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

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Basic information

Entry
Database: PDB / ID: 8tnn
TitleCrystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10
Components
  • (Envelope glycoprotein ...) x 2
  • A10 heavy chain
  • A10 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 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / 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 speciesHuman herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Macaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 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 1.1May 22, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Glycoprotein 42
D: Envelope glycoprotein H
E: Envelope glycoprotein L
F: Glycoprotein 42
G: A10 light chain
H: A10 heavy chain
I: A10 light chain
J: A10 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,85920
Polymers309,91710
Non-polymers2,94310
Water00
1
A: Envelope glycoprotein H
B: Envelope glycoprotein L
C: Glycoprotein 42
G: A10 light chain
H: A10 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,65111
Polymers154,9585
Non-polymers1,6936
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Envelope glycoprotein H
E: Envelope glycoprotein L
F: Glycoprotein 42
I: A10 light chain
J: A10 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,2099
Polymers154,9585
Non-polymers1,2504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.750, 138.960, 316.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Envelope glycoprotein ... , 2 types, 4 molecules ADBE

#1: Protein Envelope glycoprotein H


Mass: 72829.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Gene: gH / Production host: Homo sapiens (human) / References: UniProt: P03231
#2: Protein Envelope glycoprotein L


Mass: 12475.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Gene: gL / Production host: Homo sapiens (human) / References: UniProt: P03212

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Protein , 1 types, 2 molecules CF

#3: Protein Glycoprotein 42


Mass: 21626.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8))
Gene: BZLF2 / Production host: Homo sapiens (human) / References: UniProt: P03205

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Antibody , 2 types, 4 molecules GIHJ

#4: Antibody A10 light chain


Mass: 22654.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Production host: Homo sapiens (human)
#5: Antibody A10 heavy chain


Mass: 25372.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Production host: Homo sapiens (human)

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Sugars , 2 types, 10 molecules

#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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.: 8
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

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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 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM Tris pH7.5, 150mM NaCl, 0.1M citric-acid-BIS-TRIS propane, and 10% PEG 3,350

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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: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.36→54.67 Å / Num. obs: 56676 / % possible obs: 99.9 % / Redundancy: 13.4 % / Rsym value: 0.215 / Net I/σ(I): 7.3
Reflection shellResolution: 3.36→3.41 Å / Num. unique obs: 5565 / Rsym value: 3.918

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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: 3.36→45.83 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.281 2763 4.88 %
Rwork0.234 --
obs0.236 56635 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.36→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20103 0 190 0 20293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420782
X-RAY DIFFRACTIONf_angle_d0.7728439
X-RAY DIFFRACTIONf_dihedral_angle_d6.4272984
X-RAY DIFFRACTIONf_chiral_restr0.0473355
X-RAY DIFFRACTIONf_plane_restr0.0063624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.36-3.420.4391350.37592676X-RAY DIFFRACTION100
3.42-3.480.36641350.34722615X-RAY DIFFRACTION100
3.48-3.550.38421190.3292686X-RAY DIFFRACTION100
3.55-3.620.33711300.31282635X-RAY DIFFRACTION100
3.62-3.70.35851460.30472700X-RAY DIFFRACTION100
3.7-3.780.35621210.28692619X-RAY DIFFRACTION100
3.78-3.880.34091450.29152710X-RAY DIFFRACTION100
3.88-3.980.33891520.27272620X-RAY DIFFRACTION100
3.98-4.10.3091520.25522678X-RAY DIFFRACTION100
4.1-4.230.29351330.242690X-RAY DIFFRACTION100
4.23-4.380.30951310.22772650X-RAY DIFFRACTION100
4.38-4.560.29271380.212673X-RAY DIFFRACTION100
4.56-4.770.25881510.20362678X-RAY DIFFRACTION100
4.77-5.020.25981370.20722709X-RAY DIFFRACTION100
5.02-5.330.26991410.21592695X-RAY DIFFRACTION100
5.33-5.740.30131370.22892707X-RAY DIFFRACTION100
5.74-6.320.31421350.242747X-RAY DIFFRACTION100
6.32-7.230.23931380.23772721X-RAY DIFFRACTION100
7.23-9.10.23681390.21052793X-RAY DIFFRACTION100
9.1-45.830.24921480.21152870X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.5604 Å / Origin y: -17.2469 Å / Origin z: 40.5285 Å
111213212223313233
T0.8878 Å2-0.0561 Å20.2071 Å2-1.0562 Å2-0.0129 Å2--0.8578 Å2
L0.4256 °2-0.1495 °20.0969 °2-0.7097 °2-0.0244 °2--0.5354 °2
S0.0645 Å °-0.0372 Å °0.1582 Å °0.1271 Å °-0.0392 Å °-0.0052 Å °-0.2636 Å °-0.0155 Å °-0.0178 Å °
Refinement TLS groupSelection details: ALL

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