7s1b

Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with human neutralizing antibodies 769C2 and 770F7

Method: X-RAY DIFFRACTION

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

Envelope glycoprotein H

Human gammaherpesvirus 4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Envelope glycoprotein L × 1 （P03212） 770F7 Fab heavy chain × 1 770F7 Fab light chain × 1 769C2 Fab heavy chain × 1 769C2 Fab light chain × 1 Soluble gp42 × 1 （P0C6Z5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GH_EBVB9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–657； UniProt 18–674

Envelope glycoprotein L

Human gammaherpesvirus 4

UniProt P03212

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Envelope glycoprotein H × 1 （P03231） 770F7 Fab heavy chain × 1 770F7 Fab light chain × 1 769C2 Fab heavy chain × 1 769C2 Fab light chain × 1 Soluble gp42 × 1 （P0C6Z5） 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GL_EBVB9
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–114； UniProt 24–137

Soluble gp42

Human gammaherpesvirus 4

UniProt P0C6Z5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Envelope glycoprotein H × 1 （P03231） Envelope glycoprotein L × 1 （P03212） 770F7 Fab heavy chain × 1 770F7 Fab light chain × 1 769C2 Fab heavy chain × 1 769C2 Fab light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GP42_EBVG
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain C； PDBConstruct 1–33； UniProt 47–79

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	7s1b
Deposition date deposition_date	2021-09-02
Structure title title	Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with human neutralizing antibodies 769C2 and 770F7
Keywords keywords	Antibody, Fab, IMMUNE SYSTEM, gH/gL, Epstein-Barr virus, herpesvirus; 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.

7s1b__assembly_1__model_1

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

Download this curve (.dat)

7s1b__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7s1b__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	55.69 Å
Rg (electron density)	56.68 Å
Total Rg	56.36 Å
Atom count	12257
Residues	1595
Excluded volume	218330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7s1b__assembly_1__model_1`	heptameric （7）	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	Envelope glycoprotein H
Molecular weight formula_weight	72838.5 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	12257

ASLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

Source Source

Source organism organism	Human gammaherpesvirus 4
Common name common_name	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	12503.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

WAYPCCHVTQLAAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGLNVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHRGG

Source Source

Source organism organism	Human gammaherpesvirus 4
Common name common_name	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	770F7 Fab heavy chain
Molecular weight formula_weight	24626.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQFQQWGAGLLKPSETLSLTCGVYGGSLSGYYWSWIRQTPGKGLEWIGEINHTGTTNYNPSLKSRVTMSVDTSKNQFSLKMSSLTAADTALYYCAREGAPRWALKRPSNWFDPWGQGTLVTVSSASTKGPSVFPLAPSSASTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	770F7 Fab light chain
Molecular weight formula_weight	23398.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

EIVLTQSPVSLSLSPGERATLSCRASQSLSSTYLAWYQQIPGQAPRLLIYGASSRAAGIPDRFSGGGSGTDFTLTISRLEPEDFAVYYCQQYGSSPRSFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	769C2 Fab heavy chain
Molecular weight formula_weight	23840.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

EVQLVESGGGLVKPGGSLRLSCAASGFTFSTYAMDWVRQAPGKGLEWVSLISSRSSNIYYSDSVKGNFTISRDNAKNSLFLQMNSLRAEDTAVYYCAREAGGFHSHFDMWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	769C2 Fab light chain
Molecular weight formula_weight	22782.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

QSVLTQPASVSGSLGQSVTISCTGTSSDVGGYDYVSWYQQHPGKNPKLMIFEVNNRPSGVSTRFSGSKSGNTASLTISGLQAEDEADYYCNSYSTTTTWVFGGGTSLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	Soluble gp42
Molecular weight formula_weight	3766.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

KPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLP

Source Source

Source organism organism	Human gammaherpesvirus 4
Common name common_name	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	Homo sapiens

Entity 8 Entity 8 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	4

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	7s1bH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s1bH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s1bL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s1bL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7s1bY01
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	89.326 Å
Unit-cell length b length_b	107.703 Å
Unit-cell length c length_c	110.650 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.030 Å
Low-resolution limit resolution_low	71.320 Å
R factor r_factor	0.2436
R_work r_work	0.2409
R_free r_free	0.2880

Crystal structure of Epstein-Barr virus glycoproteins gH/gL/gp42-peptide in complex with human neutralizing antibodies 769C2 and 770F7

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

Envelope glycoprotein H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Envelope glycoprotein L

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Soluble gp42

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

7s1b__assembly_1__model_1

7s1b__assembly_1__model_1 | I(q)

7s1b__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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)