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- PDB-9shd: Structure of vaccinia virus A26 (residues 1-397) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9shd
TitleStructure of vaccinia virus A26 (residues 1-397) in complex with Fab 10M2146
Components
  • Anti-Fab VHH
  • Envelop protein OPG153
  • Heavy chain of Fab 10M2146
  • Light chain of Fab 10M2146
KeywordsVIRAL PROTEIN / complex antigen-antibody / vaccinia virus / A26
Function / homologyOrthopoxvirus A26L/A30L / Orthopoxvirus A26L/A30L protein / Chordopoxvirus fusion protein/multifunctional envelope protein A27 / Chordopoxvirus multifunctional envelope protein A27 / fusion of virus membrane with host plasma membrane / viral envelope / virion membrane / membrane / Envelop protein OPG153
Function and homology information
Biological speciesHomo sapiens (human)
Lama glama (llama)
Orthopoxvirus vaccinia
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBattini, L. / Guardado-Calvo, P.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0003 France
Agence Nationale de la Recherche (ANR)ANR-24-CE15- 6625 France
CitationJournal: To Be Published
Title: Structure of vaccinia virus A26 (residues 1-397) in complex with Fab 10M2146
Authors: Battini, L. / Guardado-Calvo, P.
History
DepositionAug 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain of Fab 10M2146
L: Light chain of Fab 10M2146
K: Anti-Fab VHH
H0Z0: Envelop protein OPG153


Theoretical massNumber of molelcules
Total (without water)113,7124
Polymers113,7124
Non-polymers00
Water19,2221067
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-30 kcal/mol
Surface area37430 Å2
Unit cell
Length a, b, c (Å)122.459, 157.821, 141.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11H-500-

HOH

21H-522-

HOH

31H0Z0-709-

HOH

41H0Z0-739-

HOH

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Components

#1: Antibody Heavy chain of Fab 10M2146


Mass: 24551.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain of Fab 10M2146


Mass: 23410.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Anti-Fab VHH


Mass: 13390.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#4: Protein Envelop protein OPG153


Mass: 52359.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orthopoxvirus vaccinia / Gene: OPG153, VACWR149, A26L / Production host: Escherichia coli (E. coli) / References: UniProt: P24758
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1067 / Source method: isolated from a natural source / Formula: H2O
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: 3 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MgCl2, 0.1 M Tris pH 8.5, 17% (w/v) PEG 20K

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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: Oct 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.9→39.93 Å / Num. obs: 107567 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 24.28 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 5260 / CC1/2: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.93 Å / SU ML: 0.1973 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.0491
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1903 5432 5.05 %
Rwork0.1577 102076 -
obs0.1593 107508 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.52 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7148 0 0 1067 8215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00947424
X-RAY DIFFRACTIONf_angle_d0.954810090
X-RAY DIFFRACTIONf_chiral_restr0.06451099
X-RAY DIFFRACTIONf_plane_restr0.00711293
X-RAY DIFFRACTIONf_dihedral_angle_d12.88672705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.33221830.27393397X-RAY DIFFRACTION99.92
1.92-1.940.29151760.25593371X-RAY DIFFRACTION99.97
1.94-1.970.27841810.24393357X-RAY DIFFRACTION100
1.97-1.990.261720.22883360X-RAY DIFFRACTION100
1.99-2.020.26581800.21323378X-RAY DIFFRACTION99.94
2.02-2.050.2481760.20033365X-RAY DIFFRACTION100
2.05-2.080.2351860.18283421X-RAY DIFFRACTION100
2.08-2.110.22771630.17773340X-RAY DIFFRACTION100
2.11-2.140.21281880.17033381X-RAY DIFFRACTION100
2.14-2.170.22031850.16983393X-RAY DIFFRACTION100
2.17-2.210.19561890.16393340X-RAY DIFFRACTION100
2.21-2.250.21151780.16323410X-RAY DIFFRACTION100
2.25-2.30.21121640.16063364X-RAY DIFFRACTION100
2.3-2.340.21261880.163375X-RAY DIFFRACTION100
2.34-2.390.20091820.16143415X-RAY DIFFRACTION100
2.39-2.450.18071680.15543404X-RAY DIFFRACTION99.97
2.45-2.510.18951750.14693396X-RAY DIFFRACTION99.97
2.51-2.580.19661890.14923368X-RAY DIFFRACTION99.97
2.58-2.650.18151930.15313380X-RAY DIFFRACTION100
2.65-2.740.18851670.15443398X-RAY DIFFRACTION100
2.74-2.840.19941650.15553438X-RAY DIFFRACTION100
2.84-2.950.19881840.1643402X-RAY DIFFRACTION99.97
2.95-3.090.20261960.15893377X-RAY DIFFRACTION100
3.09-3.250.1841660.15613430X-RAY DIFFRACTION99.97
3.25-3.450.19062010.15343421X-RAY DIFFRACTION100
3.45-3.720.17661830.14623430X-RAY DIFFRACTION100
3.72-4.090.13881810.13463418X-RAY DIFFRACTION100
4.09-4.680.15191540.11953504X-RAY DIFFRACTION100
4.68-5.90.14182140.1373461X-RAY DIFFRACTION100
5.9-39.930.18462050.16583582X-RAY DIFFRACTION99.68
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)
10.545024479459-0.333513085713-0.2740597507720.616093751990.3941326528390.49624689674-0.003781790820.0247391565861-0.01221727810240.0550146152585-0.03373541817960.05676236408920.0450280952706-0.1199355749970.06382593500280.1635518908750.00146245106084-0.002899428039210.2036021462660.01275989330590.162369785936.0059193334213.8136978478-12.1148399684
20.363394990554-0.1964109102230.04681144689880.5569816748950.3792977417230.4142392599910.0115406197657-0.112178467923-0.03057221668090.01850591697-0.00742570627698-0.03567560647720.0575898443782-0.04628535101330.01684088350060.149095322462-0.01037142134660.00521072020820.1835218347220.02277746492310.16504238472421.621157524422.2583589284-8.6557945682
31.194627093140.2219358293620.06492766863491.26188960470.05983138270871.03144881314-0.0186708121945-0.0442430425170.03922040531540.0462169334263-0.0367791543079-0.166111514648-0.08640564003320.158151910331-0.05044822570820.154478107263-0.0140519398128-0.002241711680570.188524030470.01060859046680.22200450659841.961748262238.4206299719-4.94518321812
40.493951214585-0.143114931443-0.05501935005520.8747083135160.3237975914280.546928045183-0.004536582949750.0364907156033-0.05057776758070.0136994313622-0.01299175648180.03598157203710.0476160707564-0.0400469988760.004217892144530.1501122485410.000845856659070.005665348026840.127685457155-0.005596392726960.13009965558439.2404027689-23.1817539836-33.5153533088
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'H' )HA20 - 2471 - 224
22(chain 'L' )LB20 - 2331 - 214
33(chain 'K' )KD2 - 1131 - 120
44(chain 'A' )H0Z0E16 - 3641 - 349

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