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- PDB-8sgn: Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) ... -

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Basic information

Entry
Database: PDB / ID: 8sgn
TitleCrystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy651H02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine
Components
  • (Cy651H02 Fab ...) x 2
  • Envelope glycoprotein gp350
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Epstein-Barr virus / immune system / monoclonal antibody / macaques / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell membrane / receptor ligand activity / symbiont entry into host cell / virion membrane / membrane
Similarity search - Function
Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal
Similarity search - Domain/homology
Envelope glycoprotein GP350
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJoyce, M.G. / Jensen, J.L. / Chen, W.H. / Kanekiyo, M.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Immunity / Year: 2025
Title: Structural basis for complement receptor engagement and virus neutralization through Epstein-Barr virus gp350.
Authors: Joyce, M.G. / Bu, W. / Chen, W.H. / Gillespie, R.A. / Andrews, S.F. / Wheatley, A.K. / Tsybovsky, Y. / Jensen, J.L. / Stephens, T. / Prabhakaran, M. / Fisher, B.E. / Narpala, S.R. / Bagchi, ...Authors: Joyce, M.G. / Bu, W. / Chen, W.H. / Gillespie, R.A. / Andrews, S.F. / Wheatley, A.K. / Tsybovsky, Y. / Jensen, J.L. / Stephens, T. / Prabhakaran, M. / Fisher, B.E. / Narpala, S.R. / Bagchi, M. / McDermott, A.B. / Nabel, G.J. / Kwong, P.D. / Mascola, J.R. / Cohen, J.I. / Kanekiyo, M.
History
DepositionApr 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Feb 19, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Feb 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Cy651H02 Fab light chain
H: Cy651H02 Fab heavy chain
G: Envelope glycoprotein gp350
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,42640
Polymers93,1523
Non-polymers4,27437
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.148, 139.148, 172.337
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11H-465-

HOH

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Components

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Protein , 1 types, 1 molecules G

#3: Protein Envelope glycoprotein gp350 / Membrane antigen / MA


Mass: 46895.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BLLF1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P03200

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Antibody , 2 types, 2 molecules LH

#1: Antibody Cy651H02 Fab light chain


Mass: 22490.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody Cy651H02 Fab heavy chain


Mass: 23765.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Cell line (production host): Expi293 / Production host: Homo sapiens (human)

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Sugars , 2 types, 10 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}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.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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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Non-polymers , 3 types, 321 molecules

#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.72M ammonium sulfate, 0.1M Tris pH 8.0

