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- PDB-8v5p: Crystal Structure of the C-terminal domain of the VZV gE ectodoma... -

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Basic information

Entry
Database: PDB / ID: 8v5p
TitleCrystal Structure of the C-terminal domain of the VZV gE ectodomain in complex with the Fab of human antibody 5A2
Components
  • 5A2 Fab Light Chain
  • 5A2 Fab heavy chain
  • Envelope glycoprotein E
KeywordsVIRAL PROTEIN / glycoprotein E / varicella / zoster / herpes / virus / antibody
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 speciesHuman alphaherpesvirus 3 (Varicella-zoster virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.33 Å
AuthorsHarshbarger, W. / Malito, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded 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
A: Envelope glycoprotein E
H: 5A2 Fab heavy chain
L: 5A2 Fab Light Chain
D: Envelope glycoprotein E
E: 5A2 Fab heavy chain
Y: 5A2 Fab Light Chain
G: Envelope glycoprotein E
J: 5A2 Fab heavy chain
X: 5A2 Fab Light Chain
C: Envelope glycoprotein E
F: 5A2 Fab heavy chain
I: 5A2 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)306,09612
Polymers306,09612
Non-polymers00
Water00
1
A: Envelope glycoprotein E
H: 5A2 Fab heavy chain
L: 5A2 Fab Light Chain


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


Theoretical massNumber of molelcules
Total (without water)76,5243
Polymers76,5243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Envelope glycoprotein E
J: 5A2 Fab heavy chain
X: 5A2 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)76,5243
Polymers76,5243
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Envelope glycoprotein E
F: 5A2 Fab heavy chain
I: 5A2 Fab Light Chain


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)274.822, 274.822, 128.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_3ens_1chain "D"
d_4ens_1chain "G"
d_1ens_2chain "E"
d_2ens_2chain "F"
d_3ens_2chain "H"
d_4ens_2chain "J"
d_1ens_3chain "I"
d_2ens_3chain "L"
d_3ens_3chain "X"
d_4ens_3chain "Y"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLNGLNPHEPHEAA305 - 47935 - 209
d_2ens_1GLNGLNPHEPHECJ305 - 47935 - 209
d_3ens_1GLNGLNPHEPHEDD305 - 47935 - 209
d_4ens_1GLNGLNPHEPHEGG305 - 47935 - 209
d_1ens_2GLNGLNPROPROEE1 - 2181 - 221
d_2ens_2GLNGLNPROPROFK1 - 2181 - 221
d_3ens_2GLNGLNPROPROHB1 - 2181 - 221
d_4ens_2GLNGLNPROPROJH1 - 2181 - 221
d_1ens_3ASPASPTHRTHRIL1 - 2091 - 210
d_2ens_3ASPASPTHRTHRLC1 - 2101 - 210
d_3ens_3ASPASPTHRTHRXI1 - 2091 - 210
d_4ens_3ASPASPTHRTHRYF1 - 2091 - 210

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

#1: Protein
Envelope glycoprotein E


Mass: 28010.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 3 (Varicella-zoster virus)
Gene: ORF68 / Production host: Homo sapiens (human) / References: UniProt: A0A1B1JEP3
#2: Antibody
5A2 Fab heavy chain


Mass: 26039.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
5A2 Fab Light Chain


Mass: 22474.045 Da / Num. of mol.: 4
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: 3.98 Å3/Da / Density % sol: 69.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.5, benzamidine hydrochloride

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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: Dec 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.33→45.8 Å / Num. obs: 33380 / % possible obs: 99 % / Redundancy: 13.6 % / Biso Wilson estimate: 46.58 Å2 / CC1/2: 0.94 / Net I/σ(I): 9.3
Reflection shellResolution: 4.33→4.485 Å / Num. unique obs: 3055 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.33→45.8 Å / SU ML: 0.4624 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0052
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2722 1999 6.04 %
Rwork0.2218 31103 -
obs0.2249 33102 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.84 Å2
Refinement stepCycle: LAST / Resolution: 4.33→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18372 0 0 0 18372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318880
X-RAY DIFFRACTIONf_angle_d0.802325808
X-RAY DIFFRACTIONf_chiral_restr0.04892924
X-RAY DIFFRACTIONf_plane_restr0.00563288
X-RAY DIFFRACTIONf_dihedral_angle_d5.7752576
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.76793725867
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.29283573572
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.55262650974
ens_2d_2EEX-RAY DIFFRACTIONTorsion NCS0.886146561368
ens_2d_3EEX-RAY DIFFRACTIONTorsion NCS1.04456574232
ens_2d_4EEX-RAY DIFFRACTIONTorsion NCS0.900348316374
ens_3d_2LIX-RAY DIFFRACTIONTorsion NCS0.97553639591
ens_3d_3LIX-RAY DIFFRACTIONTorsion NCS0.811371038583
ens_3d_4LIX-RAY DIFFRACTIONTorsion NCS0.926261671709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.33-4.440.32751250.25041953X-RAY DIFFRACTION89.07
4.44-4.560.28461410.2192193X-RAY DIFFRACTION99.74
4.56-4.690.26361410.20382199X-RAY DIFFRACTION99.91
4.69-4.840.25921420.1952201X-RAY DIFFRACTION99.7
4.84-5.010.23351420.19922213X-RAY DIFFRACTION99.92
5.01-5.210.2511420.19572219X-RAY DIFFRACTION99.96
5.22-5.450.23791420.20582208X-RAY DIFFRACTION99.96
5.45-5.740.26191440.21542238X-RAY DIFFRACTION99.96
5.74-6.10.29871440.23012248X-RAY DIFFRACTION99.96
6.1-6.570.30361440.24162228X-RAY DIFFRACTION100
6.57-7.230.30941460.25612268X-RAY DIFFRACTION99.92
7.23-8.270.30251450.23892255X-RAY DIFFRACTION100
8.27-10.390.2261470.20092290X-RAY DIFFRACTION99.71
10.39-45.80.2921540.25692390X-RAY DIFFRACTION98.26

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