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- PDB-9fja: Structure of the F13 protein (A295E mutant) of Vaccinia virus in ... -

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Basic information

Entry
Database: PDB / ID: 9fja
TitleStructure of the F13 protein (A295E mutant) of Vaccinia virus in complex with tecovirimat
ComponentsEnvelope phospholipase OPG057
KeywordsVIRAL PROTEIN / poxvirus / tecovirimat / 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
: / Envelope phospholipase OPG057
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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

Downloads & links

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Assembly

Deposited unit
A: Envelope phospholipase OPG057
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9775
Polymers42,3251
Non-polymers6534
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)281.722, 281.722, 281.722
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

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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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1ICJ / Tecovirimat / ~{N}-[(1~{R},2~{R},6~{S},7~{S},8~{S},10~{R})-3,5-bis(oxidanylidene)-4-azatetracyclo[5.3.2.0^{2,6}.0^{8,10}]dodec-11-en-4-yl]-4-(trifluoromethyl)benzamide


Mass: 376.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15F3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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

CrystalDensity Matthews: 5.5 Å3/Da / Density % sol: 77.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1 M Na3 citrate, 0.1 M Imidazole pH 8 (cryoprotected with 33% glycerol, soaked with 1 mM tecovirimat)

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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: 3.5→49.8 Å / Num. obs: 12621 / % possible obs: 100 % / Redundancy: 55 % / Biso Wilson estimate: 117.88 Å2 / CC1/2: 0.999 / Net I/σ(I): 8.4
Reflection shellResolution: 3.5→3.83 Å / Num. unique obs: 2936 / CC1/2: 0.228

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→49.8 Å / SU ML: 0.6836 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 44.0417
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.281 589 4.96 %
Rwork0.2362 11284 -
obs0.2385 11873 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 157.92 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 45 14 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.04362993
X-RAY DIFFRACTIONf_angle_d0.85914062
X-RAY DIFFRACTIONf_chiral_restr0.0615464
X-RAY DIFFRACTIONf_plane_restr0.0052514
X-RAY DIFFRACTIONf_dihedral_angle_d8.75941094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.850.51871370.5122197X-RAY DIFFRACTION76.13
3.85-4.410.39141390.34842938X-RAY DIFFRACTION99.61
4.41-5.560.28551520.2222975X-RAY DIFFRACTION100
5.56-49.80.20691610.17233174X-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)
14.630083383912.28314708854-0.6435328268882.38787034175-0.2030826849193.760533409250.08536611954640.2178372096210.344575339652-0.4876432217380.138845994085-0.0588991027539-0.5339890416-0.780975640059-0.1575953612811.160362574210.340589092009-0.08280554405451.105092053150.1395207779871.2762938227543.9615052809-22.6320962869-95.8190413299
23.97337112817-1.410771942053.510488068814.98076032745-1.560037805453.87144661315-0.1571616955-0.1781421505371.39442673822-0.2623610145160.0400739931951-0.381555621788-1.226991466580.4064930383760.1565245409881.39866817457-0.04077641374130.2176052059690.968137096312-0.05612394281291.4762833845954.6433439841-16.0919104454-84.6872182273
35.092113343710.8296916030342.985066881646.92170909737-0.1889519774589.538162534920.304147450524-0.50284676181-0.2398401340230.3924696099450.115949426697-0.2528333184070.2637360859070.431475197135-0.455012176780.8122609255850.00597237464211-0.0963099377641.02684492162-0.03576233903411.2484833873354.9697590818-31.1447558435-74.3292893686
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 255 )138 - 255133 - 250
33chain 'A' and (resid 256 through 372 )256 - 372251 - 367

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