SAXSdb — 3jcl

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

Spike glycoprotein

Murine hepatitis virus strain A59

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPIKE_CVMA5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1217； UniProt 15–1231 Author chain B； PDBConstruct 1–1217； UniProt 15–1231 Author chain C； PDBConstruct 1–1217； UniProt 15–1231

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	3jcl
Deposition date deposition_date	2015-12-21
Structure title title	Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer
Keywords keywords	Coronavirus, viral fusion proteins, viral spike, peplomer, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

3jcl__assembly_1__model_1

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

Download this curve (.dat)

3jcl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3jcl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.10 Å
Rg (electron density)	46.44 Å
Total Rg	46.71 Å
Atom count	24822
Residues	3201
Excluded volume	439860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3jcl__assembly_1__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 (1)

Entity 1 Entity 1 polymer

Description description	Spike glycoprotein
Molecular weight formula_weight	139729.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	24822

YIGDFRCIQLVNSNGANVSAPSISTETVEVSQGLGTYYVLDRVYLNATLLLTGYYPVDGSKFRNLALRGTNSVSLSWFQPPYLNQFNDGIFAKVQNLKTSTPSGATAYFPTIVIGSLFGYTSYTVVIEPYNGVIMASVCQYTICQLPYTDCKPNTNGNKLIGFWHTDVKPPICVLKRNFTLNVNADAFYFHFYQHGGTFYAYYADKPSATTFLFSVYIGDILTQYYVLPFICNPTAGSTFAPRYWVTPLVKRQYLFNFNQKGVITSAVDCASSYTSEIKCKTQSMLPSTGVYELSGYTVQPVGVVYRRVANLPACNIEEWLTARSVPSPLNWERKTFQNCNFNLSSLLRYVQAESLFCNNIDASKVYGRCFGSISVDKFAVPRSRQVDLQLGNSGFLQTANYKIDTAATSCQLHYTLPKNNVTINNHNPSSWNRRYGFNDAGVFGKNQHDVVYAQQCFTVRSSYCPCAQPDIVSPCTTQTKPKSAFVNVGDHCEGLGVLEDNCGNADPHKGCICANNSFIGWSHDTCLVNDRCQIFANILLNGINSGTTCSTDLQLPNTEVVTGICVKYDLYGITGQGVFKEVKADYYNSWQTLLYDVNGNLNGFRDLTTNKTYTIRSCYSGRVSAAFHKDAPEPALLYRNINCSYVFSNNISREENPLNYFDSYLGCVVNADNRTDEALPNCDLRMGAGLCVDYSKSRRAHSSVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK

Source Source

Source organism organism	Murine hepatitis virus strain A59
Common name common_name	MHV-A59
NCBI taxonomy ID ncbi_taxonomy_id	11142
Host organism host_organism	Drosophila melanogaster

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3jcla1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.318 — SARS receptor-binding domain-like
Superfamily Superfamily superfamily	d.318.1 — SARS receptor-binding domain-like
Family Family family	d.318.1.1 — SARS receptor-binding domain-like

Domain ID domain_id	d3jcla2
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.26 — Coronavirus spike glycoprotein S1, N-terminal domain

Domain ID domain_id	d3jcla3
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.83 — Coronavirus S1 beta-rich region
Superfamily Superfamily superfamily	e.83.1 — Coronavirus S1 beta-rich region
Family Family family	e.83.1.1 — Coronavirus S1 beta-rich region

Domain ID domain_id	d3jcla4
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.3.3.2 — Coronavirus spike glycoprotein S2 subunit

CATH v4.4 (3 domains)

Domain ID domain_id	3jclA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

Domain ID domain_id	3jclB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

Domain ID domain_id	3jclC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	960 — Spike glycoprotein, N-terminal domain

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	4.00 Å
Resolution测定Method resolution_method	Projection-matching
颗粒数 num_particles	82000

Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

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

Spike 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

3jcl__assembly_1__model_1

3jcl__assembly_1__model_1 | I(q)

3jcl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer

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

Spike 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

3jcl__assembly_1__model_1

3jcl__assembly_1__model_1 | I(q)

3jcl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)