8tnt

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2

Method: X-RAY DIFFRACTION

▼

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

Envelope glycoprotein H

Epstein-Barr virus

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） Glycoprotein 42 × 1 （P03205） 769C2 light chain × 1 769C2 heavy chain × 1 F-2-1 light chain × 1 F-2-1 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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 1–656； UniProt 19–674

Envelope glycoprotein L

Epstein-Barr virus

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） Glycoprotein 42 × 1 （P03205） 769C2 light chain × 1 769C2 heavy chain × 1 F-2-1 light chain × 1 F-2-1 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	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 1–112； UniProt 24–135

Glycoprotein 42

Epstein-Barr virus

UniProt P03205

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） 769C2 light chain × 1 769C2 heavy chain × 1 F-2-1 light chain × 1 F-2-1 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GP42_EBVB9
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–191； UniProt 33–223

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8tnt
Deposition date deposition_date	2023-08-02
Structure title title	Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2
Keywords keywords	Viral Protein, Antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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.

8tnt__assembly_1__model_1

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

Download this curve (.dat)

8tnt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8tnt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	60.80 Å
Rg (electron density)	62.02 Å
Total Rg	61.69 Å
Atom count	13731
Residues	1810
Excluded volume	244100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8tnt__assembly_1__model_1`	heptameric （7）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	72687.4 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	13731

SLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

Source Source

Source organism organism	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	12475.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGLNVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHR

Source Source

Source organism organism	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Glycoprotein 42
Molecular weight formula_weight	21626.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GGGRVAAAAITWVPKPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHWTPTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSNS

Source Source

Source organism organism	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10376
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	769C2 light chain
Molecular weight formula_weight	22842.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

QSVLTQPASVSGSLGQSVTISCTGTSSDVGGYDYVSWYQQHPGKALKLMIFEVNNRPSGVSTRFSGSKSGNTASLTISGLQAEDEADYYCNSYSTTTTWVFGGGTSLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	769C2 heavy chain
Molecular weight formula_weight	24670.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

EVQLVESGGGLVKPGGSLRLSCAASGFTFSTYAMDWVRQAPGKGLEWVSLISSRSSNIYYSDSVKGRFTISRDNAKNSLFLQMNSLRAEDTAVYYCAREAGGFHSHFDMWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	F-2-1 light chain
Molecular weight formula_weight	23723.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

DIVLTQSPASLAVSLGQRATISCRASKSVSTSGYSYMHWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSGTDFTLNIHPVEEEDAATYYCLHSRDLPPTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 7 Entity 7 polymer

Description description	F-2-1 heavy chain
Molecular weight formula_weight	24759.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

EVKLLESGGGLVQPGGSLKLSCAASGFDFSRYWMSWVRQAPGKGLEWIGEINPDSSTINYTSSLKDKFIISRDNAKNTLYLQMSKVRSEDTALYYCARQGDWWYFDVWGAGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
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	2

▶

Unit-cell length a length_a	117.317 Å
Unit-cell length b length_b	85.172 Å
Unit-cell length c length_c	119.714 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.09 °
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	3.150 Å
Low-resolution limit resolution_low	46.320 Å
R factor r_factor	0.2562
R_work r_work	0.2545
R_free r_free	0.2866

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with antibodies F-2-1 and 769C2

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

Glycoprotein 42

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

8tnt__assembly_1__model_1

8tnt__assembly_1__model_1 | I(q)

8tnt__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

7. Citations (1)