1wnc

Crystal structure of the SARS-CoV Spike protein fusion core

Method: X-RAY DIFFRACTION

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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	water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	water × 3	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
Chains and sequence ranges	Author chain A； PDBConstruct 1–49； UniProt 900–948 Author chain A； PDBConstruct 71–112； UniProt 1144–1185 Author chain B； PDBConstruct 1–49； UniProt 900–948 Author chain B； PDBConstruct 71–112； UniProt 1144–1185 Author chain C； PDBConstruct 1–49； UniProt 900–948 Author chain C； PDBConstruct 71–112； UniProt 1144–1185 Author chain D； PDBConstruct 1–49； UniProt 900–948 Author chain D； PDBConstruct 71–112； UniProt 1144–1185 Author chain E； PDBConstruct 1–49； UniProt 900–948 Author chain E； PDBConstruct 71–112； UniProt 1144–1185 Author chain F； PDBConstruct 1–49； UniProt 900–948 Author chain F； PDBConstruct 71–112； UniProt 1144–1185

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1wnc
Deposition date deposition_date	2004-07-29
Structure title title	Crystal structure of the SARS-CoV Spike protein fusion core
Keywords keywords	SARS-CoV, Spike protein, Fusion Core, Heptad repeat, Viral protein; 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.

1wnc__assembly_1__model_1

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

Download this curve (.dat)

1wnc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wnc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.57 Å
Rg (electron density)	28.42 Å
Total Rg	28.99 Å
Atom count	3480
Residues	454
Excluded volume	61588 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wnc__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wnc__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1wnc__assembly_3__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 (2)

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1wnca_
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	d1wncb_
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	d1wncc_
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	d1wncd_
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	d1wnce_
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	d1wncf_
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	1wncA00
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	1wncB00
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	1wncC00
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	1wncD00
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	1wncE00
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	1wncF00
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 —

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Unit-cell length a length_a	121.215 Å
Unit-cell length b length_b	66.316 Å
Unit-cell length c length_c	69.976 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2330
R_work r_work	0.2330
R_free r_free	0.2730

Description description	E2 glycoprotein
Molecular weight formula_weight	11892.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4131

Crystal structure of the SARS-CoV Spike protein fusion core

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

1wnc__assembly_1__model_1

1wnc__assembly_1__model_1 | I(q)

1wnc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	SARS coronavirus
NCBI taxonomy ID ncbi_taxonomy_id	227859
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	651

Crystal structure of the SARS-CoV Spike protein fusion core

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

1wnc__assembly_1__model_1

1wnc__assembly_1__model_1 | I(q)

1wnc__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)