832.9959-0.38550.18170.1259-0.53820.20950.42090.05370.10910.35870.66880.0442-0.11420.8037-0.05030.39874.49913.241819.8123
26.25062.79031.55166.82142.03277.45430.1397-0.22780.8820.4430.1958-0.153-0.60460.9269-0.37670.6635-0.13180.05050.7538-0.08840.500389.053527.83874.7412
36.36321.8678-1.62775.1342-4.47693.8040.0966-1.08781.09070.78830.3098-0.0666-0.39680.115-0.4620.6841-0.07870.03510.5481-0.2090.581984.532627.33319.3474
43.4885-2.68961.65424.16730.7122.92420.01791.25711.13870.0067-0.6907-0.1777-0.0553-0.63330.61871.0567-0.04260.14010.72860.02550.649984.430225.0992-6.5493
52.7041-0.17051.22533.3683-3.69064.4318-0.59511.58051.8084-0.43630.6493-0.2362-1.64672.48720.36931.026-0.1709-0.15791.4591-0.06881.238197.17732.8979-0.5536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 30 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 31 THROUGH 87 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 88 THROUGH 117 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 118 THROUGH 138 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 56 THROUGH 73 )

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