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

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 1	Cy651H02 Fab light chain × 1 Cy651H02 Fab heavy chain × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1,2-ETHANEDIOL × 23 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GP350_EBVB9
Isoform	—
PDB entities	3
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8sgn
Deposition date deposition_date	2023-04-12
Structure title title	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
Keywords keywords	Epstein-Barr virus, immune system, monoclonal antibody, macaques, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8sgn__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8sgn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8sgn__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	36.23 Å
Rg (electron density)	36.39 Å
Total Rg	36.66 Å
Atom count	6590
Residues	837
Excluded volume	116990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8sgn__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Cy651H02 Fab light chain
Molecular weight formula_weight	22490.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	6884

QAALTQPPSVSGSPGQSVTISCTGTSSDIGGYNYVSWYQQHPGKAPKVMIYEVSKRPSGVSDRFSGSKSGNIASLTISGLQAEDEADYYCSSYAGSNTFLFGGGTRLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVEVAWKADGSAVNAGVETTKPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPAE

Source Source

Source organism organism	Macaca fascicularis
NCBI taxonomy ID ncbi_taxonomy_id	9541
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Cy651H02 Fab heavy chain
Molecular weight formula_weight	23765.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QLQLQESGPGVVKPSETLSLTCTISGGSFSTYYWTWIRQPPGKGLEWVGYIGNGGRSLNYNPSLKSRITLSVDASKNQFSLKVTSVTAADTAVYYCGRARGLRGNWFDVWGPGVLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTC

Source Source

Source organism organism	Macaca fascicularis
NCBI taxonomy ID ncbi_taxonomy_id	9541
Host organism 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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MEAALLVCQYTIQSLIHLTGEDPGFFNVEIPEFPFYPTCNVCTADVNVTINFDVGGKKHQLDLDFGQLTPHTKAVYQPRGAFGGSENATNLFLLELLGAGELALTMRSKKLPINVTTGEEQQVSLESVDVYFQDVFGTMWCHHAEMQNPVYLIPETVPYIKWDNCNSTNITAVVRAQGLDVTLPLSLPTSAQDSNFSVKTEMLGNEIDIECIMEDGEISQVLPGDNKFNITCSGYESHVPSGGILTSTSPVATPIPGTGYAYSLRLTPRPVSRFLGNNSILYVFYSGNGPKASGGDYCIQSNIVFSDEIPASQDMPTNTTDITYVGDNATYSVPMVTSEDANSPNVTVTAFWAWPNNTETDFKCKWTLTSGTPSGCENISGAFASNRTFDITVSGLGTAPKTLIITRTATNATTTTHKVIFSKAPHHHHHH

Source Source

Source organism organism	Human herpesvirus 4
Common name common_name	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10377
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 branched

Description description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	367.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	23

Entity 6 Entity 6 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 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	9

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	294

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Unit-cell length a length_a	139.148 Å
Unit-cell length b length_b	139.148 Å
Unit-cell length c length_c	172.337 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	32.920 Å
R factor r_factor	0.1954
R_work r_work	0.1931
R_free r_free	0.2366

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8sgn__assembly_1__model_1

8sgn__assembly_1__model_1 | I(q)

8sgn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

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

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8sgn__assembly_1__model_1

8sgn__assembly_1__model_1 | I(q)

8sgn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)