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- PDB-9qqv: Structure of the F13 protein of Vaccinia virus in complex with G2... -

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Basic information

Entry
Database: PDB / ID: 9qqv
TitleStructure of the F13 protein of Vaccinia virus in complex with G243-1720
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 / D-type glycerophospholipase 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: 3.4 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 Commun / Year: 2025
Title: Development of a replication-defective mpox virus platform for fundamental and therapeutic research
Authors: Chen, J. / Hu, L. / Vernuccio, R. / Shi, N. / Tian, J. / Zhang, Y. / Tian, S. / Cao, X. / Ha, Z. / Lu, J. / Battini, L. / Raynal, B. / Haouz, A. / Xue, J. / Cai, Q. / Zhao, Y. / Lu, Y. / ...Authors: Chen, J. / Hu, L. / Vernuccio, R. / Shi, N. / Tian, J. / Zhang, Y. / Tian, S. / Cao, X. / Ha, Z. / Lu, J. / Battini, L. / Raynal, B. / Haouz, A. / Xue, J. / Cai, Q. / Zhao, Y. / Lu, Y. / Smith, G.L. / Xie, Y. / Lu, H. / Guardado-Calvo, P. / Zhang, P. / Zhang, R.
History
DepositionApr 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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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)45,2696
Polymers44,3631
Non-polymers9065
Water27015
1
A: Envelope phospholipase OPG057
hetero molecules

A: Envelope phospholipase OPG057
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,53912
Polymers88,7262
Non-polymers1,81310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation51_554-x+1/2,y,-z-1/21
Buried area3380 Å2
ΔGint-8 kcal/mol
Surface area27730 Å2
Unit cell
Length a, b, c (Å)281.495, 281.495, 281.495
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-405-

A1I9D

21A-405-

A1I9D

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-A1I9D / 4-(azepan-1-ylcarbonyl)-~{N}-(2-chloranyl-4-methyl-phenyl)-1,2,5-trimethyl-pyrrole-3-sulfonamide


Mass: 437.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28ClN3O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 5.24 Å3/Da / Density % sol: 76.52 % / Description: Cubic crystals
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 G243-1720)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978564977646 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564977646 Å / Relative weight: 1
ReflectionResolution: 3.4→39.42 Å / Num. obs: 13691 / % possible obs: 99.9 % / Redundancy: 78.7 % / Biso Wilson estimate: 166.12 Å2 / CC1/2: 1 / Net I/σ(I): 17.7
Reflection shellResolution: 3.4→3.67 Å / Num. unique obs: 2755 / CC1/2: 0.763

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→39.42 Å / SU ML: 0.5591 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.1257
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273 650 4.79 %
Rwork0.2262 12909 -
obs0.2283 13559 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 153.1 Å2
Refinement stepCycle: LAST / Resolution: 3.4→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 60 15 2901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152942
X-RAY DIFFRACTIONf_angle_d0.4353987
X-RAY DIFFRACTIONf_chiral_restr0.0406448
X-RAY DIFFRACTIONf_plane_restr0.003504
X-RAY DIFFRACTIONf_dihedral_angle_d9.46241069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.660.49981280.43662408X-RAY DIFFRACTION95.2
3.66-4.030.30791220.28662542X-RAY DIFFRACTION100
4.03-4.610.31511330.26682569X-RAY DIFFRACTION100
4.62-5.810.25671310.21412598X-RAY DIFFRACTION100
5.81-39.420.23921360.19262792X-RAY DIFFRACTION99.9
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)
14.245747877631.361561653081.405550563333.076273923780.5569335648793.460328645230.007752951664390.3329071403510.471446846828-0.1240436348960.0767256261460.145272413767-0.322882026644-0.245026653557-7.40973147086E-61.663558518480.162308330641-0.07172541979431.452481194150.08907029623021.7515361797144.1533010256-21.4268537773-94.6794649259
20.0999094749326-0.07216368706430.04256879116190.0649856026293-0.01612368282840.0316800161984-0.414221402763-0.123998393213-0.580494424303-0.244363470435-0.907401391369-1.28916970315-0.09738707387260.0412360928718-6.26323847581E-62.72647408156-0.3906907154290.463040623791.930888894240.006550437090062.7377289242358.3171809755-7.14620815653-101.048487515
35.409813679670.5400680127872.894947155453.395184663660.9066298210834.661349053130.209855071285-0.6154663450480.02382430210360.150558235269-0.00385756733031-0.3854351374910.01230930439490.08125140961980.0001424279768371.54117612165-0.0374671227563-0.0676319291511.52890488518-0.04509020741731.6347489793455.8979197165-25.853930225-75.7833190469
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 189 )171 - 189166 - 174
33chain 'A' and (resid 190 through 372 )190 - 372175 - 357

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