SAXSdb — 9ma7

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

Envelope glycoprotein GP350

human gammaherpesvirus 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 × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain A； UniProt 1–470	Not recorded	1H5 heavy chain no-CH2CH3 × 1 1H5 light chain × 1 1A12 heavy chain no-CH2CH3 × 1 1A12 light chain × 1 2E9 heavy chain no-CH2CH3 × 1 2E9 light chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 3.14 Å

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 9MA7	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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 oligomeric state 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

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 A； PDBConstruct 1–470； UniProt 1–470

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	9ma7
Deposition date deposition_date	2025-03-14
Structure title title	Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9
Keywords keywords	;Envelope glycoprotein GP350, Membrane antigen (MA), neutralizing antibody, 1A22, 1E5, 2E9, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex ;; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	40.24 Å
Radius of gyration Rg (electron density) rg_electron	40.11 Å
Forward intensity I(0) i0	225051000.00
Molecular weight molecular_weight	119750.0 kDa
Excluded volume excluded_volume	148770 Å³
Envelope volume envelope_volume	206030 Å³
Hydration-shell volume shell_volume	44957 Å³
Envelope diameter envelope_diameter	135.3 Å
Shell Rg shell_rg	43.44 Å
Envelope Rg envelope_rg	39.42 Å
Shape Rg shape_rg	40.08 Å
Total Rg total_rg	40.40 Å
Total atoms total_atoms	8435
Residues n_residues	1111
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	132.9 Å
Rg (real space) rg_real	40.27 Å
Rg uncertainty (real space) rg_real_error	1.34 Å
I(0) (real space) i0_real	2.2510e+08
I(0) uncertainty (real space) i0_real_error	4.0270e+06
Rg (reciprocal space) rg_reciprocal	40.24 Å
I(0) (reciprocal space) i0_reciprocal	225000000.0000
Solution quality estimate total_estimate	0.8893
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.9 Å
Skewness Skewness skewness	0.229
Kurtosis Kurtosis kurtosis	-0.707
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20260000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.897

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein GP350
Molecular weight formula_weight	51454.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8435

MEAALLVCQYTIQSLIHLTGEDPGFFNVEIPEFPFYPTCNVCTADVNVTINFDVGGKKHQLDLDFGQLTPHTKAVYQPRGAFGGSENATNLFLLELLGAGELALTMRSKKLPINVTTGEEQQVSLESVDVYFQDVFGTMWCHHAEMQNPVYLIPETVPYIKWDNCNSTNITAVVRAQGLDVTLPLSLPTSAQDSNFSVKTQMLGNEIDIECIMEDGEISQVLPGDNKFNITCSGYESHVPSGGILTSTSPVATPIPGTGYAYSLRLTPRPVSRFLGNNSILYVFYSGNGPKASGGDYCIQSNIVFSDEIPASQDMPTNTTDITYVGDNATYSVPMVTSEDANSPNVTVTAFWAWPNNTETDFKCKWTLTSGTPSGCENISGAFASNRTFDITVSGLGTAPKTLIITRTATNATTTTHKVIFSKAPESTTTSPTLNTTGFADPNTTTGLPSSTHVPTNLTAPASTGPTVSTGSHHHHHH

来源 Source

来源生物 organism	human gammaherpesvirus 4
通用名 common_name	Epstein-Barr virus
NCBI Class编号 ncbi_taxonomy_id	10376
宿主生物 host_organism	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 2 Entity 2 polymer

Description description	1H5 heavy chain no-CH2CH3
Molecular weight formula_weight	26271.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGWSCIILFLVATATGVHSQVQLVQSGAEVRKPGSSVKVSCEFSGGPFKNSAFSWVRQAPGQGPEWMGGIIPPFVRGKYAQGFQGRVTITADEHLSTTYMELTGLRSDDTAVYYCARGPSSGNYNYYYGMDVWGQGTPVSVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 3 Entity 3 polymer

Description description	1H5 light chain
Molecular weight formula_weight	24930.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGWSCIILFLVATATGSWAQSVLTQPPSASGTPGQRVTISCSGSSSNIGSNYVYWYQQLPGTAPKLLIYRNNQRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCAAWDDSLSGWVFGGGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 4 Entity 4 polymer

Description description	1A12 heavy chain no-CH2CH3
Molecular weight formula_weight	26621.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGWSCIILFLVATATGVHSQVQLVQSGAEVKKPGASMKVSCKASGYTFAGYYIHWVRQAPGQGLEWMGSINPNSGKATYAQRFHGRVTLTREMSINTAYMELTRLTSDDTAIYYCARDATYSTSFSPRWFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 5 Entity 5 polymer

Description description	1A12 light chain
Molecular weight formula_weight	24901.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MGWSCIILFLVATATGSWAEIVLTQSPGTLSLSPGERATLSCRASQSISSNSLAWYQQRPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPRTFGPGTKVDIKGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 6 Entity 6 polymer

Description description	2E9 heavy chain no-CH2CH3
Molecular weight formula_weight	25906.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MGWSCIILFLVATATGVHSQVQLQESGPGLVKPSETLSLICTVSGYSISSGYNWGWIRQPPGKGLEWIGSINHSGSTYYNPSLKSRVTTSVDTSTNQFSLKLSSVTAADTAVYYCARDSIMIGYRGLDYWGQGTLVSVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 7 Entity 7 polymer

Description description	2E9 light chain
Molecular weight formula_weight	24774.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MGWSCIILFLVATATGSWAQSVVTQPPSVSAAPGQKVTISCSGSSSNIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAYVFGTGTQLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Mammalian expression vector Flag-MCS-pcDNA3.1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.140 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.14 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	673171

fit	/app/data/saxs_computation/ma/9ma7/9ma7.fit
pddf	/app/data/pr_computation/ma/9ma7/9ma7.pr.out
profile	/app/data/saxs_computation/ma/9ma7/9ma7.dat

Cryo-EM structure of EBV gp350 D123 in complex with neutralizing antibody 1A12 and 1H5 and non-neutralizing antibody 2E9

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

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Entity 2 Entity 2 polymer

Polymer Polymer

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Entity 3 Entity 3 polymer

Polymer Polymer

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Entity 4 Entity 4 polymer

Polymer Polymer

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Entity 5 Entity 5 polymer

Polymer Polymer

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Entity 6 Entity 6 polymer

Polymer Polymer

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Entity 7 Entity 7 polymer

Polymer Polymer

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8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)