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- PDB-5ua5: Crystal structure of A179L:Bid BH3 complex -

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Basic information

Entry
Database: PDB / ID: 5ua5
TitleCrystal structure of A179L:Bid BH3 complex
Components
  • 5-HL
  • Uncharacterized protein
KeywordsAPOPTOSIS / Bcl-2
Function / homology
Function and homology information


Release of apoptotic factors from the mitochondria / Activation, translocation and oligomerization of BAX / Pyroptosis / : / suppression by virus of host autophagy / mitochondrial fusion / channel activity / host cell endoplasmic reticulum / host cell mitochondrion / extrinsic apoptotic signaling pathway in absence of ligand ...Release of apoptotic factors from the mitochondria / Activation, translocation and oligomerization of BAX / Pyroptosis / : / suppression by virus of host autophagy / mitochondrial fusion / channel activity / host cell endoplasmic reticulum / host cell mitochondrion / extrinsic apoptotic signaling pathway in absence of ligand / : / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / membrane => GO:0016020 / oxidoreductase activity / positive regulation of apoptotic process / protein heterodimerization activity / nucleotide binding / protein homodimerization activity
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / 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. ...Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Apoptosis regulator Bcl-2 homolog / Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase / Apoptosis regulator Bcl-2 homolog
Similarity search - Component
Biological speciesAfrican swine fever virus
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBanjara, S. / Caria, S. / Kvansakul, M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1007918 Australia
Australian Research Council (ARC)FT130101349 Australia
CitationJournal: J. Virol. / Year: 2017
Title: Structural Insight into African Swine Fever Virus A179L-Mediated Inhibition of Apoptosis.
Authors: Banjara, S. / Caria, S. / Dixon, L.K. / Hinds, M.G. / Kvansakul, M.
History
DepositionDec 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Mar 15, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: 5-HL
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)20,8622
Polymers20,8622
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-14 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.126, 94.126, 40.834
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsDimer as determined by size exclusion chromatography

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Components

#1: Protein 5-HL / A179L / Bcl-2-like protein / PA179L


Mass: 17709.230 Da / Num. of mol.: 1 / Fragment: residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: 5-HL, A179L / Production host: Escherichia coli (E. coli) / References: UniProt: D0Q0E8, UniProt: P42485*PLUS
#2: Protein/peptide Uncharacterized protein


Mass: 3152.553 Da / Num. of mol.: 1 / Fragment: residues 50-77 / Source method: obtained synthetically / Source: (synth.) Sus scrofa (pig) / References: UniProt: F1RIQ4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.75 Å3/Da / Density % sol: 55.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1.6 M Ammonium Sulphate, 0.1M Sodium acetate pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9573 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9573 Å / Relative weight: 1
ReflectionResolution: 2.5→36.51 Å / Num. obs: 7316 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.1
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.122 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
xia2data reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→36.51 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.59
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 368 5.03 %random selection
Rwork0.2464 ---
obs0.2474 7316 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 0 2 1333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031357
X-RAY DIFFRACTIONf_angle_d0.5441829
X-RAY DIFFRACTIONf_dihedral_angle_d12.68805
X-RAY DIFFRACTIONf_chiral_restr0.039206
X-RAY DIFFRACTIONf_plane_restr0.002227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.86190.3191220.29312287X-RAY DIFFRACTION100
2.8619-3.60530.30851330.28812283X-RAY DIFFRACTION100
3.6053-36.510.2431130.22572378X-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)
16.55834.8435-1.18444.75820.55682.93290.30880.6713-0.1749-0.20.4084-0.53930.49020.0886-0.31460.6640.0679-0.0180.543-0.10770.930342.8743-10.2729-9.113
20.4301-1.3776-1.57395.13454.96099.1932-1.151-0.8082-1.30212.01391.6543-0.32830.50653.09240.24761.10380.0995-0.74170.66210.06662.285250.1862-16.60341.1002
37.18321.36282.1165.28460.91336.80880.6359-1.3694-0.28641.5686-0.8098-1.6390.2935-0.45980.16280.8873-0.1711-0.24940.64820.02470.785636.9031-12.54816.4027
47.16413.387-0.89549.63575.13457.59590.5588-0.2404-0.46580.4424-0.8516-0.18820.6817-1.04790.05080.4948-0.1265-0.14420.6835-0.05310.569831.5097-16.1586-4.0955
54.10682.01780.54684.4974-1.03677.77450.2748-0.40851.11530.3976-0.2891-0.2881-1.44810.04540.35330.8520.0655-0.02630.59750.01340.941138.43380.7876-1.7516
68.31745.96424.46744.95361.53246.9286-0.1358-0.77491.74481.3972-0.6162.5487-0.0948-2.51970.54940.9271-0.05980.12291.4123-0.25480.954125.5671-6.44866.1287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 146 )
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 48 )

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