8tnn

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10

Method: X-RAY DIFFRACTION

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

Envelope glycoprotein H

Human herpesvirus 4 strain B95-8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Envelope glycoprotein L × 1 （P03212） Glycoprotein 42 × 1 （P03205） A10 light chain × 1 A10 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count
2	Other combination	Heteromer	Protein 5 其他Polymer 1	Envelope glycoprotein L × 1 （P03212） Glycoprotein 42 × 1 （P03205） A10 light chain × 1 A10 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	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 1–658； UniProt 17–674 Author chain D； PDBConstruct 1–658； UniProt 17–674

Envelope glycoprotein L

Human herpesvirus 4 strain B95-8

UniProt P03212

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Envelope glycoprotein H × 1 （P03231） Glycoprotein 42 × 1 （P03205） A10 light chain × 1 A10 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count
2	Other combination	Heteromer	Protein 5 其他Polymer 1	Envelope glycoprotein H × 1 （P03231） Glycoprotein 42 × 1 （P03205） A10 light chain × 1 A10 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	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 Author chain E； PDBConstruct 1–112； UniProt 24–135

Glycoprotein 42

Human herpesvirus 4 strain B95-8

UniProt P03205

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 5 其他Polymer 1	Envelope glycoprotein H × 1 （P03231） Envelope glycoprotein L × 1 （P03212） A10 light chain × 1 A10 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count
2	Other combination	Heteromer	Protein 5 其他Polymer 1	Envelope glycoprotein H × 1 （P03231） Envelope glycoprotein L × 1 （P03212） A10 light chain × 1 A10 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	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 Author chain F； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8tnn
Deposition date deposition_date	2023-08-02
Structure title title	Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10
Keywords keywords	Viral Protein, Antibody, IMMUNE SYSTEM; 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.

8tnn__assembly_1__model_1

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

Download this curve (.dat)

8tnn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8tnn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.63 Å
Rg (electron density)	47.82 Å
Total Rg	47.76 Å
Atom count	10274
Residues	1359
Excluded volume	182210 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8tnn__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8tnn__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	72829.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	20293

AASLSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

Source Source

Source organism organism	Human herpesvirus 4 strain B95-8
Common name common_name	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10377
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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGLNVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHR

Source Source

Source organism organism	Human herpesvirus 4 strain B95-8
Common name common_name	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10377
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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

GGGRVAAAAITWVPKPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHWTPTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSNS

Source Source

Source organism organism	Human herpesvirus 4 strain B95-8
Common name common_name	Epstein-Barr virus
NCBI taxonomy ID ncbi_taxonomy_id	10377
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	A10 light chain
Molecular weight formula_weight	22654.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,I

NSYELTQPPSVSAASGQTARITCGGDNIGSKNVQWYQQKPAQAPVLVIYADSKRPSGVPERFSGSNSGNTATLTISGVEAGDEADYYCQVWDRSSNIFGVGTRLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source Source

Source organism organism	Macaca fascicularis
NCBI taxonomy ID ncbi_taxonomy_id	9541
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	A10 heavy chain
Molecular weight formula_weight	25372.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,J

NSQVQLQESGPGLVKPSQTLSLTCAISGDSVSSNSATWNWIRQSPSRGLEWLGRTYYRSKWYYDYAQSVQNRISINPDTSKNQFSLQLNSVTPEDMAVYYCARGDFDAFDFWGQGLRVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Source Source

Source organism organism	Macaca fascicularis
NCBI taxonomy ID ncbi_taxonomy_id	9541
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 7 Entity 7 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	8

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Unit-cell length a length_a	88.750 Å
Unit-cell length b length_b	138.960 Å
Unit-cell length c length_c	316.264 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.360 Å
Low-resolution limit resolution_low	45.830 Å
R factor r_factor	0.2360
R_work r_work	0.2340
R_free r_free	0.2810

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10

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

Envelope glycoprotein L

State in the Current Structure

Other States of the Same Protein in the Database

Glycoprotein 42

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

8tnn__assembly_1__model_1

8tnn__assembly_1__model_1 | I(q)

8tnn__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 (7)

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 branched

Entity 7 Entity 7 non-polymer

7. Citations (1)

Crystal structure of Epstein-Barr virus gH/gL/gp42 in complex with gp42 antibody A10

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

8tnn__assembly_1__model_1

8tnn__assembly_1__model_1 | I(q)

8tnn__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 (7)

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 branched

Entity 7 Entity 7 non-polymer

7. Citations (1)