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- PDB-9fhk: Structure of the F13 protein of Vaccinia virus (P21 crystal form) -

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Basic information

Entry
Database: PDB / ID: 9fhk
TitleStructure of the F13 protein of Vaccinia virus (P21 crystal form)
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: 2.1 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 27, 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
B: Envelope phospholipase OPG057
A: Envelope phospholipase OPG057


Theoretical massNumber of molelcules
Total (without water)88,7262
Polymers88,7262
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-9 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.350, 94.111, 73.197
Angle α, β, γ (deg.)90.000, 98.941, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 6 through 173 or resid 193 through 372))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERILEILEAB6 - 37233 - 399
d_21SERSERALAALABA6 - 17333 - 200
d_22TYRTYRILEILEBA193 - 372220 - 399

NCS oper: (Code: givenMatrix: (-0.623590169669, -0.00293911942302, 0.781745906206), (1.0598630179E-5, -0.999992964148, -0.00375120549905), (0.781751431198, -0.00233092943786, 0.623585813331)Vector: - ...NCS oper: (Code: given
Matrix: (-0.623590169669, -0.00293911942302, 0.781745906206), (1.0598630179E-5, -0.999992964148, -0.00375120549905), (0.781751431198, -0.00233092943786, 0.623585813331)
Vector: -0.148163217436, -47.6510688804, -0.0808868741021)

