SAXSdb — 1wdf

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

E2 glycoprotein

Murine hepatitis virus

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGL2_CVMA5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–56； UniProt 969–1024 Author chain A； PDBConstruct 57–95； UniProt 1216–1254 Author chain B； PDBConstruct 1–56； UniProt 969–1024 Author chain B； PDBConstruct 57–95； UniProt 1216–1254

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	1wdf
Deposition date deposition_date	2004-05-14
Structure title title	crystal structure of MHV spike protein fusion core
Keywords keywords	MHV, coronavirus, heptad repeat, fusion core, viral entry, 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.

1wdf__assembly_2__model_1

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

Download this curve (.dat)

1wdf__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wdf__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.14 Å
Rg (electron density)	24.20 Å
Total Rg	24.83 Å
Atom count	2103
Residues	273
Excluded volume	37452 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wdf__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wdf__assembly_2__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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1wdfa_
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	d1wdfb_
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 (2 domains)

Domain ID domain_id	1wdfA00
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	1wdfB00
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	48.300 Å
Unit-cell length b length_b	48.300 Å
Unit-cell length c length_c	199.600 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	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.2240
R_work r_work	0.2220
R_free r_free	0.2910

Description description	E2 glycoprotein
Molecular weight formula_weight	10455.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1589

crystal structure of MHV 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

1wdf__assembly_2__model_1

1wdf__assembly_2__model_1 | I(q)

1wdf__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Murine hepatitis virus
NCBI taxonomy ID ncbi_taxonomy_id	11142
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	168

crystal structure of MHV 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

1wdf__assembly_2__model_1

1wdf__assembly_2__model_1 | I(q)

1wdf__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)