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- PDB-6xy4: Structural insight into sheep-pox virus mediated inhibition of ap... -

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Basic information

Entry
Database: PDB / ID: 6xy4
TitleStructural insight into sheep-pox virus mediated inhibition of apoptosis
Components
  • Activator of apoptosis harakiri
  • anti-apoptotic membrane protein
KeywordsAPOPTOSIS / Pox virus / Bcl-2
Function / homology
Function and homology information


cellular response to potassium ion starvation / symbiont-mediated suppression of host apoptosis / positive regulation of release of cytochrome c from mitochondria / positive regulation of protein-containing complex assembly / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / apoptotic process / mitochondrion / membrane
Similarity search - Function
Activator of apoptosis harakiri / Activator of apoptosis harakiri / 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. / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Anti-apoptotic membrane protein / Activator of apoptosis harakiri
Similarity search - Component
Biological speciesSheeppox virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04623155256 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1007918 Australia
CitationJournal: Febs Lett. / Year: 2020
Title: Crystal structures of the sheeppox virus encoded inhibitor of apoptosis SPPV14 bound to the proapoptotic BH3 peptides Hrk and Bax.
Authors: Suraweera, C.D. / Burton, D.R. / Hinds, M.G. / Kvansakul, M.
History
DepositionJan 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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: anti-apoptotic membrane protein
B: Activator of apoptosis harakiri


Theoretical massNumber of molelcules
Total (without water)20,4492
Polymers20,4492
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-19 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.280, 70.660, 115.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein anti-apoptotic membrane protein


Mass: 17476.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sheeppox virus (strain Turkey/TU-V02127)
Gene: SPPV_14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A3F2YKH3
#2: Protein/peptide Activator of apoptosis harakiri / BH3-interacting domain-containing protein 3 / Neuronal death protein DP5


Mass: 2973.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00198
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/vPEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.046→31.07 Å / Num. obs: 11236 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 39.8950367928 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Net I/σ(I): 8.7
Reflection shellResolution: 2.05→8.92 Å / Num. unique obs: 782 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Coot0.8.0-3model building
XDS20180427data reduction
Aimless7data scaling
PHASER1.11.1_2575-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJY

2bjy


Resolution: 2.04623155256→31.0657632133 Å / SU ML: 0.237702211781 / Cross valid method: FREE R-VALUE / σ(F): 1.38553218358 / Phase error: 26.211733487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233810671103 568 5.05517977928 %
Rwork0.219930444744 10668 -
obs0.220603579671 11236 97.6958525346 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.7478958779 Å2
Refinement stepCycle: LAST / Resolution: 2.04623155256→31.0657632133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 28 1257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002384084319851245
X-RAY DIFFRACTIONf_angle_d0.3977592978351673
X-RAY DIFFRACTIONf_chiral_restr0.0332360412731200
X-RAY DIFFRACTIONf_plane_restr0.00140794756101211
X-RAY DIFFRACTIONf_dihedral_angle_d16.9358529231787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04623155265-2.25210.2731022405161590.2573813541462523X-RAY DIFFRACTION95.0726692662
2.2521-2.57780.2591322272281220.2397820022942689X-RAY DIFFRACTION99.1534391534
2.5778-3.24730.2500136083211530.2366133398562677X-RAY DIFFRACTION98.812849162
3.2473-31.06576321330.215540740211340.2040902909842779X-RAY DIFFRACTION97.7188862798
Refinement TLS params.Method: refined / Origin x: -18.4590111381 Å / Origin y: -12.5771924003 Å / Origin z: -11.1701382726 Å
111213212223313233
T0.356873017009 Å20.0201448405319 Å20.0175253669372 Å2-0.344584880018 Å20.0014601194472 Å2--0.341014260961 Å2
L4.45340416183 °21.53913903174 °20.823391120508 °2-2.58557950292 °2-0.853219529095 °2--4.65257779361 °2
S-0.0564594308793 Å °0.365321035451 Å °0.0211249438113 Å °-0.278965474825 Å °0.153017389009 Å °0.0900464395735 Å °0.0812525005108 Å °-0.05125301716 Å °0.00420459506247 Å °
Refinement TLS groupSelection details: all

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