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8sm1

CRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN-BARR VIRUS MAJOR GLYCOPROTEIN GP350

Method: X-RAY DIFFRACTION Dmax: 134.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp350

Human herpesvirus 4

UniProt P03200

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain G； UniProt 1–425 Not recorded 769A9 Fab heavy chain × 1 769A9 Fab light chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；1.60M AMMONIUM SULFATE, 2% PEG 400, 0.5% GLYCEROL, 0.1M SODIUM ACETATE PH5.5 Resolution 3.29 Å R-free 0.298

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8SM1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8SGN Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy651H02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine Deposited 2023-04-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–425（425 aa）
Not recorded EDO 1,2-ETHANEDIOL × 23 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.72M ammonium sulfate, 0.1M Tris pH 8.0
Resolution 2.20 Å R-free 0.237
8SIC Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine Deposited 2023-04-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–425（425 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；18% PEG 8000, 0.22 M sodium acetate, 0.1 M sodium cacodylate pH 6.5
Resolution 2.76 Å R-free 0.295
8SIC Crystal structure of Epstein-Barr virus glycoprotein 350 (gp350) in complex with Cy137C02, a monoclonal antibody isolated from macaques immunized with a gp350 nanoparticle vaccine Deposited 2023-04-14 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–425（425 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；18% PEG 8000, 0.22 M sodium acetate, 0.1 M sodium cacodylate pH 6.5
Resolution 2.76 Å R-free 0.295
8SM0 Crystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr virus major glycoprotein gp350 Deposited 2023-04-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–425（425 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；1.60M AMMONIUM SULFATE, 2% PEG 400, 0.5% GLYCEROL, 0.1M SODIUM ACETATE PH5.5
Resolution 1.68 Å R-free 0.241
9MA0 Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 4A11 Deposited 2025-03-13 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–470（470 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.33 Å
9MA7 Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9 Deposited 2025-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–470（470 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.14 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GP350_EBVB9
Isoform —
PDB entities 1
Chains and sequence ranges Author chain G； PDBConstruct 1–425； UniProt 1–425

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8sm1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8sm1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8sm1
Deposition date deposition_date2023-04-25
Structure title titleCRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN-BARR VIRUS MAJOR GLYCOPROTEIN GP350
Keywords keywordsVIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.02 Å
Radius of gyration Rg (electron density) rg_electron37.41 Å
Forward intensity I(0) i0134844000.00
Molecular weight molecular_weight92509.0 kDa
Excluded volume excluded_volume115390 ų
Envelope volume envelope_volume159360 ų
Hydration-shell volume shell_volume38981 ų
Envelope diameter envelope_diameter141.9 Å
Shell Rg shell_rg39.01 Å
Envelope Rg envelope_rg37.73 Å
Shape Rg shape_rg37.38 Å
Total Rg total_rg37.60 Å
Total atoms total_atoms6512
Residues n_residues831
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax134.7 Å
Rg (real space) rg_real37.56 Å
Rg uncertainty (real space) rg_real_error1.90 Å
I(0) (real space) i0_real1.3480e+08
I(0) uncertainty (real space) i0_real_error2.4000e+06
Rg (reciprocal space) rg_reciprocal37.23 Å
I(0) (reciprocal space) i0_reciprocal134800000.0000
Solution quality estimate total_estimate0.7841
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.5 Å
Skewness Skewness skewness0.682
Kurtosis Kurtosis kurtosis0.040
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19690000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.631; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.522; Smooth: 0.777
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)