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- PDB-9fiz: Structure of the F13 protein (mutant A295E) of Vaccinia virus -

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Basic information

Entry
Database: PDB / ID: 9fiz
TitleStructure of the F13 protein (mutant A295E) of Vaccinia virus
ComponentsEnvelope phospholipase OPG057
KeywordsVIRAL PROTEIN / poxvirus / phospholipase D / vaccinia virus
Function / homology
Function and homology information


viral membrane / viral budding from Golgi membrane / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / phospholipase D / phospholipase D activity / viral budding via host ESCRT complex / host cell Golgi apparatus / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane
Similarity search - Function
PLD-like domain / PLD-like domain / : / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
CITRIC ACID / Envelope phospholipase OPG057
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVernuccio, R. / Guardado-Calvo, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0003 France
CitationJournal: Nat Microbiol / Year: 2025
Title: Structural insights into tecovirimat antiviral activity and poxvirus resistance.
Authors: Vernuccio, R. / Martinez Leon, A. / Poojari, C.S. / Buchrieser, J. / Selverian, C.N. / Jaleta, Y. / Meola, A. / Guivel-Benhassine, F. / Porrot, F. / Haouz, A. / Chevreuil, M. / Raynal, B. / ...Authors: Vernuccio, R. / Martinez Leon, A. / Poojari, C.S. / Buchrieser, J. / Selverian, C.N. / Jaleta, Y. / Meola, A. / Guivel-Benhassine, F. / Porrot, F. / Haouz, A. / Chevreuil, M. / Raynal, B. / Mercer, J. / Simon-Loriere, E. / Chandran, K. / Schwartz, O. / Hub, J.S. / Guardado-Calvo, P.
History
DepositionMay 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope phospholipase OPG057
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,71415
Polymers42,3251
Non-polymers1,38914
Water1,06359
1
A: Envelope phospholipase OPG057
hetero molecules

A: Envelope phospholipase OPG057
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,42830
Polymers84,6502
Non-polymers2,77928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
Buried area2380 Å2
ΔGint-6 kcal/mol
Surface area28890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)280.979, 280.979, 280.979
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Space group name HallF423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x,y+1/2,z+1/2
#26: x,-z+1/2,y+1/2
#27: x,z+1/2,-y+1/2
#28: z,y+1/2,-x+1/2
#29: -z,y+1/2,x+1/2
#30: -y,x+1/2,z+1/2
#31: y,-x+1/2,z+1/2
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y,x+1/2,-z+1/2
#44: -y,-x+1/2,-z+1/2
#45: z,-y+1/2,x+1/2
#46: -z,-y+1/2,-x+1/2
#47: -x,z+1/2,y+1/2
#48: -x,-z+1/2,-y+1/2
#49: x+1/2,y,z+1/2
#50: x+1/2,-z,y+1/2
#51: x+1/2,z,-y+1/2
#52: z+1/2,y,-x+1/2
#53: -z+1/2,y,x+1/2
#54: -y+1/2,x,z+1/2
#55: y+1/2,-x,z+1/2
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+1/2,x,-z+1/2
#68: -y+1/2,-x,-z+1/2
#69: z+1/2,-y,x+1/2
#70: -z+1/2,-y,-x+1/2
#71: -x+1/2,z,y+1/2
#72: -x+1/2,-z,-y+1/2
#73: x+1/2,y+1/2,z
#74: x+1/2,-z+1/2,y
#75: x+1/2,z+1/2,-y
#76: z+1/2,y+1/2,-x
#77: -z+1/2,y+1/2,x
#78: -y+1/2,x+1/2,z
#79: y+1/2,-x+1/2,z
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+1/2,x+1/2,-z
#92: -y+1/2,-x+1/2,-z
#93: z+1/2,-y+1/2,x
#94: -z+1/2,-y+1/2,-x
#95: -x+1/2,z+1/2,y
#96: -x+1/2,-z+1/2,-y
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

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Components

#1: Protein Envelope phospholipase OPG057 / 37 kDa protein / Envelope phospholipase F13 / Palmitoylated EV membrane protein / p37K


Mass: 42324.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG057, VACWR052, F13L / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P04021, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases, phospholipase D
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1 M Na3 citrate, 0.1 M Imidazole pH 8 (cryoprotected with 33% glycerol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2.6→49.67 Å / Num. obs: 29768 / % possible obs: 96.14 % / Redundancy: 80.7 % / Biso Wilson estimate: 73.64 Å2 / CC1/2: 1 / Net I/σ(I): 21.2
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 2921 / CC1/2: 0.644

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.67 Å / SU ML: 0.5764 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.8533
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 1396 4.88 %
Rwork0.2159 27236 -
obs0.218 28632 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 91 59 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023024
X-RAY DIFFRACTIONf_angle_d0.48394079
X-RAY DIFFRACTIONf_chiral_restr0.0424459
X-RAY DIFFRACTIONf_plane_restr0.0034514
X-RAY DIFFRACTIONf_dihedral_angle_d10.43291099
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.73991020.83181723X-RAY DIFFRACTION62.41
2.69-2.80.64731180.60642756X-RAY DIFFRACTION99.1
2.8-2.930.43121480.38792753X-RAY DIFFRACTION99.93
2.93-3.080.36071480.28752791X-RAY DIFFRACTION100
3.08-3.280.32281410.26372775X-RAY DIFFRACTION99.9
3.28-3.530.33651390.26982821X-RAY DIFFRACTION99.97
3.53-3.880.22841500.19362810X-RAY DIFFRACTION99.97
3.89-4.450.23891390.17232851X-RAY DIFFRACTION100
4.45-5.60.2071430.15982882X-RAY DIFFRACTION99.97
5.6-49.670.19651680.17993074X-RAY DIFFRACTION99.85
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)
11.81946768976-0.3387578915090.9692729199772.48435438536-0.2640894941663.320341551930.1052373356020.153160034654-0.237268133491-0.177235231445-0.064739827592-0.1896305945810.2526046061350.131545249885-0.02878940299140.4778760961750.03979781052020.09246698523720.635234010182-0.03250671102590.599780713055-22.50303424844.923297260743.894816888
24.166216134410.779702297995-0.737625601565.373896413241.264339598022.28600628278-0.0792280421675-0.225185502029-0.05364610192980.449908614243-0.0255992271306-0.9999782155490.06603375653410.6739764350350.09432074580430.4543051120910.0179995704219-0.02496452181720.7689739605750.09887434866940.612271454821-12.40172691754.104408837151.966185879
32.80999794759-0.191450304771.119621450464.035261838230.7987782999474.597504848910.0122529851835-0.0807666771333-0.03113516895230.165272155932-0.2242312165230.329626245268-0.344285956029-0.4874149589070.1763789078230.4714446943930.01424180936610.02242540931710.522037910828-0.07705739364720.515957473066-30.362454906465.889308976656.2949868353
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 137 )6 - 1371 - 132
22chain 'A' and (resid 138 through 229 )138 - 229133 - 224
33chain 'A' and (resid 230 through 372 )230 - 372225 - 367

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