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- PDB-7qtx: Kaposi sarcoma associated herpes virus (KSHV) encoded apoptosis i... -

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Basic information

Entry
Database: PDB / ID: 7qtx
TitleKaposi sarcoma associated herpes virus (KSHV) encoded apoptosis inhibitor, KsBcl-2 in complex with Puma BH3
Components
  • Bcl-2
  • Bcl-2-binding component 3, isoforms 1/2
KeywordsAPOPTOSIS / viral Bcl-2 protein / gamma herpes virus / Kaposi sarcoma virus
Function / homology
Function and homology information


positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / symbiont-mediated suppression of host apoptosis / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process / Activation of PUMA and translocation to mitochondria / execution phase of apoptosis ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / symbiont-mediated suppression of host apoptosis / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process / Activation of PUMA and translocation to mitochondria / execution phase of apoptosis / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway / intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / cellular response to ionizing radiation / determination of adult lifespan / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / positive regulation of neuron apoptotic process / regulation of apoptotic process / cellular response to hypoxia / mitochondrial outer membrane / DNA damage response / mitochondrion / membrane / cytosol
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / Blc2-like / Apoptosis Regulator Bcl-x / 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 ...Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / Blc2-like / Apoptosis Regulator Bcl-x / 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
BROMIDE ION / Bcl-2 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesHuman gammaherpesvirus 8
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11598861103 Å
AuthorsSuraweera, C.D. / Hinds, M.G. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: Viruses / Year: 2022
Title: Structural Insight into KsBcl-2 Mediated Apoptosis Inhibition by Kaposi Sarcoma Associated Herpes Virus.
Authors: Suraweera, C.D. / Hinds, M.G. / Kvansakul, M.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2
B: Bcl-2-binding component 3, isoforms 1/2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2748
Polymers19,8482
Non-polymers4266
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-13 kcal/mol
Surface area8690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.229, 48.529, 57.386
Angle α, β, γ (deg.)90.000, 97.065, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-364-

HOH

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Components

#1: Protein Bcl-2 / ORF 16 / ORF16 / ORF16 protein


Mass: 16637.180 Da / Num. of mol.: 1 / Mutation: V117A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 8 / Gene: ORF16, HHV8GK18_gp19 / Production host: Escherichia coli (E. coli) / Variant (production host): Codon plus (RIL) / References: UniProt: Q76RI8
#2: Protein/peptide Bcl-2-binding component 3, isoforms 1/2 / JFY-1 / p53 up-regulated modulator of apoptosis


Mass: 3210.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.41 % / Description: single long rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium bromide, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.937 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 2.11→32.4632234192 Å / Num. obs: 9148 / % possible obs: 98.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 32.4290222293 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.2
Reflection shellResolution: 2.11→2.17 Å / Num. unique obs: 409 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DIALSdata reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: KsBcl-2_Bid

Resolution: 2.11598861103→32.4632234192 Å / SU ML: 0.312535587486 / Cross valid method: FREE R-VALUE / σ(F): 1.35034511599 / Phase error: 30.1945594635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.257493681771 425 4.65090829503 %
Rwork0.217695316985 8713 -
obs0.219570195451 9138 97.9841303882 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.4042455698 Å2
Refinement stepCycle: LAST / Resolution: 2.11598861103→32.4632234192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1310 0 15 95 1420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001780086085391349
X-RAY DIFFRACTIONf_angle_d0.4349861884741819
X-RAY DIFFRACTIONf_chiral_restr0.0332056062118192
X-RAY DIFFRACTIONf_plane_restr0.00313875011317236
X-RAY DIFFRACTIONf_dihedral_angle_d14.544474644795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.116-2.42210.3291778336251280.2851127465112890X-RAY DIFFRACTION98.370273794
2.4221-3.05120.2771647345551480.2463064873272880X-RAY DIFFRACTION98.1841763943
Refinement TLS params.Method: refined / Origin x: 6.14585868528 Å / Origin y: 33.5559067189 Å / Origin z: 13.458405656 Å
111213212223313233
T0.231351741179 Å2-0.00841820419553 Å2-0.0339621853634 Å2-0.230956636113 Å20.0170571467953 Å2--0.244014954663 Å2
L1.641420665 °20.182971807205 °2-1.33289707334 °2-0.0284435627164 °2-0.0587074463572 °2--4.09663548438 °2
S-0.011070792682 Å °-0.361899604009 Å °-0.0322536910352 Å °0.0865258042161 Å °-0.0427268117346 Å °-0.0568500118068 Å °-0.00171322795031 Å °0.580117284834 Å °0.0507385278557 Å °
Refinement TLS groupSelection details: all

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