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- PDB-9hpa: Structure of A16/G9 (vaccinia virus) in complex with VHH D07 and ... -

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Basic information

Entry
Database: PDB / ID: 9hpa
TitleStructure of A16/G9 (vaccinia virus) in complex with VHH D07 and VHH E12
Components
  • Entry-fusion complex protein OPG094
  • VHH D07
  • VHH E12
  • Virion membrane protein OPG143
KeywordsVIRAL PROTEIN / poxvirus / viral fusion / vaccinia virus / mpox virus
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / helicase activity / DNA-templated transcription termination / hydrolase activity / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / virion membrane / DNA binding / ATP binding / membrane
Similarity search - Function
Pox virus entry-fusion-complex G9/A16 / Pox virus entry-fusion-complex G9/A16
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Entry-fusion complex protein OPG094 / Virion membrane protein OPG143
Similarity search - Component
Biological speciesVaccinia virus Western Reserve
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsVernuccio, R. / Meola, A. / Guardado-Calvo, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0003 France
CitationJournal: Cell / Year: 2025
Title: Structural basis of poxvirus fusion regulation and anti-A16/G9 antibody-mediated neutralization and protection.
Authors: Annalisa Meola / Riccardo Vernuccio / Leandro Battini / Guillermo Albericio / Pilar Delgado / Rebecca Bamford / Laura Pokorny / Manon Broutin / Alejandro Martínez León / Sébastien Gallien ...Authors: Annalisa Meola / Riccardo Vernuccio / Leandro Battini / Guillermo Albericio / Pilar Delgado / Rebecca Bamford / Laura Pokorny / Manon Broutin / Alejandro Martínez León / Sébastien Gallien / María Gil / María A Noriega / Florence Guivel-Benhassine / Françoise Porrot / Jeanne Postal / Julian Buchrieser / Mathieu Hubert / Ahmed Haouz / Pierre Lafaye / Mariano Esteban / Jochen S Hub / Matthieu Mahévas / Pascal Chappert / Jason Mercer / Juan Garcia-Arriaza / Olivier Schwartz / Pablo Guardado-Calvo /
Abstract: Monkeypox virus (MPXV) is a poxvirus endemic to Central and West Africa with high epidemic potential. Poxviruses enter host cells via a conserved entry-fusion complex (EFC), which mediates viral ...Monkeypox virus (MPXV) is a poxvirus endemic to Central and West Africa with high epidemic potential. Poxviruses enter host cells via a conserved entry-fusion complex (EFC), which mediates viral fusion to the cell membrane. The EFC is a promising therapeutic target, but the absence of structural data has limited the development of fusion-inhibiting treatments. Here, we investigated A16/G9, a subcomplex of the EFC that controls fusion timing. Using cryo-electron microscopy, we showed how A16/G9 interacts with A56/K2, a viral fusion suppressor that prevents superinfection. Immunization with A16/G9 elicited a protective immune response in mice. Using X-ray crystallography, we characterized two neutralizing antibodies and engineered a chimeric antibody that cross-neutralizes several poxviruses more efficiently than 7D11, the most potent antibody targeting the EFC described to date. These findings highlight the potential of A16/G9 as a candidate for subunit vaccines and identify regions of the EFC as targets for antiviral development.
History
DepositionDec 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virion membrane protein OPG143
B: Entry-fusion complex protein OPG094
D: VHH E12
C: VHH D07
E: Virion membrane protein OPG143
F: Entry-fusion complex protein OPG094
H: VHH E12
G: VHH D07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,99519
Polymers224,8918
Non-polymers1,10511
Water1,78399
1
A: Virion membrane protein OPG143
B: Entry-fusion complex protein OPG094
D: VHH E12
C: VHH D07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,04110
Polymers112,4454
Non-polymers5956
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Virion membrane protein OPG143
F: Entry-fusion complex protein OPG094
H: VHH E12
G: VHH D07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,9559
Polymers112,4454
Non-polymers5095
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.204, 148.041, 185.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein Virion membrane protein OPG143


Mass: 40941.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG143, VACWR136, A16L / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P16710
#2: Protein Entry-fusion complex protein OPG094 / EFC protein OPG094 / Myristoylated protein G9 / Protein F1


