1zv8

A structure-based mechanism of SARS virus membrane fusion

Method: X-RAY DIFFRACTION

▼

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

E2 glycoprotein

SARS coronavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	SODIUM ION × 2 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	SODIUM ION × 4 CACODYLATE ION × 1 ZINC ION × 2 ACETATE ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGL2_CVHSA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–50； UniProt 901–950 Author chain C； PDBConstruct 1–50； UniProt 901–950 Author chain E； PDBConstruct 1–50； UniProt 901–950 Author chain G； PDBConstruct 1–50； UniProt 901–950 Author chain I； PDBConstruct 1–50； UniProt 901–950 Author chain K； PDBConstruct 1–50； UniProt 901–950 Author chain B； PDBConstruct 1–36； UniProt 1150–1185 Author chain D； PDBConstruct 1–36； UniProt 1150–1185 Author chain F； PDBConstruct 1–36； UniProt 1150–1185 Author chain H； PDBConstruct 1–36； UniProt 1150–1185 Author chain J； PDBConstruct 1–36； UniProt 1150–1185 Author chain L； PDBConstruct 1–36； UniProt 1150–1185

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	1zv8
Deposition date deposition_date	2005-06-01
Structure title title	A structure-based mechanism of SARS virus membrane fusion
Keywords keywords	SARS coronavirus, membrane fusion, S2, virus entry, coiled coils, conformational change, VIRAL PROTEIN; VIRAL PROTEIN
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.

1zv8__assembly_1__model_1

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

Download this curve (.dat)

1zv8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zv8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.44 Å
Rg (electron density)	21.05 Å
Total Rg	21.93 Å
Atom count	1774
Residues	230
Excluded volume	31674 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zv8__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zv8__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	E2 glycoprotein
Molecular weight formula_weight	5433.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	3861

NQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSS

Source Source

Source organism organism	SARS coronavirus
NCBI taxonomy ID ncbi_taxonomy_id	227859
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	E2 glycoprotein
Molecular weight formula_weight	4011.5 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

DISGINASVVNIQKEIDRLNEVAKNLNESLIDLQEL

Source Source

Source organism organism	SARS coronavirus
NCBI taxonomy ID ncbi_taxonomy_id	227859
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 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	176

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1zv8.1
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.3 — Coronavirus S2 glycoprotein
Family Family family	h.3.3.1 — Coronavirus spike glycoprotein S2 fragments

Domain ID domain_id	d1zv8.2
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.3 — Coronavirus S2 glycoprotein
Family Family family	h.3.3.1 — Coronavirus spike glycoprotein S2 fragments

Domain ID domain_id	d1zv8.3
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.3 — Coronavirus S2 glycoprotein
Family Family family	h.3.3.1 — Coronavirus spike glycoprotein S2 fragments

Domain ID domain_id	d1zv8.4
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.3 — Coronavirus S2 glycoprotein
Family Family family	h.3.3.1 — Coronavirus spike glycoprotein S2 fragments

Domain ID domain_id	d1zv8.5
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.3 — Coronavirus S2 glycoprotein
Family Family family	h.3.3.1 — Coronavirus spike glycoprotein S2 fragments

Domain ID domain_id	d1zv8.6
Class class	h — Coiled coil proteins
Fold Fold fold	h.3 — Stalk segment of viral fusion proteins
Superfamily Superfamily superfamily	h.3.3 — Coronavirus S2 glycoprotein
Family Family family	h.3.3.1 — Coronavirus spike glycoprotein S2 fragments

CATH v4.4 (6 domains)

Domain ID domain_id	1zv8A00
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	300 —

Domain ID domain_id	1zv8C00
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	300 —

Domain ID domain_id	1zv8E00
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	300 —

Domain ID domain_id	1zv8G00
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	300 —

Domain ID domain_id	1zv8I00
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	300 —

Domain ID domain_id	1zv8K00
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	300 —

▶

Unit-cell length a length_a	31.054 Å
Unit-cell length b length_b	55.565 Å
Unit-cell length c length_c	71.678 Å
Unit-cell angle α angle_alpha	81.26 °
Unit-cell angle β angle_beta	87.08 °
Unit-cell angle γ angle_gamma	84.10 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	70.710 Å
R factor r_factor	0.2070
R_work r_work	0.2032
R_free r_free	0.2743

A structure-based mechanism of SARS virus membrane fusion

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

E2 glycoprotein

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

1zv8__assembly_1__model_1

1zv8__assembly_1__model_1 | I(q)

1zv8__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 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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

A structure-based mechanism of SARS virus membrane fusion

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

E2 glycoprotein

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

1zv8__assembly_1__model_1

1zv8__assembly_1__model_1 | I(q)

1zv8__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 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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)