1ixr

RuvA-RuvB complex

Method: X-RAY DIFFRACTION

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

Holliday junction DNA helicase ruvA

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	RuvB × 4 （Q5SL87） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUVA_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–191； UniProt 1–191 Author chain B； PDBConstruct 1–191； UniProt 1–191

RuvB

Thermus thermophilus

UniProt Q5SL87

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 12	Holliday junction DNA helicase ruvA × 8 （Q9F1Q3） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUVB_THET8
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–312； UniProt 1–312

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	1ixr
Deposition date deposition_date	2002-07-04
Structure title title	RuvA-RuvB complex
Keywords keywords	heterooligomeric complex, octameric RuvA, AAA-ATPase domain, complex with nucleotide, Hydrolase; HYDROLASE
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.

1ixr__assembly_1__model_1

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

Download this curve (.dat)

1ixr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ixr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	75.75 Å
Rg (electron density)	75.34 Å
Total Rg	74.76 Å
Atom count	19616
Residues	2536
Excluded volume	354240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ixr__assembly_1__model_1`	dodecameric （12）	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	Holliday junction DNA helicase ruvA
Molecular weight formula_weight	20441.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4904

MIRYLRGLVLKKEAGGFVLLAGGVGFFLQAPTPFLQALEEGKEVGVHTHLLLKEEGLSLYGFPDEENLALFELLLSVSGVGPKVALALLSALPPRLLARALLEGDARLLTSASGVGRRLAERIALELKGKVPPHLLAGEKVESEAAEEAVMALAALGFKEAQARAVVLDLLAQNPKARAQDLIKEALKRLR

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	RuvB
Molecular weight formula_weight	34801.3 kDa
EC 编号 ec_number	3.6.1.3
Mutation mutation	Y309R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MEDLALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALEALAALGLDELGLEKRDREILEVLILRFGGGPVGLATLATALSEDPGTLEEVHEPYLIRQGLLKRTPRGRVATELARRHL

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d1ixra1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.2 — RuvA domain 2-like
Family Family family	a.60.2.1 — DNA helicase RuvA subunit, middle domain

Domain ID domain_id	d1ixra2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

Domain ID domain_id	d1ixrb1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.1 — DNA helicase RuvA subunit, C-terminal domain
Family Family family	a.5.1.1 — DNA helicase RuvA subunit, C-terminal domain

Domain ID domain_id	d1ixrb2
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.2 — RuvA domain 2-like
Family Family family	a.60.2.1 — DNA helicase RuvA subunit, middle domain

Domain ID domain_id	d1ixrb3
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.2 — DNA helicase RuvA subunit, N-terminal domain

Domain ID domain_id	d1ixrc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.11 — Helicase DNA-binding domain

Domain ID domain_id	d1ixrc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (8 domains)

Domain ID domain_id	1ixrA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1ixrA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	1ixrB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1ixrB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	1ixrB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	1ixrC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1ixrC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	60 —

Domain ID domain_id	1ixrC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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Unit-cell length a length_a	61.581 Å
Unit-cell length b length_b	195.113 Å
Unit-cell length c length_c	246.244 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	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	—
R_work r_work	0.2680
R_free r_free	0.3350

RuvA-RuvB complex

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

Holliday junction DNA helicase ruvA

State in the Current Structure

Other States of the Same Protein in the Database

RuvB

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

1ixr__assembly_1__model_1

1ixr__assembly_1__model_1 | I(q)

1ixr__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

CATH v4.4 (8 domains)

7. Citations (1)

RuvA-RuvB complex

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

Holliday junction DNA helicase ruvA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RuvB

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

1ixr__assembly_1__model_1

1ixr__assembly_1__model_1 | I(q)

1ixr__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

CATH v4.4 (8 domains)

7. Citations (1)