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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	3A3 heavy chain × 1 3A3 light chain × 1 3A5 light chain × 1 3A5 heavy chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

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. 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.

7fbi__assembly_1__model_1

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

Download this curve (.dat)

7fbi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7fbi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.67 Å
Rg (electron density)	61.75 Å
Total Rg	61.54 Å
Atom count	7777
Residues	1005
Excluded volume	137780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7fbi__assembly_1__model_1`	pentameric （5）	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 (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

Source Source

Source organism organism	Oryctolagus cuniculus
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism 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

Source Source

Source organism organism	Oryctolagus cuniculus
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism 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

Source Source

Source organism organism	Epstein-Barr virus (strain GD1)
Common name common_name	HHV-4, Human herpesvirus 4
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism 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

Source Source

Source organism organism	Oryctolagus cuniculus
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism 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

Source Source

Source organism organism	Oryctolagus cuniculus
NCBI taxonomy ID ncbi_taxonomy_id	9986
Host organism host_organism	Homo sapiens

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6. 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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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Method resolution_method	—
颗粒数 num_particles	367966

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7fbi__assembly_1__model_1

7fbi__assembly_1__model_1 | I(q)

7fbi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7fbi__assembly_1__model_1

7fbi__assembly_1__model_1 | I(q)

7fbi__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)