Mass: 37432.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve / Gene: OPG094, VACWR087, G9R / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P07611

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Antibody , 2 types, 4 molecules DHCG

#3: Antibody VHH E12


Mass: 17105.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Antibody VHH D07


Mass: 16965.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 110 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20 % w/v PEG 1K, 0.1 M Na Phos Cit pH 4.2, 0.2 M LiSO4 (cryoprotected with 33% Ethylene glycol)

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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: Sep 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 3.1→39.33 Å / Num. obs: 38737 / % possible obs: 97.4 % / Redundancy: 7.9 % / Biso Wilson estimate: 70.7 Å2 / CC1/2: 0.989 / Net I/σ(I): 6.8
Reflection shellResolution: 3.1→3.24 Å / Num. unique obs: 4739 / CC1/2: 0.373

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→39.33 Å / SU ML: 0.4769 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2652 1982 5.13 %
Rwork0.2225 36656 -
obs0.2248 38638 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.56 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12624 0 65 99 12788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002312976
X-RAY DIFFRACTIONf_angle_d0.468517535
X-RAY DIFFRACTIONf_chiral_restr0.04061824
X-RAY DIFFRACTIONf_plane_restr0.00372288
X-RAY DIFFRACTIONf_dihedral_angle_d10.64924824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.180.38151340.33952594X-RAY DIFFRACTION97.85
3.18-3.260.35281470.32962650X-RAY DIFFRACTION98.14
3.26-3.360.38251270.3152605X-RAY DIFFRACTION98.06
3.36-3.470.30161260.29592615X-RAY DIFFRACTION97.86
3.47-3.590.33911500.27012582X-RAY DIFFRACTION96.88
3.59-3.740.29471410.25062613X-RAY DIFFRACTION96.9
3.74-3.910.29981340.23222625X-RAY DIFFRACTION97.63
3.91-4.110.25341460.22972618X-RAY DIFFRACTION97.56
4.11-4.370.26731460.1982601X-RAY DIFFRACTION97.2
4.37-4.70.23861480.17462592X-RAY DIFFRACTION96.82
4.71-5.180.23861490.17812620X-RAY DIFFRACTION96.21
5.18-5.920.24651430.19292606X-RAY DIFFRACTION95.52
5.92-7.450.22121460.20612640X-RAY DIFFRACTION95.64
7.46-39.330.20621450.18212695X-RAY DIFFRACTION93.02
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)
12.09010395394-0.6028643226422.361027260441.68350165456-0.7815178196581.656346543730.14367223201-0.1383640269-0.02952943249760.2328435932680.114552063491-0.1698698899010.01846502126480.00506325585435-0.0001459179638680.8522321904040.0115553265242-0.06787542187140.809724030790.04304838024440.692056817495-10.1902403228-15.748796754560.4270666139
21.44056584982-0.1601106357722.77161346460.255336722881-0.4567387965255.56214848352-0.126144587984-0.134061217201-0.08128877118060.1191538474070.0219221346995-0.0216689789467-0.150511859748-0.2310353480486.99917084551E-50.770423526999-0.0098324684417-0.0187952209140.713427736064-0.00231666699040.733521774229-26.2361472194-18.830425772526.9062010071
32.16253628544-0.663338000785-0.4932921017390.988668495657-0.3329107389822.43623347921-0.129961956892-0.4477794177160.303636084042-0.0427634882193-0.3341183439470.0958629538049-0.0371887003969-0.2448463485950.000240064772740.710751484246-0.145946410602-0.04680812137040.8202613424060.0003835662178560.734378148705-41.4387162442-14.7100820039-12.3742216074
40.87174095360.249931902095-0.4735056619670.4795733799041.210974980413.044061678180.2060683879260.150232084455-0.0123432917730.011627849381-0.017924114746-0.09236978413860.2575797139290.195810270537-1.131504289E-50.8674777121620.0286959612063-0.0992100281090.6381289015510.01650217634530.779949887402-19.5523364569-30.677198399733.2418248541
