SAXSdb — 5w0k

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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	Protein heterocomplex	Heteromer	Protein 5	Envelope glycoprotein L × 1 （P03212） CL40 IgG heavy chain × 1 CL40 IgG light chain × 1 Glycoprotein 42 × 1 （P03205）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Envelope glycoprotein L × 1 （P03212） CL40 IgG heavy chain × 1 CL40 IgG light chain × 1 Glycoprotein 42 × 1 （P03205）	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 1–660； UniProt 20–679 Author chain C； PDBConstruct 1–660； UniProt 20–679

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	Protein heterocomplex	Heteromer	Protein 5	Envelope glycoprotein H × 1 （P03231） CL40 IgG heavy chain × 1 CL40 IgG light chain × 1 Glycoprotein 42 × 1 （P03205）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Envelope glycoprotein H × 1 （P03231） CL40 IgG heavy chain × 1 CL40 IgG light chain × 1 Glycoprotein 42 × 1 （P03205）	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 Author chain D； PDBConstruct 1–114； UniProt 24–137

Glycoprotein 42

OrganismNot specified

UniProt P03205

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Envelope glycoprotein H × 1 （P03231） Envelope glycoprotein L × 1 （P03212） CL40 IgG heavy chain × 1 CL40 IgG light chain × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Envelope glycoprotein H × 1 （P03231） Envelope glycoprotein L × 1 （P03212） CL40 IgG heavy chain × 1 CL40 IgG light chain × 1	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	5
Chains and sequence ranges	Author chain X； PDBConstruct 1–35； UniProt 47–81 Author chain Y； PDBConstruct 1–35； UniProt 47–81

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	5w0k
Deposition date deposition_date	2017-05-31
Structure title title	Crystal structure of EBV gHgL/CL40/gp42 N-domain
Keywords keywords	receptor binding, herpesvirus entry, Epstein-Barr Virus, membrane fusion, VIRAL PROTEIN, VIRAL PROTEIN-Immune system complex; VIRAL PROTEIN/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.

5w0k__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5w0k__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5w0k__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	39.35 Å
Rg (electron density)	39.01 Å
Total Rg	39.31 Å
Atom count	18484
Residues	1204
Excluded volume	166450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5w0k__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5w0k__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 (5)

Entity 1 Entity 1 polymer

Description description	Envelope glycoprotein H
Molecular weight formula_weight	73225.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	37028

LSEVKLHLDIEGHASHYTIPWTELMAKVPGLSPEALWREANVTEDLASMLNRYKLIYKTSGTLGIALAEPVDIPAVSEGSMQVDASKVHPGVISGLNSPACMLSAPLEKQLFYYIGTMLPNTRPHSYVFYQLRCHLSYVALSINGDKFQYTGAMTSKFLMGTYKRVTEKGDEHVLSLVFGKTKDLPDLRGPFSYPSLTSAQSGDYSLVIVTTFVHYANFHNYFVPNLKDMFSRAVTMTAASYARYVLQKLVLLEMKGGCREPELDTETLTTMFEVSVAFFKVGHAVGETGNGCVDLRWLAKSFFELTVLKDIIGICYGATVKGMQSYGLERLAAMLMATVKMEELGHLTTEKQEYALRLATVGYPKAGVYSGLIGGATSVLLSAYNRHPLFQPLHTVMRETLFIGSHVVLRELRLNVTTQGPNLALYQLLSTALCSALEIGEVLRGLALGTESGLFSPCYLSLRFDLTRDKLLSMAPQEATLDQAAVSNAVDGFLGRLSLEREDRDAWHLPAYKCVDRLDKVLMIIPLINVTFIISSDREVRGSALYEASTTYLSSSLFLSPVIMNKCSQGAVAGEPRQIPKIQNFTRTQKSCIFCGFALLSYDEKEGLETTTYITSQEVQNSILSSNYFDFDNLHVHYLLLTTNGTVMEIAGLYEERAH

Source Source

Source organism organism	Human herpesvirus 4 (strain B95-8)
Common name common_name	HHV-4
NCBI taxonomy ID ncbi_taxonomy_id	10377
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein L
Molecular weight formula_weight	12589.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

WAYPCCHVTQLRAQHLLALENISDIYLVSNQTCDGFSLASLNSPKNGSNQLVISRCANGLNVVSFFISILKRSSSALTGHLRELLTTLETLYGSFSVEDLFGANLNRYAWHRGG

Source Source

Source organism organism	Human herpesvirus 4 (strain B95-8)
Common name common_name	HHV-4
NCBI taxonomy ID ncbi_taxonomy_id	10377
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	CL40 IgG heavy chain
Molecular weight formula_weight	23347.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EVKLQQSGAELVMPGASVKMSCKASGYTFTDYWMHWVKQRPGQGLEWIGAIDTSDSYTSYNQKFKGKATLTVDESSSTAYMQLSSLTSEDSAVYYCARGLLPFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

Source Source

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

Entity 4 Entity 4 polymer

Description description	CL40 IgG light chain
Molecular weight formula_weight	23601.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DIVMTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAKYFCQQYNSYPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Source Source

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

Entity 5 Entity 5 polymer

Description description	Glycoprotein 42
Molecular weight formula_weight	4090.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y

KPNVEVWPVDPPPPVNFNKTAEQEYGDKEVKLPHW

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	5w0kA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	380 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Herpesvirus glycoprotein H, domain D-II

Domain ID domain_id	5w0kB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	390 — SAND domain
Homologous superfamily homologous superfamily	20 — Viral glycoprotein L

Domain ID domain_id	5w0kC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	380 — Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — Herpesvirus glycoprotein H, domain D-II

Domain ID domain_id	5w0kD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	390 — SAND domain
Homologous superfamily homologous superfamily	20 — Viral glycoprotein L

Domain ID domain_id	5w0kE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5w0kF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5w0kF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5w0kH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5w0kL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5w0kL02
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	96.380 Å
Unit-cell length b length_b	133.130 Å
Unit-cell length c length_c	254.130 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	3.100 Å
Low-resolution limit resolution_low	22.763 Å
R factor r_factor	0.2445
R_work r_work	0.2416
R_free r_free	0.2991

Crystal structure of EBV gHgL/CL40/gp42 N-domain

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

5w0k__assembly_2__model_1

5w0k__assembly_2__model_1 | I(q)

5w0k__assembly_2__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 (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

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of EBV gHgL/CL40/gp42 N-domain

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

5w0k__assembly_2__model_1

5w0k__assembly_2__model_1 | I(q)

5w0k__assembly_2__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 (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

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)