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- PDB-8tnt: Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8tnt
TitleCrystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2
Components
  • (Envelope glycoprotein ...) x 2
  • 769C2 heavy chain
  • 769C2 light chain
  • F-2-1 heavy chain
  • F-2-1 light chain
  • Glycoprotein 42
KeywordsIMMUNE SYSTEM / Viral Protein / Antibody
Function / homology
Function and homology information


host cell membrane / host cell endosome membrane / carbohydrate binding / host cell Golgi apparatus / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus glycoprotein L, rhadinovirus-type / Herpesvirus glycoprotein L, rhadinovirus-type superfamily / Viral glycoprotein L / Envelope glycoprotein L / Herpesvirus glycoprotein H main domain / Herpesvirus glycoprotein H / Herpesvirus glycoprotein H, C-terminal / Herpesvirus glycoprotein H, C-terminal domain superfamily / Herpesvirus glycoprotein H C-terminal domain / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Glycoprotein 42 / Envelope glycoprotein L / Envelope glycoprotein H
Similarity search - Component
Biological speciesEpstein-Barr virus (Epstein-Barr virus)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBu, W. / Kumar, A. / Board, N. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. ...Bu, W. / Kumar, A. / Board, N. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. / Pittaluga, S. / Marcotrigiano, J. / Cohen, J.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Immunity / Year: 2024
Title: Epstein-Barr virus gp42 antibodies reveal sites of vulnerability for receptor binding and fusion to B cells.
Authors: Bu, W. / Kumar, A. / Board, N.L. / Kim, J. / Dowdell, K. / Zhang, S. / Lei, Y. / Hostal, A. / Krogmann, T. / Wang, Y. / Pittaluga, S. / Marcotrigiano, J. / Cohen, J.I.
History
DepositionAug 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Glycoprotein 42
D: 769C2 light chain
E: 769C2 heavy chain
F: F-2-1 light chain
G: F-2-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,2289
Polymers202,7857
Non-polymers4422
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.317, 85.172, 119.714
Angle α, β, γ (deg.)90.00, 105.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein H


Mass: 72687.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Gene: gH / Production host: Homo sapiens (human) / References: UniProt: P03231
#2: Protein Envelope glycoprotein L


Mass: 12475.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Gene: gL / Production host: Homo sapiens (human) / References: UniProt: P03212

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Antibody , 4 types, 4 molecules DEFG

#4: Antibody 769C2 light chain


Mass: 22842.115 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 769C2 heavy chain


Mass: 24670.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody F-2-1 light chain


Mass: 23723.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#7: Antibody F-2-1 heavy chain


Mass: 24759.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 3 molecules C

#3: Protein Glycoprotein 42


Mass: 21626.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Epstein-Barr virus (Epstein-Barr virus)
Gene: BZLF2 / Production host: Homo sapiens (human) / References: UniProt: P03205
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
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: 2.85 Å3/Da / Density % sol: 56.81 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
Details: 20mM Tris pH7.5, 150mM NaCl, 4% Tacsimate pH 7.0, and 10% PEG 3,350
PH range: 7.0 - 7.5

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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 PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→47.28 Å / Num. obs: 39158 / % possible obs: 98.7 % / Redundancy: 1.9 % / Rsym value: 0.101 / Net I/σ(I): 7.4
Reflection shellResolution: 3.15→3.28 Å / Num. unique obs: 3913 / Rsym value: 0.767

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→46.32 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2866 1984 5.08 %
Rwork0.2545 --
obs0.2562 39052 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13703 0 28 0 13731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214062
X-RAY DIFFRACTIONf_angle_d0.56519171
X-RAY DIFFRACTIONf_dihedral_angle_d4.5231947
X-RAY DIFFRACTIONf_chiral_restr0.0412209
X-RAY DIFFRACTIONf_plane_restr0.0052435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.230.3791500.35332612X-RAY DIFFRACTION99
3.23-3.320.37791500.34712596X-RAY DIFFRACTION98
3.32-3.410.37991330.33212664X-RAY DIFFRACTION98
3.41-3.520.35671300.30892680X-RAY DIFFRACTION100
3.52-3.650.38791050.29342656X-RAY DIFFRACTION99
3.65-3.80.31491260.28452662X-RAY DIFFRACTION99
3.8-3.970.32511270.26112687X-RAY DIFFRACTION99
3.97-4.180.26841400.2422660X-RAY DIFFRACTION99
4.18-4.440.27221750.2182641X-RAY DIFFRACTION99
4.44-4.780.22641720.2142646X-RAY DIFFRACTION99
4.78-5.260.25461430.22412632X-RAY DIFFRACTION98
5.26-6.020.29091720.252677X-RAY DIFFRACTION100
6.02-7.580.26441270.26132728X-RAY DIFFRACTION100
7.58-46.320.23861340.20782527X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 2.7982 Å / Origin y: 4.6949 Å / Origin z: 44.211 Å
111213212223313233
T0.4457 Å2-0.0182 Å2-0.0042 Å2-0.3502 Å2-0.0009 Å2--0.2777 Å2
L0.9079 °2-0.2448 °20.3437 °2-0.3574 °2-0.0411 °2--0.5906 °2
S0.0113 Å °0.0167 Å °-0.1018 Å °-0.1015 Å °-0.0124 Å °0.0633 Å °-0.069 Å °-0.1262 Å °-0.0028 Å °
Refinement TLS groupSelection details: all

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