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- PDB-5wos: Structural and functional insights into Canarypox Virus CNP058 re... -

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Basic information

Entry
Database: PDB / ID: 5wos
TitleStructural and functional insights into Canarypox Virus CNP058 regulation of apoptosis
Components
  • Bcl-2-like protein 11
  • CNPV058 bcl-2 like protein
KeywordsVIRAL PROTEIN / Avipoxvirus / apoptosis / Bcl-2 / Bim
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 / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process ...: / 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 / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / Bcl-2 family protein complex / 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 / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / host cell membrane / 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 / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / spermatogenesis / microtubule binding / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / membrane => GO:0016020 / positive regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / cytosol
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Apoptosis regulator, Mcl-1 / Bcl-2 family / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl-2-like protein 11 / Apoptosis regulator Bcl-2 homolog
Similarity search - Component
Biological speciesCanarypox virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsAnasir, M.I. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Viruses / Year: 2017
Title: Structural and Functional Insight into Canarypox Virus CNP058 Mediated Regulation of Apoptosis.
Authors: Anasir, M.I. / Baxter, A.A. / Poon, I.K.H. / Hulett, M.D. / Kvansakul, M.
History
DepositionAug 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CNPV058 bcl-2 like protein
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)20,5572
Polymers20,5572
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-11 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.786, 34.670, 71.726
Angle α, β, γ (deg.)90.00, 114.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CNPV058 bcl-2 like protein


Mass: 17282.715 Da / Num. of mol.: 1 / Fragment: UNP residues 1-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canarypox virus / Gene: CNPV058 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6VZT9
#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 domain (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.: 10 / 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: 2.07 Å3/Da / Density % sol: 40.6 % / Description: Needle-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.2 M calcium chloride dihydrate, 0.1 M MES pH 6.0, 20% w/v PEG6000
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.45→33.46 Å / Num. obs: 6021 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 40.9 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.084 / Net I/σ(I): 6.1
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 703 / CC1/2: 0.455 / Rpim(I) all: 0.71 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TZP

5tzp


Resolution: 2.45→33.459 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.62
RfactorNum. reflection% reflection
Rfree0.2452 274 4.55 %
Rwork0.2124 --
obs0.214 6018 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→33.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 0 10 1339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031367
X-RAY DIFFRACTIONf_angle_d0.5431849
X-RAY DIFFRACTIONf_dihedral_angle_d13.715820
X-RAY DIFFRACTIONf_chiral_restr0.039203
X-RAY DIFFRACTIONf_plane_restr0.002235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4502-3.08670.29281500.25612856X-RAY DIFFRACTION97
3.0867-33.46170.22671240.1972888X-RAY DIFFRACTION95

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