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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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20%(w/v) PEG 3350, 0.1M Hepes 7.5, 2%(v/v) Tacsimate (cryoprotected in 20% glycerol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978564321995 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564321995 Å / Relative weight: 1
ReflectionResolution: 2.1→39.44 Å / Num. obs: 40522 / % possible obs: 99.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 54.21 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 3297 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.44 Å / SU ML: 0.3353 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2487 2009 4.96 %
Rwork0.2181 38474 -
obs0.2197 40483 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5533 0 0 70 5603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195647
X-RAY DIFFRACTIONf_angle_d0.46257651
X-RAY DIFFRACTIONf_chiral_restr0.0419873
X-RAY DIFFRACTIONf_plane_restr0.0034975
X-RAY DIFFRACTIONf_dihedral_angle_d11.0572051
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.69038835267 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.39061660.35982693X-RAY DIFFRACTION99.2
2.15-2.210.34261260.33522712X-RAY DIFFRACTION97.76
2.21-2.280.38091460.31372718X-RAY DIFFRACTION97.78
2.28-2.350.32221310.28372774X-RAY DIFFRACTION99.52
2.35-2.430.28621250.27882726X-RAY DIFFRACTION98.41
2.43-2.530.28771340.28252736X-RAY DIFFRACTION98.56
2.53-2.650.33511460.28482748X-RAY DIFFRACTION98.7
2.65-2.790.29811350.26722742X-RAY DIFFRACTION99.04
2.79-2.960.29911290.2742762X-RAY DIFFRACTION99.14
2.96-3.190.31861620.26142756X-RAY DIFFRACTION99.32
3.19-3.510.25441300.24082778X-RAY DIFFRACTION99.11
3.51-4.020.23151590.20682752X-RAY DIFFRACTION99.56
4.02-5.060.19341640.16492763X-RAY DIFFRACTION99.59
5.06-39.440.21831560.17262814X-RAY DIFFRACTION99.1
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)
12.45110539307-0.306120245483-0.6784415339842.94431917249-0.1942287673273.150981580170.130338227230.308882089983-0.509448378459-0.12712029646-0.1730257899660.07363264539990.60022768293-0.239399078937-1.88797948591E-50.6616933566240.00173566915528-0.06953076570540.502755234056-0.1425966146010.6024108367135.17654161842-56.0161024102-22.8614306033
21.73205453988-1.40781028926-0.6024067493631.325015993670.2776535883341.509646722810.00653484057371-0.8247196644480.380214355460.359823460287-0.02826945892180.0763932706938-0.2035564792590.194102170578-9.39547831261E-50.652628003463-0.0335889624937-0.02570898669540.7166651372220.003942572153520.5944537501236.11264914111-41.0658972729-9.77319320473
32.11398270949-1.81192296813-1.032957631653.17158207437-0.4776823773942.424964046760.2285932747920.396777878378-0.122330787028-0.146911028465-0.2658193881390.3404170364580.0833774957338-0.171616883148-0.0001515457767550.54144907428-0.00643361500251-0.01007658751760.600888290351-0.06904315942360.4698109129-4.01839084647-30.3795430533-25.100551462
41.72385960845-2.0253325869-0.3574387056572.30911432350.2292572365582.050245434130.3970186942180.8676595003070.0578541327922-0.632924320627-0.4247369472560.2349333813130.00451708984579-0.07606932107671.80075658208E-50.5867556100670.0722748529014-0.05044347336150.647951415578-0.0115498970640.501008155645-1.91420568009-31.2658297653-31.9529887065
51.126046712920.2445929675610.1944180262323.14443003271-0.4017068004941.6468277810.3625888690170.671673477689-0.181748540201-0.403964585964-0.267858700115-0.0366961356961-0.0494501572094-0.0845723226110.0001022036238480.5809882644590.08326993139280.03753188201110.682032688813-0.06032622242540.5118467699794.21900356835-37.2952015089-28.9852119823
61.98284116046-0.4253236266750.5266487527873.0105058226-0.1552708117682.18767575108-0.398306872427-0.02932094067350.3444056222890.1984318277930.1996481930680.374004069872-0.68759691199-0.505617024213-8.33735920626E-50.7442001892910.246550179278-0.04499744683530.657021145659-0.005116147762510.691654405017-25.92495500329.57364268934-10.398196003
71.54414795450.8147420318450.2986174077131.873561601820.2100944820771.33997732573-0.4959930855280.1559195946140.7303598037750.05461976393730.3799217548130.114028990827-0.9403981160440.219043720909-0.0006308611276530.8289270315640.0677646236755-0.08036729698040.5375854817260.04256835807790.609648776566-13.370171026810.170313968-12.3321797656
80.7600119494550.0374336872691-0.2301843516821.130941453820.156523182990.0870312663664-0.168396777219-0.2667012062670.2123048973850.3195389777030.09248018583020.0565829167956-0.591741134962-0.0697426565244-0.0002018980871380.6557872395370.139051972991-0.05075238224210.607940872867-0.03148052909110.621621284334-19.97695394964.02547727401-7.02579950603
91.10252074856-0.6482048609980.1779810616951.095816668750.5235208585660.7604386883950.51334914688-1.09132161263-0.3353049718711.26530756355-0.414056220909-0.104085645483-0.5481935230330.675154023240.001038821712670.8745474134690.09514733773550.0430008935930.802493374584-0.00733860484410.557673094019-15.2485373239-7.368907807810.340226915391
100.828039994667-0.357061794322-0.5637747915841.11587526466-0.2321302311151.26004652297-0.16110479221-0.283243459839-0.06561286365750.2389942092280.18671441790.1786408492750.329704435764-0.2369436330155.63272096727E-50.5446372916780.02857495401250.08255072875370.5106571254210.002724222960020.548878331585-15.0128652188-13.4840387448-9.54600899322
112.14601526193-1.552554149170.3671684762081.69354506940.5058208848821.07937454410.2406307236310.06222409115360.165408241535-0.00924890966343-0.01283390458180.109016281133-0.1571314658250.1313801671720.0006206946838710.518434582086-0.09162771531030.0988610892120.507184658837-0.07996101149360.565933808149-11.6460560939-18.3204050193-20.4435800831
121.05679868268-0.6114717880990.08636308920270.7959448200770.3141587620930.3483515662740.2029184400971.245374057440.0634860105654-1.26577571765-0.04062724689860.4979334389610.0771203443269-0.115819606732-0.003222766602510.7367782572160.009393256444680.03926595948750.879489324493-0.04093016786740.806602778558-20.8203886516-17.8377445428-28.1142101136
132.33416241904-0.5734653165690.4391977225452.03595694752-0.1067400722662.03866839339-0.2428525297590.169694547439-0.322642139385-0.03214491343930.1099101396680.34211647640.0178459053729-0.350261110897-9.35847125349E-50.450812752305-0.01258027467730.08488156602210.536872927774-0.0251138717550.581836520918-21.6889278921-11.4176106429-14.8888460035
140.7168575046160.3851437264230.2517763577631.425256632060.1520039477170.745005884419-0.2873825368890.028005206545-1.08916453190.0640219816347-0.4103652643020.919597487951-0.0530605548834-0.221361121786-0.05312443923610.436846028284-0.03294268514170.01415770379880.883684425842-0.00086554260820.992544420504-33.4899065583-12.4131769778-17.3405845157
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 170 )AB6 - 1701 - 165
22chain 'A' and (resid 171 through 218 )AB171 - 218166 - 194
33chain 'A' and (resid 219 through 283 )AB219 - 283195 - 259
44chain 'A' and (resid 284 through 325 )AB284 - 325260 - 301
55chain 'A' and (resid 326 through 372 )AB326 - 372302 - 348
66chain 'B' and (resid 6 through 87 )BA6 - 871 - 82
77chain 'B' and (resid 88 through 132 )BA88 - 13283 - 127
88chain 'B' and (resid 133 through 170 )BA133 - 170128 - 165
99chain 'B' and (resid 171 through 207 )BA171 - 207166 - 184
1010chain 'B' and (resid 208 through 243 )BA208 - 243185 - 220
1111chain 'B' and (resid 244 through 268 )BA244 - 268221 - 245
1212chain 'B' and (resid 269 through 297 )BA269 - 297246 - 274
1313chain 'B' and (resid 298 through 347 )BA298 - 347275 - 324
1414chain 'B' and (resid 348 through 372 )BA348 - 372325 - 349

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