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- PDB-8v5s: VZV glycoprotein E C-terminal domain (cleaved) in complex with hu... -

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Basic information

Entry
Database: PDB / ID: 8v5s
TitleVZV glycoprotein E C-terminal domain (cleaved) in complex with human Fab 5A2
Components
  • 5A2 Fab Heavy Chain
  • 5A2 Fab Light Chain
  • Envelope glycoprotein E
KeywordsVIRAL PROTEIN / varicella zoster / virus / antibody / immune / herpes
Function / homology
Function and homology information


host cell junction / host cell Golgi membrane / host cell endosome membrane / viral envelope / virion membrane / 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: 3.53 Å
AuthorsHarshbarger, W. / Malito, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
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

Downloads & links

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Assembly

Deposited unit
H: 5A2 Fab Heavy Chain
L: 5A2 Fab Light Chain
A: 5A2 Fab Heavy Chain
B: 5A2 Fab Light Chain
C: Envelope glycoprotein E
D: Envelope glycoprotein E


Theoretical massNumber of molelcules
Total (without water)153,0486
Polymers153,0486
Non-polymers00
Water00
1
H: 5A2 Fab Heavy Chain
L: 5A2 Fab Light Chain
C: Envelope glycoprotein E


Theoretical massNumber of molelcules
Total (without water)76,5243
Polymers76,5243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 5A2 Fab Heavy Chain
B: 5A2 Fab Light Chain
D: Envelope glycoprotein E


Theoretical massNumber of molelcules
Total (without water)76,5243
Polymers76,5243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.077, 60.410, 114.667
Angle α, β, γ (deg.)90.000, 93.890, 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

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Components

#1: Antibody 5A2 Fab Heavy Chain


Mass: 26039.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody 5A2 Fab Light Chain


Mass: 22474.045 Da / Num. of mol.: 2
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: 28010.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: gE / Production host: Homo sapiens (human) / References: UniProt: A0A1B1JEP3
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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.02 M Sodium/potassium phosphate 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350

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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: Apr 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.53→40.02 Å / Num. obs: 16382 / % possible obs: 90.73 % / Redundancy: 3.8 % / Biso Wilson estimate: 53.04 Å2 / CC1/2: 0.96 / Net I/σ(I): 15.2
Reflection shellResolution: 3.53→3.66 Å / Num. unique obs: 1136 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
PHASERphasing
HKL-3000data scaling
HKL-3000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.53→40.02 Å / SU ML: 0.5352 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.8766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3074 805 4.91 %
Rwork0.2611 15577 -
obs0.2634 16382 90.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.88 Å2
Refinement stepCycle: LAST / Resolution: 3.53→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8421 0 0 0 8421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00268647
X-RAY DIFFRACTIONf_angle_d0.691111815
X-RAY DIFFRACTIONf_chiral_restr0.0461348
X-RAY DIFFRACTIONf_plane_restr0.00461494
X-RAY DIFFRACTIONf_dihedral_angle_d6.04871179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.53-3.750.3859970.33422006X-RAY DIFFRACTION70.57
3.75-4.040.33931330.30682510X-RAY DIFFRACTION88.22
4.04-4.440.33711240.26012602X-RAY DIFFRACTION92.09
4.44-5.090.28151590.23552782X-RAY DIFFRACTION98.2
5.09-6.40.28061440.24942831X-RAY DIFFRACTION98.58
6.4-40.020.28131480.23432846X-RAY DIFFRACTION96.08

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