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- PDB-8v5q: Varicella Zoster Virus (VZV) glycoprotein E (gE) gI binding domai... -

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Basic information

Entry
Database: PDB / ID: 8v5q
TitleVaricella Zoster Virus (VZV) glycoprotein E (gE) gI binding domain in complex with human Fab 1E3
Components
  • Envelope glycoprotein E
  • Fab 1E3 Heavy Chain
  • Fab 1E3 Light Chain
KeywordsVIRAL PROTEIN / Varicella Zoster Virus / VZV / gE / glycoprotein E / gI binding domain / fab / 1E3
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
DI(HYDROXYETHYL)ETHER / Envelope glycoprotein E
Similarity search - Component
Biological speciesHomo sapiens (human)
Human alphaherpesvirus 3 (Varicella-zoster virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHolzapfel, G. / Seraj, N. / Harshbarger, W.
Funding support1items
OrganizationGrant numberCountry
Other private
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 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 1E3 Heavy Chain
L: Fab 1E3 Light Chain
G: Envelope glycoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6679
Polymers73,0503
Non-polymers6176
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-46 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.621, 193.755, 179.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
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

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Components

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Protein , 1 types, 1 molecules G

#3: Protein Envelope glycoprotein E


Mass: 23281.025 Da / Num. of mol.: 1 / Fragment: gl binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: HHV3_E_SVETAgp69 / Production host: Homo sapiens (human) / References: UniProt: A6XEF7

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab 1E3 Heavy Chain


Mass: 26445.350 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 1E3 Light Chain


Mass: 23323.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 183 molecules

#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.6 / Details: 0.1M citric acid, pH 3.6 ; 1.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→89.927 Å / Num. obs: 61689 / % possible obs: 99.8 % / Redundancy: 13.7 % / Biso Wilson estimate: 30.61 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.052 / Rrim(I) all: 0.191 / Net I/σ(I): 8.9
Reflection shellResolution: 1.9→1.937 Å / Redundancy: 13 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 38641 / CC1/2: 0.62 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.72 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 1995 3.25 %
Rwork0.2263 --
obs0.2266 61391 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4236 0 38 177 4451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.219
X-RAY DIFFRACTIONf_dihedral_angle_d15.5931565
X-RAY DIFFRACTIONf_chiral_restr0.077669
X-RAY DIFFRACTIONf_plane_restr0.014750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.42221350.40744019X-RAY DIFFRACTION95
1.95-20.30571400.31114147X-RAY DIFFRACTION99
2-2.060.25691420.28644213X-RAY DIFFRACTION99
2.06-2.130.26911410.27154194X-RAY DIFFRACTION100
2.13-2.210.25351410.24654198X-RAY DIFFRACTION100
2.21-2.290.28981400.29354201X-RAY DIFFRACTION99
2.29-2.40.24181410.24814214X-RAY DIFFRACTION100
2.4-2.520.30271420.24644237X-RAY DIFFRACTION100
2.52-2.680.24461450.24494283X-RAY DIFFRACTION100
2.68-2.890.26951400.24254230X-RAY DIFFRACTION100
2.89-3.180.26781450.24554299X-RAY DIFFRACTION100
3.18-3.640.26321440.21574277X-RAY DIFFRACTION100
3.64-4.580.18621460.17814362X-RAY DIFFRACTION100
4.59-33.720.16841530.1924522X-RAY DIFFRACTION100

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