3nw8

Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH

Method: X-RAY DIFFRACTION

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

Envelope glycoprotein B

Human herpesvirus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MESO-ERYTHRITOL × 6 SODIUM ION × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-glucopyranose × 12 MESO-ERYTHRITOL × 12 CHLORIDE ION × 3 water × 3	Consistent with protein count
3	Other combination	Homooligomer	Protein 3 其他Polymer 3	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MESO-ERYTHRITOL × 9 SODIUM ION × 6 water × 3	Consistent with protein count
4	Other combination	Homooligomer	Protein 3 其他Polymer 3	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 MESO-ERYTHRITOL × 3 SODIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GB_HHV1K
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–703； UniProt 30–730 Author chain B； PDBConstruct 3–703； UniProt 30–730 Author chain C； PDBConstruct 3–703； UniProt 30–730 Author chain D； PDBConstruct 3–703； UniProt 30–730

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	3nw8
Deposition date deposition_date	2010-07-09
Structure title title	Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH
Keywords keywords	ENVELOPE GLYCOPROTEIN, MEMBRANE FUSION, VIRAL PROTEIN, Glycoprotein B, Herpesvirus 1, HSV-1, Membrane; VIRAL PROTEIN
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.

3nw8__assembly_1__model_1

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

Download this curve (.dat)

3nw8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nw8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.44 Å
Rg (electron density)	50.75 Å
Total Rg	50.70 Å
Atom count	14748
Residues	1818
Excluded volume	259630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nw8__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3nw8__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3nw8__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3nw8__assembly_4__model_1`	trimeric （3）	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 B
Molecular weight formula_weight	78797.2 kDa
Mutation mutation	Y179S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A,C,D
Atom count atom_count	19958

DPAAPTSPGTPGVAAATQAANGGPATPAPPALGAAPTGDPKPKKNKKPKNPTPPRPAGDNATVAAGHATLREHLRDIKAENTDANFYVCPPPTGATVVQFEQPRRCPTRPEGQNYTEGIAVVFKENIAPYKFKATMYYKDVTVSQVWFGHRSSQFMGIFEDRAPVPFEEVIDKINAKGVCRSTAKYVRNNLETTAFHRDDHETDMELKPANAATRTSRGWHTTDLKYNPSRVEAFHRYGTTVNCIVEEVDARSVYPYDEFVLATGDFVYMSPFYGYREGSHTEHTSYAADRFKQVDGFYARDLTTKARATAPTTRNLLTTPKFTVAWDWVPKRPSVCTMTKWQEVDEMLRSEYGGSFRFSSDAISTTFTTNLTEYPLSRVDLGDCIGKDARDAMDRIFARRYNATHIKVGQPQYYLANGGFLIAYQPLLSNTLAELYVREHLREQSRKPPNPTPPPPGASANASVERIKTTSSIEFARLQFTYNHIQRHVNDMLGRVAIAWCELQNHELTLWNEARKLNPNAIASVTVGRRVSARMLGDVMAVSTCVPVAADNVIVQNSMRISSRPGACYSRPLVSFRYEDQGPLVEGQLGENNELRLTRDAIEPCTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTVSTFIDLNITMLEDHEFVPLEVYTRHEIKDSGLLDYTEVQRRNQLHDLRFADIDTVIHADANAA

Source Source

Source organism organism	Human herpesvirus 1
Common name common_name	HHV-1
NCBI taxonomy ID ncbi_taxonomy_id	10306
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 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	11

Entity 4 Entity 4 non-polymer

Description description	MESO-ERYTHRITOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3nw8a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamily	e.76.1 — Viral glycoprotein ectodomain-like
Family Family family	e.76.1.1 — Glycoprotein B-like

Domain ID domain_id	d3nw8b_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamily	e.76.1 — Viral glycoprotein ectodomain-like
Family Family family	e.76.1.1 — Glycoprotein B-like

Domain ID domain_id	d3nw8c_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamily	e.76.1 — Viral glycoprotein ectodomain-like
Family Family family	e.76.1.1 — Glycoprotein B-like

Domain ID domain_id	d3nw8d_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.76 — Viral glycoprotein ectodomain-like
Superfamily Superfamily superfamily	e.76.1 — Viral glycoprotein ectodomain-like
Family Family family	e.76.1.1 — Glycoprotein B-like

CATH v4.4 (16 domains)

Domain ID domain_id	3nw8A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1230 —

Domain ID domain_id	3nw8A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1890 —

Domain ID domain_id	3nw8A03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3nw8A05
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3280 —

Domain ID domain_id	3nw8B01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1230 —

Domain ID domain_id	3nw8B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1890 —

Domain ID domain_id	3nw8B03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3nw8B05
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3280 —

Domain ID domain_id	3nw8C01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1230 —

Domain ID domain_id	3nw8C02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1890 —

Domain ID domain_id	3nw8C03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3nw8C05
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3280 —

Domain ID domain_id	3nw8D01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1230 —

Domain ID domain_id	3nw8D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1890 —

Domain ID domain_id	3nw8D03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3nw8D05
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3280 —

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Unit-cell length a length_a	117.985 Å
Unit-cell length b length_b	117.985 Å
Unit-cell length c length_c	321.537 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	2.759 Å
Low-resolution limit resolution_low	48.690 Å
R factor r_factor	0.2037
R_work r_work	0.2015
R_free r_free	0.2425

Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH

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

Envelope glycoprotein B

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

3nw8__assembly_1__model_1

3nw8__assembly_1__model_1 | I(q)

3nw8__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Glycoprotein B from Herpes simplex virus type 1, Y179S mutant, high-pH

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

Envelope glycoprotein B

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

3nw8__assembly_1__model_1

3nw8__assembly_1__model_1 | I(q)

3nw8__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (4 domains)

CATH v4.4 (16 domains)

7. Citations (1)