SAXSdb — 7fbi

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

Envelope glycoprotein B

Epstein-Barr virus (strain GD1)

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 22–674	Not recorded	3A3 heavy chain × 1 3A3 light chain × 1 3A5 light chain × 1 3A5 heavy chain × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 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 7FBI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8YY6 Structure of a murine monoclonal antibody Fab5 targeting Epstein-Barr virus gB Deposited 2024-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 23–683（661 aa） Chain B 23–683（661 aa） Chain C 23–683（661 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9YKA Cryo-EM structure of post-fusion EBV gB in complex with AMMO2 fab Deposited 2025-10-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–688（688 aa） Chain B 1–688（688 aa） Chain C 1–688（688 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	R4R670_EBVG
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–653； UniProt 22–674

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	7fbi
Deposition date deposition_date	2021-07-10
Structure title title	Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5
Keywords keywords	EBV, Glycoprotein B, Neutralizing antibody, Cryo-EM, VIRAL PROTEIN; VIRAL PROTEIN
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	60.67 Å
Radius of gyration Rg (electron density) rg_electron	61.75 Å
Forward intensity I(0) i0	182600000.00
Molecular weight molecular_weight	110580.0 kDa
Excluded volume excluded_volume	137780 Å³
Envelope volume envelope_volume	259790 Å³
Hydration-shell volume shell_volume	39360 Å³
Envelope diameter envelope_diameter	196.4 Å
Shell Rg shell_rg	52.73 Å
Envelope Rg envelope_rg	58.51 Å
Shape Rg shape_rg	61.71 Å
Total Rg total_rg	61.54 Å
Total atoms total_atoms	7777
Residues n_residues	1005
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	186.4 Å
Rg (real space) rg_real	61.52 Å
Rg uncertainty (real space) rg_real_error	1.98 Å
I(0) (real space) i0_real	1.8260e+08
I(0) uncertainty (real space) i0_real_error	3.8360e+06
Rg (reciprocal space) rg_reciprocal	59.83 Å
I(0) (reciprocal space) i0_reciprocal	182100000.0000
Solution quality estimate total_estimate	0.6722
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	35.8 Å
Skewness Skewness skewness	0.331
Kurtosis Kurtosis kurtosis	-1.063
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7143000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.477; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.304; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	3A3 heavy chain
Molecular weight formula_weight	11744.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	7777

QSVKESGGRLVTPGTPLTLTCTVSGFSLSSYAMSWVRQAPGKGLEYIGVIYASGSTYYASWAKGRFTISRTATTVDLKITSPTTEDTATYFCGRGVSTNMWGPGTLVTVSS

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	3A3 light chain
Molecular weight formula_weight	11572.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DLVMTQTPSSVSAAVGGTVTIKCQASQSLGGGLAWYQQKPGQRPKLLIYSASTLESGVPSRFRGSGSGTEFTLTISDLECADAATYYCQSAYGPTSNGLFNAFGGGTKVVIK

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein B
Molecular weight formula_weight	73456.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

AQTPEQPAPPATTVQPTATRQQTSFPFRVCELSSHGDLFRFSSDIQCPSFGTRENHTEGLLMVFKDNIIPYSFKVRSYTKIVTNILIYNGHRADSVTNRHEEKFSVESYETDQMDTIYQCYNAVKMTKDGLTRVYVDRDGVNITVNLKPTGGLANGVRRYASQTELYDAPGRVEATYRTRTTVNCLITDMMAKSNSPFDFFVTTTGQTVEMSPFYDGKNTETFHERADSFHVRTNYKIVDYDNRGTNPQGERRAFLDKGTYTLSWKLENRTAYCPLQHWQTFDSTIATETGKSIHFVTDEGTSSFVTNTTVGIELPDAFKCIEEQVNKTMHEKYEAVQDRYTKGQEAITYFITSGGLLLAWLPLTPRSLATVKNLTELTTPTSSPPSSPSPPAPPAARGSTSAAVLRRRRRNAGNATTPVPPAAPGKSLGTLNNPATVQIQFAYDSLRRQINRMLGDLARAWCLEQKRQNMVLRELTKINPTTVMSSIYGKAVAAKRLGDVISVSQCVPVNQATVTLRKSMRVPGSETMCYSRPLVSFSFINDTKTYEGQLGTDNEIFLTKKMTEVCQATSQYYFQSGNEIHVYNDYHHFKTIELDGIATLQTFISLNTSLIENIDFASLELYSRDEQRASNVFDLEGIFREYNFQAQNIAGL

来源 Source

来源生物 organism	Epstein-Barr virus (strain GD1)
通用名 common_name	HHV-4, Human herpesvirus 4
NCBI Class编号 ncbi_taxonomy_id	10376
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	3A5 light chain
Molecular weight formula_weight	11673.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

ALVMTQTPSSVSEPVGGTVTIKCQASQSISSYLAWYQRKPGQRPKLLIYGTSTLASGVPSRFIGSGSGTDYTLTISDLECDDAATYYCQQGFSTSNVYNSFGGGTKVDIK

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	3A5 heavy chain
Molecular weight formula_weight	12513.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

QSVKESGGRLVTPGTPLTLTCTVSGFSLSSYEMGWVRQAPGEGLEWIGTISTGGSSYYASWAKGRFTISRTSTTVDLKMTSLTTADTATYFCARGYGGYGIGAGYFNIWGPGTLVTVSS

来源 Source

来源生物 organism	Oryctolagus cuniculus
NCBI Class编号 ncbi_taxonomy_id	9986
宿主生物 host_organism	Homo sapiens

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7fbiH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7fbiL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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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	3.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	367966

fit	/app/data/saxs_computation/fb/7fbi/7fbi.fit
pddf	/app/data/pr_computation/fb/7fbi/7fbi.pr.out
profile	/app/data/saxs_computation/fb/7fbi/7fbi.dat

Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5

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

Envelope glycoprotein B

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

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 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)