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- PDB-8v5l: Structure of the Varicella Zoster Virus (VZV) gI binding domain o... -

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Basic information

Entry
Database: PDB / ID: 8v5l
TitleStructure of the Varicella Zoster Virus (VZV) gI binding domain of glycoprotein E (gE) in complex with human Fab 1A2 and 1E12
Components
  • Envelope glycoprotein E
  • Fab 1A2 Heavy Chain
  • Fab 1A2 Light Chain
  • Fab 1E12 Heavy Chain
  • Fab 1E12 Light Chain
KeywordsVIRAL PROTEIN / glycoprotein / gE / VZV / Varicella Zoster
Function / homology
Function and homology information


host cell junction / anchoring junction / host cell Golgi membrane / host cell endosome membrane / viral envelope / virion membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein E, Fc-binding domain / Envelope glycoprotein E, N-terminal / Alphaherpesvirus glycoprotein E / Alphaherpesvirus glycoprotein E N-terminal / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein E
Similarity search - Component
Biological speciesHomo sapiens (human)
Human alphaherpesvirus 3 (Varicella-zoster virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsSeraj, N. / Holzapfel, G. / Harshbarger, W.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Vaccines (Basel) / Year: 2024
Title: Structures of the Varicella Zoster Virus Glycoprotein E and Epitope Mapping of Vaccine-Elicited Antibodies.
Authors: Harshbarger, W.D. / Holzapfel, G. / Seraj, N. / Tian, S. / Chesterman, C. / Fu, Z. / Pan, Y. / Harelson, C. / Peng, D. / Huang, Y. / Chandramouli, S. / Malito, E. / Bottomley, M.J. / Williams, J.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab 1A2 Heavy Chain
L: Fab 1A2 Light Chain
A: Envelope glycoprotein E
B: Fab 1E12 Heavy Chain
C: Fab 1E12 Light Chain


Theoretical massNumber of molelcules
Total (without water)123,5905
Polymers123,5905
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.776, 63.493, 96.484
Angle α, β, γ (deg.)90.000, 99.960, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Antibody Fab 1A2 Heavy Chain


Mass: 26711.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab 1A2 Light Chain


Mass: 23477.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Envelope glycoprotein E


Mass: 23281.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Production host: Homo sapiens (human) / References: UniProt: Q77JX0
#4: Antibody Fab 1E12 Heavy Chain


Mass: 26685.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody Fab 1E12 Light Chain


Mass: 23434.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% w/v PEG 3350, 0.1 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→47.57 Å / Num. obs: 35605 / % possible obs: 94.14 % / Redundancy: 3 % / Biso Wilson estimate: 59.18 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.109 / Net I/σ(I): 16
Reflection shellResolution: 3.09→3.2 Å / Num. unique obs: 1958 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
autoPROCdata reduction
PHASERphasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→47.57 Å / SU ML: 0.4303 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 3103 8.72 %
Rwork0.233 32502 -
obs0.2362 35605 76.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.43 Å2
Refinement stepCycle: LAST / Resolution: 3.09→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7752 0 0 0 7752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327939
X-RAY DIFFRACTIONf_angle_d0.655910812
X-RAY DIFFRACTIONf_chiral_restr0.04541217
X-RAY DIFFRACTIONf_plane_restr0.00671381
X-RAY DIFFRACTIONf_dihedral_angle_d4.97291090
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.140.4889680.3894711X-RAY DIFFRACTION37.02
3.14-3.190.4198890.3591958X-RAY DIFFRACTION48.49
3.19-3.240.3353910.3232949X-RAY DIFFRACTION49.9
3.24-3.30.3491000.2976996X-RAY DIFFRACTION51.55
3.3-3.370.3045960.26541034X-RAY DIFFRACTION52.12
3.37-3.440.29891240.2611234X-RAY DIFFRACTION63.94
3.44-3.510.30441240.24721317X-RAY DIFFRACTION67.56
3.51-3.590.25411270.26241405X-RAY DIFFRACTION72.57
3.59-3.680.34851440.26441498X-RAY DIFFRACTION77.13
3.68-3.780.3631490.27771585X-RAY DIFFRACTION81.41
3.78-3.890.28431620.26131636X-RAY DIFFRACTION84.41
3.89-4.020.2831510.24841681X-RAY DIFFRACTION85.93
4.02-4.160.28371580.22981652X-RAY DIFFRACTION86.64
4.16-4.330.27861610.21611702X-RAY DIFFRACTION87.38
4.33-4.530.21651670.20341716X-RAY DIFFRACTION86.53
4.53-4.760.24821510.19871632X-RAY DIFFRACTION84.78
4.76-5.060.23981630.1871689X-RAY DIFFRACTION86.62
5.06-5.450.26271780.20091855X-RAY DIFFRACTION94.69
5.45-60.25691730.23141843X-RAY DIFFRACTION95.41
6-6.870.27651760.23671842X-RAY DIFFRACTION94.43
6.87-8.640.25491780.23611785X-RAY DIFFRACTION92.25
8.64-47.570.18961730.20211782X-RAY DIFFRACTION91.87

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