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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: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 55717 / % possible obs: 88 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.45
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 1165 / % possible all: 45.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.92 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2366 2951 5.3 %
Rwork0.1931 --
obs0.1954 55717 87.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 124 294 6884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036715
X-RAY DIFFRACTIONf_angle_d0.6449118
X-RAY DIFFRACTIONf_dihedral_angle_d8.953992
X-RAY DIFFRACTIONf_chiral_restr0.0491065
X-RAY DIFFRACTIONf_plane_restr0.0051147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.3247930.27351165X-RAY DIFFRACTION42
2.23-2.270.3406660.28221411X-RAY DIFFRACTION49
2.27-2.310.3238940.27611592X-RAY DIFFRACTION56
2.31-2.360.3128930.27291908X-RAY DIFFRACTION66
2.36-2.410.31481140.27632172X-RAY DIFFRACTION75
2.41-2.460.33291430.27332306X-RAY DIFFRACTION82
2.46-2.520.31491810.26422509X-RAY DIFFRACTION90
2.52-2.580.29541950.25192669X-RAY DIFFRACTION95
2.58-2.650.31851860.25032758X-RAY DIFFRACTION97
2.65-2.730.32611360.24232847X-RAY DIFFRACTION99
2.73-2.810.28431700.23152854X-RAY DIFFRACTION100
2.81-2.910.26671520.22842844X-RAY DIFFRACTION100
2.91-3.030.24941280.21092870X-RAY DIFFRACTION100
3.03-3.170.27991400.22082893X-RAY DIFFRACTION100
3.17-3.340.23461220.20672869X-RAY DIFFRACTION100
3.34-3.540.25071990.18932818X-RAY DIFFRACTION100
3.55-3.820.2597850.17352926X-RAY DIFFRACTION100
3.82-4.20.23321690.16792828X-RAY DIFFRACTION100
4.2-4.810.16391960.13872818X-RAY DIFFRACTION100
4.81-6.050.18851300.16022879X-RAY DIFFRACTION100
6.05-32.920.2071590.1872830X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.26283.4426-3.21228.2880.56776.6936-0.15110.28690.1118-0.17080.18050.02470.08050.00670.00070.2003-0.0001-0.03190.3094-0.0070.1865-43.97034.359140.2414
23.09690.6594-0.96162.2756-1.55822.86810.1754-0.0540.1886-0.0418-0.13010.2415-0.0687-0.343-0.0770.25450.02350.00640.32-0.03620.264-46.53584.759551.5586
33.60931.2843-0.34121.1252-0.0090.52830.05110.07540.31360.089-0.014-0.0146-0.16990.0362-0.0410.36880.0068-0.02990.3566-0.03340.2571-27.204115.001242.2221
46.4560.72160.08622.23680.11423.3854-0.09920.72770.2834-0.23210.065-0.158-0.35280.44120.00890.4137-0.0844-0.01480.45150.04930.2902-13.266322.569330.937
54.5664-0.2847-1.34871.70060.12442.4090.0284-0.4246-0.04250.2686-0.0301-0.16550.05950.13840.02660.2654-0.0161-0.02230.3332-0.00810.2272-27.56850.389161.2552
64.6251-0.1004-1.35875.44114.20515.74220.35170.18680.6034-0.4204-0.40850.5958-0.92140.04120.08790.4442-0.0717-0.01230.4380.01630.5322-10.387326.471244.9999
76.5754-1.25430.35417.52760.26976.65290.1488-0.96720.45790.5792-0.0651-0.1153-0.4477-0.7039-0.14180.2899-0.02230.06490.5883-0.07430.4051-13.64722.421750.5928
83.6823-0.5053-0.39311.43760.14851.7401-0.21390.3714-0.4296-0.0971-0.11290.42660.3407-0.520.32680.4424-0.15260.0080.6312-0.17010.519-73.1961-13.20863.9963
96.8151-1.6975-2.24476.12712.04856.4465-0.09490.3012-0.2812-0.24640.0625-0.0650.7434-0.2905-0.03470.4434-0.12040.03190.4174-0.15060.4227-65.2131-17.330764.3109
104.4813-1.2545-3.99073.77111.19894.0834-0.26130.6082-0.0791-0.15620.089-0.00170.2447-0.22260.27470.5321-0.1132-0.06640.7742-0.18920.4824-68.7841-11.413257.4139
117.89761.62712.05391.86140.18164.13570.10820.3844-0.1129-0.1762-0.3566-0.24920.72220.70610.16290.48580.09170.09310.48920.10440.3968-49.1663-8.904781.973
124.86630.33841.58016.00872.30348.5531-0.17330.09720.41260.1924-0.05020.1839-0.75020.54390.1510.3509-0.0478-0.00360.35780.03530.2524-49.70513.793878.3508
133.28722.0091.2969.47254.30627.0375-0.1187-0.23280.0071-0.0897-0.19840.1313-0.22040.45540.33590.2803-0.02080.05260.37760.11660.1676-50.1811-4.323480.3511
141.5524-1.21921.353.6077-1.63063.36050.0468-0.4971-0.6298-0.03010.09470.65160.3438-0.3175-0.1020.46230.00570.03230.4485-0.12310.3505-63.274-8.686581.6465
153.6671-1.2883-0.03254.67970.28454.3309-0.20480.16850.0808-0.1404-0.08520.72090.1125-0.85840.21590.4006-0.0091-0.0550.9396-0.13230.7102-96.03781.75473.1352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 24 )
2X-RAY DIFFRACTION2chain 'L' and (resid 25 through 75 )
3X-RAY DIFFRACTION3chain 'L' and (resid 76 through 140 )
4X-RAY DIFFRACTION4chain 'L' and (resid 141 through 211 )
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 119 )
6X-RAY DIFFRACTION6chain 'H' and (resid 120 through 145 )
7X-RAY DIFFRACTION7chain 'H' and (resid 146 through 213 )
8X-RAY DIFFRACTION8chain 'G' and (resid 7 through 87 )
9X-RAY DIFFRACTION9chain 'G' and (resid 88 through 117 )
10X-RAY DIFFRACTION10chain 'G' and (resid 118 through 156 )
11X-RAY DIFFRACTION11chain 'G' and (resid 157 through 187 )
12X-RAY DIFFRACTION12chain 'G' and (resid 188 through 259 )
13X-RAY DIFFRACTION13chain 'G' and (resid 260 through 296 )
14X-RAY DIFFRACTION14chain 'G' and (resid 297 through 317 )
15X-RAY DIFFRACTION15chain 'G' and (resid 318 through 424 )

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