1q3s

Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)

Method: X-RAY DIFFRACTION

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

Thermosome alpha subunit

Thermococcus sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 16	MAGNESIUM ION × 14 ADENOSINE-5'-DIPHOSPHATE × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THSA_PYRKOX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–548； UniProt 1–548 Author chain B； PDBConstruct 1–548； UniProt 1–548 Author chain C； PDBConstruct 1–548； UniProt 1–548 Author chain D； PDBConstruct 1–548； UniProt 1–548 Author chain E； PDBConstruct 1–548； UniProt 1–548 Author chain F； PDBConstruct 1–548； UniProt 1–548 Author chain G； PDBConstruct 1–548； UniProt 1–548 Author chain H； PDBConstruct 1–548； UniProt 1–548

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	1q3s
Deposition date deposition_date	2003-07-31
Structure title title	Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)
Keywords keywords	chaperone, chaperonin, thermosome; CHAPERONE
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.

1q3s__assembly_1__model_1

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

Download this curve (.dat)

1q3s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1q3s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	66.65 Å
Rg (electron density)	65.55 Å
Total Rg	65.66 Å
Atom count	63502
Residues	8272
Excluded volume	1144100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1q3s__assembly_1__model_1`	hexadecameric （16）	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 (3)

Entity 1 Entity 1 polymer

Description description	Thermosome alpha subunit
Molecular weight formula_weight	59296.6 kDa
EC 编号 ec_number	3.6.4.9
Mutation mutation	G65C
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	31751

MAQLSGQPVVILPEGTQRYVGRDAQRLNILAARIIAETVRTTLGPKGMDKMLVDSLGDIVVTNDCATILDKIDLQHPAAKMMVEVAKTQDKEAGDGTTTAVVIAGELLRKAEELLDQNIHPSIIIKGYALAAEKAQEILDEIAIRVDPDDEETLLKIAATSITGKNAESHKELLAKLAVEAVKQVAEKKDGKYVVDLDNIKFEKKAGEGVEESELVRGVVIDKEVVHPRMPKRVENAKIALINEALEVKKTETDAKINITSPDQLMSFLEQEEKMLKDMVDHIAQTGANVVFVQKGIDDLAQHYLAKYGIMAVRRVKKSDMEKLAKATGAKIVTNVKDLTPEDLGYAEVVEERKLAGENMIFVEGCKNPKAVTILIRGGTEHVIDEVERALEDAVKVVKDVMEDGAVLPAGGAPEIELAIRLDEYAKQVGGKEALAIENFADALKIIPKTLAENAGLDTVEMLVKVISEHKNRGLGIGIDVFEGKPADMLEKGIIEPLRVKKQAIKSASEAAIMILRIDDVIAAKATKPEGGQGGGMPGGMGGMDMGM

Source Source

Source organism organism	Thermococcus sp.
NCBI taxonomy ID ncbi_taxonomy_id	79679
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d1q3sa1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1q3sa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1q3sa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

Domain ID domain_id	d1q3sb1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1q3sb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1q3sb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

Domain ID domain_id	d1q3sc1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1q3sc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1q3sc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

Domain ID domain_id	d1q3sd1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1q3sd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1q3sd3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

Domain ID domain_id	d1q3se1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1q3se2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1q3se3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

Domain ID domain_id	d1q3sf1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1q3sf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1q3sf3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

Domain ID domain_id	d1q3sg1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1q3sg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1q3sg3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

Domain ID domain_id	d1q3sh1
Class class	a — All alpha proteins
Fold Fold fold	a.129 — GroEL equatorial domain-like
Superfamily Superfamily superfamily	a.129.1 — GroEL equatorial domain-like
Family Family family	a.129.1.2 — Group II chaperonin (CCT, TRIC), ATPase domain

Domain ID domain_id	d1q3sh2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.2 — Group II chaperonin (CCT, TRIC), apical domain

Domain ID domain_id	d1q3sh3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.56 — GroEL-intermediate domain like
Superfamily Superfamily superfamily	d.56.1 — GroEL-intermediate domain like
Family Family family	d.56.1.2 — Group II chaperonin (CCT, TRIC), intermediate domain

CATH v4.4 (24 domains)

Domain ID domain_id	1q3sA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1q3sA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1q3sA03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1q3sB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1q3sB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1q3sB03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1q3sC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1q3sC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1q3sC03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1q3sD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1q3sD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1q3sD03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1q3sE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1q3sE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1q3sE03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1q3sF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1q3sF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1q3sF03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1q3sG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1q3sG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1q3sG03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1q3sH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	1q3sH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	1q3sH03
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

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Unit-cell length a length_a	207.425 Å
Unit-cell length b length_b	236.230 Å
Unit-cell length c length_c	234.106 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	64

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	73.620 Å
R factor r_factor	0.2510
R_work r_work	0.2510
R_free r_free	0.2880

Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)

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

Thermosome alpha subunit

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

1q3s__assembly_1__model_1

1q3s__assembly_1__model_1 | I(q)

1q3s__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (2)

Crystal structure of the chaperonin from Thermococcus strain KS-1 (FormIII crystal complexed with ADP)

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

Thermosome alpha subunit

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

1q3s__assembly_1__model_1

1q3s__assembly_1__model_1 | I(q)

1q3s__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (2)