SAXSdb — 8khr

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

Soluble gp42

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	2C1 heavy chain × 1 2C1 light chain × 1 Envelope glycoprotein H × 1 （A0A0C7TVV8） Envelope glycoprotein L × 1 （A0A0C7TRA4）	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	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–190； UniProt 34–223

Envelope glycoprotein H

Epstein-Barr virus (strain GD1)

UniProt A0A0C7TVV8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Soluble gp42 × 1 （P0C6Z5） 2C1 heavy chain × 1 2C1 light chain × 1 Envelope glycoprotein L × 1 （A0A0C7TRA4）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0C7TVV8_EBVG
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–655； UniProt 20–674

Envelope glycoprotein L

Epstein-Barr virus (strain GD1)

UniProt A0A0C7TRA4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Soluble gp42 × 1 （P0C6Z5） 2C1 heavy chain × 1 2C1 light chain × 1 Envelope glycoprotein H × 1 （A0A0C7TVV8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0C7TRA4_EBVG
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain B； PDBConstruct 1–107； UniProt 27–133

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	8khr
Deposition date deposition_date	2023-08-22
Structure title title	Cryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1
Keywords keywords	Human gammaherpesvirus 4, Neutralizing antibody, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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.

8khr__assembly_1__model_1

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

Download this curve (.dat)

8khr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8khr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.22 Å
Rg (electron density)	39.89 Å
Total Rg	40.09 Å
Atom count	8320
Residues	1138
Excluded volume	147680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8khr__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	Soluble gp42
Molecular weight formula_weight	22398.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	8320

GGRVAAAAITWVPKPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHWTPTLHTFQVPQNYTKANCTYCNTREYTFSYKGCCFYFTKKKHTWNGCFQACAELYPCTYFYGPTPDILPVVTRNLNAIESLWVGVYRVGEGNWTSLDGGTFKVYQIFGSHCTYVSKFSTVPVSHHECSFLKPCLCVSQRSNSHHHHHH

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 2 Entity 2 polymer

Description description	2C1 heavy chain
Molecular weight formula_weight	11978.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QLVQSGAEVKKPGSSVKVSCRASGGTFDTYAISWVRQAPGHGLEWMGGIIPVSGTANYAQKFQGRVTITADESTGTAYMDLSSLRSEDTAVYYCARVPDYGTNTPFDYWGQ

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 3 Entity 3 polymer

Description description	2C1 light chain
Molecular weight formula_weight	11849.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIRLTQSPSSLPASVGDRVTITCRASQDIATYLAWYQQKPGRAPNLLIYATSTLQSGVPPRFSGSRSGTDFTLTISSLQPEDFATYYCQQLRTYPITFGQGTRLEIK

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 4 Entity 4 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	72600.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

LSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLY

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 5 Entity 5 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	11759.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGLNVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAW

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

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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	3.25 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	227428

Cryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1

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

Soluble gp42

State in the Current Structure

Other States of the Same Protein in the Database

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8khr__assembly_1__model_1

8khr__assembly_1__model_1 | I(q)

8khr__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

7. Citations (1)

Cryo-EM structure of EBV gH/gL-gp42 in complex with fab 2C1

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

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8khr__assembly_1__model_1

8khr__assembly_1__model_1 | I(q)

8khr__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

7. Citations (1)