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- PDB-2vvx: Structure of Vaccinia virus protein A52 -

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Basic information

Entry
Database: PDB / ID: 2vvx
TitleStructure of Vaccinia virus protein A52
ComponentsPROTEIN A52
KeywordsVIRAL PROTEIN / IRAK2 / TRAF6 / BCL-2 FAMILY / VACCINIA VIRUS / IMMUNOMODULATOR / NF-KB ACTIVATION / HOST-VIRUS INTERACTION
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / protein sequestering activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / symbiont-mediated suppression of host innate immune response
Similarity search - Function
dsDNA poxvirus / Poxvirus Bcl-2-like / Poxvirus domain superfamily / Poxvirus Bcl-2-like proteins / Apoptosis Regulator Bcl-x / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.746 Å
AuthorsGraham, S.C. / Bahar, M.W. / Cooray, S. / Chen, R.A.-J. / Whalen, D.M. / Abrescia, N.G.A. / Alderton, D. / Owens, R.J. / Stuart, D.I. / Smith, G.L. / Grimes, J.M.
CitationJournal: Plos Pathog. / Year: 2008
Title: Vaccinia Virus Proteins A52 and B14 Share a Bcl-2-Like Fold But Have Evolved to Inhibit NF-kappaB Rather Than Apoptosis
Authors: Graham, S.C. / Bahar, M.W. / Cooray, S. / Chen, R.A.-J. / Whalen, D.M. / Abrescia, N.G.A. / Alderton, D. / Owens, R.J. / Stuart, D.I. / Smith, G.L. / Grimes, J.M.
History
DepositionJun 12, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN A52
B: PROTEIN A52


Theoretical massNumber of molelcules
Total (without water)39,1792
Polymers39,1792
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-16.7 kcal/mol
Surface area18480 Å2
MethodPQS
2
A: PROTEIN A52


Theoretical massNumber of molelcules
Total (without water)19,5901
Polymers19,5901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: PROTEIN A52


Theoretical massNumber of molelcules
Total (without water)19,5901
Polymers19,5901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.075, 126.075, 124.058
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 42:54 OR RESSEQ 56:75 OR RESSEQ 79:98 OR RESSEQ 106:116 OR RESSEQ 128:183 )
211CHAIN B AND (RESSEQ 42:54 OR RESSEQ 56:75 OR RESSEQ 79:98 OR RESSEQ 106:116 OR RESSEQ 128:183 )

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Components

#1: Protein PROTEIN A52 / A52


Mass: 19589.703 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3) PLYSS / References: UniProt: Q01220
Sequence detailsRESIDUES 1-36 ARE REMOVED, AN N-TERMINAL START CODON IS ADDED AND A C-TERMINAL LYS-HIS6 ...RESIDUES 1-36 ARE REMOVED, AN N-TERMINAL START CODON IS ADDED AND A C-TERMINAL LYS-HIS6 PURIFICATION TAG IS ADDED.

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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: 4.88 Å3/Da / Density % sol: 74.83 %
Description: MODEL WAS STRIPPED OF SOLVENT AND ALTERNATE CONFORMATIONS PRIOR TO MOLECULAR REPLACEMENT.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: HANGING DROPS CONTAINING 1 UL PROTEIN (5.4 MG/ML IN 20 MM TRIS, 200 MM NACL, PH 7.5) AND 1 UL RESERVOIR SOLUTION (0.2 M SODIUM PHOSPHATE, 22% (W/V) PEG 3350) WERE EQUILIBRATED AGAINST 500 UL ...Details: HANGING DROPS CONTAINING 1 UL PROTEIN (5.4 MG/ML IN 20 MM TRIS, 200 MM NACL, PH 7.5) AND 1 UL RESERVOIR SOLUTION (0.2 M SODIUM PHOSPHATE, 22% (W/V) PEG 3350) WERE EQUILIBRATED AGAINST 500 UL RESERVOIRS AT 21 C. CRYSTALS WERE CRYOPROTECTED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 20% (V/V) GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 11, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 19184 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 56.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVW, CHAIN A

2vvw


Resolution: 2.746→40.981 Å / SU ML: 0.23 / Phase error: 21.3 / Stereochemistry target values: ML / Details: B VALUES INCLUDE TLS CONTRIBUTIONS.
RfactorNum. reflection% reflection
Rfree0.1918 988 5.2 %
Rwork0.1814 --
obs0.182 19183 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.898 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso mean: 81.77 Å2
Baniso -1Baniso -2Baniso -3
1--9.6646 Å2-0 Å2-0 Å2
2---9.6646 Å2-0 Å2
3----36.0821 Å2
Refinement stepCycle: LAST / Resolution: 2.746→40.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 0 0 2516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052574
X-RAY DIFFRACTIONf_angle_d0.8163465
X-RAY DIFFRACTIONf_dihedral_angle_d16.895950
X-RAY DIFFRACTIONf_chiral_restr0.056381
X-RAY DIFFRACTIONf_plane_restr0.003437
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A995X-RAY DIFFRACTIONPOSITIONAL
12B995X-RAY DIFFRACTIONPOSITIONAL0.028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7463-2.89110.30211350.28682611X-RAY DIFFRACTION50
2.8911-3.07220.25171390.24362578X-RAY DIFFRACTION50
3.0722-3.30930.23141350.2162604X-RAY DIFFRACTION50
3.3093-3.64210.2061520.18182610X-RAY DIFFRACTION50
3.6421-4.16870.16071520.15432582X-RAY DIFFRACTION50
4.1687-5.25040.17361290.14412622X-RAY DIFFRACTION50
5.2504-40.98540.16741460.16862588X-RAY DIFFRACTION50
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)
12.383-0.5922-1.78944.8348-0.02163.7080.0955-0.21330.21370.02690.01220.0844-0.53920.2159-0.00020.7634-0.0830.01990.8043-0.08620.7526.7173-11.37016.0799
23.03421.8176-0.60273.6440.45314.82630.05360.1660.1834-0.04360.05720.0773-0.3242-0.0458-0.00040.63180.01560.03930.7248-0.02180.71732.9718-25.3207-19.0064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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