52.33669095435-1.12449790272-0.03420156844151.77267651430.8377618657533.03347572491-0.01390745404880.0486207063725-0.265604810947-0.079026061629-0.01168889307730.2550175444520.2648947771390.350568756329-5.16111815773E-60.918362759505-0.0389597500191-0.07551944803140.6983392243310.09533180338260.931803864547-22.1465632322-30.36325974135.87972471245
62.69272375034-1.275151027391.191719694632.56819185374-1.111271648474.046685839330.1350454359270.3194970403270.115650708977-0.0117706698957-0.24598684285-0.1641956984370.5829474131690.481666371353-3.45328497144E-50.681633169224-0.02688015119660.06818444344040.7904586104430.02806332598490.702654512667-25.6654611621-22.869220593-20.0880489972
71.20236501335-0.38888271788-0.9523657678862.08988499271-0.755976514753.222221768470.334729262976-0.09916844061450.00818521402576-0.196310798725-0.365027181139-0.06523569386370.08934628777390.0606447285185-3.78476214237E-50.5441093922710.0274391016213-0.01949943787330.610346265116-0.1156494284950.679111415233-18.2716758124-11.490588435-43.8417742926
81.37718926506-0.0661546955129-1.429812342290.162790122908-0.1295437621641.830233838340.0264078841611-0.302885027503-0.2912975800230.4322068004460.005527748167960.05653616702980.0783736544792-0.414308067846.33985880342E-50.5868121037340.0984752386649-0.02908035801380.8076100735170.06024205481030.619452673698-19.0282572616-14.6021422793-37.4472117158
90.777412548190.456949707587-0.3224669123440.545043246259-0.4163244620841.65705777658-0.140312419142-1.146550821170.253085671941-0.3126533378970.4321733880330.378561064425-0.239320096691-0.2573127146050.0003983385146370.776372772980.0955705267897-0.1028199383621.09230725410.09529654712580.977860388099-23.4352645627-11.2295662621-46.424717339
102.969937403570.791262120070.7941656137230.576125475589-0.5073692204442.484507542580.289331946734-0.5018367689940.2281815258820.223077664560.3617651361850.00557550312278-0.140652192061-1.271425598340.010777898260.6755604038920.09171415733650.04376814550931.455158054240.08338077802480.943568151774-59.948351375-10.8450259318-19.2066785308
110.6148457416680.327586013990.125425550051.274111171280.2623604194150.0322639158431-0.182516153919-0.509703303084-0.2887820183270.255111644885-0.02239100806350.539068080423-0.692955112488-0.3528591884810.000143443735680.7560498433960.001853111253830.03240243462221.865048351480.05929223274580.949745055377-65.6480160826-13.5520563202-16.2479447084
121.070118147340.966269463397-0.4715515234091.80558803649-1.068478773230.829329644748-0.01960721142820.4816349186520.7180598898240.135129863676-0.3478385969040.108935066729-1.18310139516-0.7865755863260.01942249144850.6184469482130.0910949368584-0.05597718897241.50708173845-0.01351807504240.736314717261-52.3261280487-8.294389097-24.2550188319
130.7471095091550.242630718910.1324059993871.937839993042.512934324552.794209411840.1951558167380.243467710740.0718511547853-0.8256919550310.3265521445730.7915091085151.02871848925-0.3593177539940.01373276938131.82842106833-0.131528370824-0.3563716448960.7803095936090.2336674658161.0726608879213.1094853209-15.734563005533.1912315932
142.207820841840.9702487823150.9014552409410.3966295335230.3949339638420.357163613588-0.2449185120780.03916802081460.710329965589-1.637999995140.2388645360950.9766345157210.495785509395-1.648374876330.004593204493642.27551170437-0.4700340633-0.5981569597341.222125227630.2145716176821.031181433827.16138757167-20.522138069336.3380054449
150.746061008152-0.3013186488682.03605274465-0.09828861887020.624083673114.79977645405-0.1371449549660.2478391297410.216818396451-0.1654908077830.105176652386-0.105460151212-0.1642212779320.7454630289655.58113275612E-50.764540286388-0.0225014424166-0.09532531099320.787615508281-0.05286635419880.9886396019237.8657059378-16.93811266690.3941420549
