SAXSdb — 8sic

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp350

Human herpesvirus 4

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 E； UniProt 1–425	Not recorded	Cy137C02 Fab heavy chain × 1 Cy137C02 Fab light chain × 1 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 1–425	Not recorded	Cy137C02 Fab heavy chain × 1 Cy137C02 Fab light chain × 1 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

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 8SIC	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
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 experimental conditions 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
8SM1 CRYSTAL STRUCTURE OF HUMAN ANTIBODY 769A9 IN COMPLEX WITH EPSTEIN-BARR VIRUS MAJOR GLYCOPROTEIN GP350 Deposited 2023-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–425（425 aa）	Not recorded	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
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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GP350_EBVB9
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–425； UniProt 1–425 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8sic
Deposition date deposition_date	2023-04-14
Structure title title	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
Keywords keywords	;viral protein, envelope glycoprotein, monoclonal antibody, antiviral, immune system, macaques, Epstein-Barr virus, VIRAL PROTEIN-IMMUNE SYSTEM complex ;; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	64.66 Å
Radius of gyration Rg (electron density) rg_electron	67.50 Å
Forward intensity I(0) i0	510828000.00
Molecular weight molecular_weight	186240.0 kDa
Excluded volume excluded_volume	232120 Å³
Envelope volume envelope_volume	345310 Å³
Hydration-shell volume shell_volume	52318 Å³
Envelope diameter envelope_diameter	252.5 Å
Shell Rg shell_rg	48.43 Å
Envelope Rg envelope_rg	68.55 Å
Shape Rg shape_rg	67.49 Å
Total Rg total_rg	66.97 Å
Total atoms total_atoms	13106
Residues n_residues	1670
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	230.9 Å
Rg (real space) rg_real	66.76 Å
Rg uncertainty (real space) rg_real_error	3.23 Å
I(0) (real space) i0_real	5.1060e+08
I(0) uncertainty (real space) i0_real_error	1.3090e+07
Rg (reciprocal space) rg_reciprocal	62.80 Å
I(0) (reciprocal space) i0_reciprocal	507300000.0000
Solution quality estimate total_estimate	0.6605
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.729
Kurtosis Kurtosis kurtosis	-0.204
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0010
Highest regularization parameter α highest_alpha	15780000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.303; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.211; Smooth: 0.468

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cy137C02 Fab heavy chain
Molecular weight formula_weight	23805.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,H
Atom count atom_count	13230

QLQLQESGPGLVKPSETLSLTCAVSGGSISGYYWSWIRQPPGKGPEWIGFIDGNTVGTNYNPSLKSRVTLSKDTSKNQFSLKVSSVTAADTAVYYCARKPLRRYFWFDVWGPGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEIKT

来源 Source

来源生物 organism	Macaca fascicularis
NCBI Class编号 ncbi_taxonomy_id	9541
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Cy137C02 Fab light chain
Molecular weight formula_weight	22806.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,L

QSVLTQPPSVSGDPGQRVTISCTGSSSNIGAGYYVYWYQQFPGTAPKLLIYQDNKRPSGVSDRFSGSKSGTSASLTITGLQPGDEADYYCSAWDSSLSAVMFGRGTRLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVEVAWKADGSAVNAGVETTKPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPAE

来源 Source

来源生物 organism	Macaca fascicularis
NCBI Class编号 ncbi_taxonomy_id	9541
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein gp350
Molecular weight formula_weight	46895.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G

MEAALLVCQYTIQSLIHLTGEDPGFFNVEIPEFPFYPTCNVCTADVNVTINFDVGGKKHQLDLDFGQLTPHTKAVYQPRGAFGGSENATNLFLLELLGAGELALTMRSKKLPINVTTGEEQQVSLESVDVYFQDVFGTMWCHHAEMQNPVYLIPETVPYIKWDNCNSTNITAVVRAQGLDVTLPLSLPTSAQDSNFSVKTEMLGNEIDIECIMEDGEISQVLPGDNKFNITCSGYESHVPSGGILTSTSPVATPIPGTGYAYSLRLTPRPVSRFLGNNSILYVFYSGNGPKASGGDYCIQSNIVFSDEIPASQDMPTNTTDITYVGDNATYSVPMVTSEDANSPNVTVTAFWAWPNNTETDFKCKWTLTSGTPSGCENISGAFASNRTFDITVSGLGTAPKTLIITRTATNATTTTHKVIFSKAPHHHHHH

来源 Source

来源生物 organism	Human herpesvirus 4
通用名 common_name	Epstein-Barr virus
NCBI Class编号 ncbi_taxonomy_id	10377
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	17

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

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8. Citations (1)

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Unit-cell length a length_a	69.047 Å
Unit-cell length b length_b	71.377 Å
Unit-cell length c length_c	395.083 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.760 Å
Low-resolution limit resolution_low	71.380 Å
R factor r_factor	0.2480
R_work r_work	0.2455
R_free r_free	0.2949

fit	/app/data/saxs_computation/si/8sic/8sic.fit
pddf	/app/data/pr_computation/si/8sic/8sic.pr.out
profile	/app/data/saxs_computation/si/8sic/8sic.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Envelope glycoprotein gp350

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)