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- PDB-9fj1: Structure of the F13 protein of Vaccinia virus in complex with IMCBH -

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Basic information

Entry
Database: PDB / ID: 9fj1
TitleStructure of the F13 protein of Vaccinia virus in complex with IMCBH
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: 3.8 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)45,0295
Polymers44,3631
Non-polymers6664
Water00
1
A: Envelope phospholipase OPG057
hetero molecules

A: Envelope phospholipase OPG057
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,05810
Polymers88,7262
Non-polymers1,3328
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation28_544x,-y-1/2,-z-1/21
Buried area4670 Å2
ΔGint-15 kcal/mol
Surface area28700 Å2
Unit cell
Length a, b, c (Å)282.805, 282.805, 282.805
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: 44363.062 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1IDM / ~{N}'-(4-chloranyl-3-methyl-phenyl)carbonylpyridine-4-carbohydrazide


Mass: 289.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12ClN3O2 / Feature type: SUBJECT OF INVESTIGATION
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: 5.31 Å3/Da / Density % sol: 76.84 %
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 IMCBH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980112240579 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980112240579 Å / Relative weight: 1
ReflectionResolution: 3.8→47.8 Å / Num. obs: 10019 / % possible obs: 99.7 % / Redundancy: 46 % / Biso Wilson estimate: 158.11 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.1
Reflection shellResolution: 3.8→4.25 Å / Num. unique obs: 2745 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→47.13 Å / SU ML: 0.3821 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.247 502 5.03 %
Rwork0.2079 9484 -
obs0.2099 9986 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 161.16 Å2
Refinement stepCycle: LAST / Resolution: 3.8→47.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 45 0 2929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172986
X-RAY DIFFRACTIONf_angle_d0.42234047
X-RAY DIFFRACTIONf_chiral_restr0.0406459
X-RAY DIFFRACTIONf_plane_restr0.0035517
X-RAY DIFFRACTIONf_dihedral_angle_d9.5431077
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.190.36611230.30512264X-RAY DIFFRACTION98.31
4.19-4.790.2641290.22382314X-RAY DIFFRACTION100
4.79-6.030.25991160.22552370X-RAY DIFFRACTION100
6.03-47.130.21541340.17522536X-RAY DIFFRACTION99.81
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)
11.540144760.356436730597-1.32257645721.75401441789-0.5082281245832.88727986838-0.0356827924322-0.2300053606670.3568622890690.3055675326430.0400218743484-0.630232192441-0.03513630962430.6461972942520.05143075586631.11187536841-0.152026896271-0.2568866323491.51508500881-0.1168369808481.35888926361-21.6458774486-46.4919485099-44.346584228
23.6834681235-1.62087949099-3.392950321810.9703535574511.738603460333.449412484390.04566742506381.877198954770.137557828738-2.18324210673-0.38757436084-1.315680783620.2933055979871.253937661720.9120003115342.844828979580.1318257692150.5105675843052.788347072020.411739413032.23725795179-6.07799439623-41.3088318889-60.6852466543
34.860333704480.874763492117-0.2370669156114.886066433230.9856851305785.354248663840.224129474003-0.01702299666160.2519958388030.172948385499-0.204914678638-0.5705213118940.1595831136510.397130057167-0.06611936458980.9977421857680.0815630135181-0.05872265225611.09120283921-0.04521475523591.07407172402-26.4866254283-65.3341440642-56.2518706293
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 170 )6 - 1701 - 165
22chain 'A' and (resid 171 through 190 )171 - 190166 - 185
33chain 'A' and (resid 191 through 372 )191 - 372186 - 367

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