160.6317129302310.889055501733-0.8854136422491.91467467751-0.2588435008342.130722316210.122030233020.1014783823040.095364816388-0.9548666206520.0502043563556-0.112457204986-0.00164056351543-0.1519407065510.01693044482581.308350350140.0272175948865-0.1317122824040.6419467975870.01897206832810.83478973677320.0544348974-29.249199775756.0592980462
170.9368059752861.267189536110.2470700180181.77336638088-0.4280451478434.305768834160.02778092651810.0765115306452-0.139278992104-0.01590612310620.0850156147493-0.05290390355880.7697277965530.1404213376031.42097790983E-50.9135451204230.0723690307461-0.2422379677750.656955731602-0.07643151996460.92756800049222.3425958932-31.134944715588.3181608126
181.2733035150.15521197041-0.3859038724331.73114996221-0.3954773306843.39813583370.0330426959988-0.3801133601870.07536348292450.2822470764270.0582406482198-0.003021354149340.4701457512640.0397117745044-2.63266300977E-50.6952968054280.106753049065-0.1323045023560.724082695626-0.08109349122110.81379372170827.4143694637-21.807968741118.311738069
195.135454898034.737297639932.341282610586.491394472851.611141330631.270809508340.9113832873-0.8162164677511.868011617980.350530423409-1.452188658242.44662648103-0.456116129141-0.844542841362-0.1173589066990.8564021532110.05372208710470.1291204600790.6163649834250.01045576473170.77914744364913.3650181691-6.07964449538143.075257645
204.238452052780.934343333012-1.757813186122.437862156451.08243427792.956571445780.157470249429-0.107487855942-0.392254606922-0.156406656494-0.26047197639-0.1130235438850.1268897806-0.0956411574014-1.30787118123E-50.599671782488-0.0169162683255-0.109677231190.825608497997-0.09147011632480.73227905262417.5150977706-12.9249948142133.63742295
212.6699351537-2.40291123633-1.698584740322.546555370030.9992252252273.067684943220.167338595381-0.7620604975590.804623602817-0.2255596877480.05708267646560.6215515096730.07430456447120.3715156733329.53552758884E-50.672557959625-0.0139812492911-0.1605957993680.801233560831-0.03885741577380.79844632204320.2455544812-12.3920427832140.900808818
220.394063151980.2820810905420.5323751374970.2193065071920.3818912119930.7213152161520.9994094897061.8378214514-0.134874090459-0.155944023533-0.0307503132993-1.13359487706-1.593213111120.3337788654290.004965331121930.972408432342-0.1774680345760.08807614040281.56674973102-0.4131499699351.319629361964.6138015846-4.48497995245119.597125811
231.61883619856-0.6090480620820.1599496875222.793655221910.5227257539391.422530485460.02277396864880.3197941582260.242927612839-0.2903600402450.3254800457480.085856779160.1937110175781.73664644831-5.18173739319E-50.68760370781-0.04603218721-0.02071198972941.24759171341-0.08611836760410.97488275694561.1808377454-13.1573393491114.908009667
240.700248092003-0.620077300653-0.06688499847541.111162194490.1870998793420.02552999382350.02801522889830.273434578191.23654045635-0.5752246940850.00705034413209-0.411707300369-0.2454080620760.7915796297660.0003083359444430.707583616182-0.0780022949668-0.01486289095531.127322895970.03076963226951.1547486982353.9934480584-6.72706426787118.90794241
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 5:94)AA5 - 941 - 90
22(chain A and resid 95:241)AA95 - 24191 - 237
33(chain A and resid 242:294)AA242 - 294238 - 290
44(chain B and resid 7:107)BB7 - 1071 - 101
55(chain B and resid 108:158)BB108 - 158102 - 152
66(chain B and resid 159:271)BB159 - 271153 - 265
77(chain C and resid 3:47)CG3 - 471 - 45
88(chain C and resid 48:100)CG48 - 10046 - 98
99(chain C and resid 101:120)CG101 - 12099 - 118
1010(chain D and resid 3:62)DF3 - 621 - 60
1111(chain D and resid 63:96)DF63 - 9661 - 94
1212(chain D and resid 97:119)DF97 - 11995 - 117
1313(chain E and resid 5:81)EI5 - 811 - 77
1414(chain E and resid 82:133)EI82 - 13378 - 129
1515(chain E and resid 134:294)EI134 - 294130 - 290
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