← Back to search
3gqb

Crystal Structure of the A3B3 complex from V-ATPase

Method: X-RAY DIFFRACTION
▼

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

V-type ATP synthase alpha chain

Thermus thermophilus HB8

UniProt Q56403

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 V-type ATP synthase beta chain × 1 （Q56404） water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 V-type ATP synthase beta chain × 1 （Q56404） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3a5c 3a5c 3a5d 3a5d 3gqb 3gqb 3j0j 3w3a 3w3a 3w3a 3w3a 5gar

57 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VATA_THET8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–578； UniProt 1–578 Author chain C； PDBConstruct 1–578； UniProt 1–578

V-type ATP synthase beta chain

Thermus thermophilus HB8

UniProt Q56404

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 V-type ATP synthase alpha chain × 1 （Q56403） water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 V-type ATP synthase alpha chain × 1 （Q56403） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3a5c 3a5c 3a5d 3a5d 3gqb 3gqb 3j0j 3w3a 3w3a 3w3a 3w3a 5y5x

54 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VATB_THET8
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–464； UniProt 1–464 Author chain D； PDBConstruct 1–464； UniProt 1–464

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3gqb
Deposition date deposition_date2009-03-24
Structure title titleCrystal Structure of the A3B3 complex from V-ATPase
Keywords keywordsA3B3, V-ATPase, ATP synthesis, ATP-binding, Hydrogen ion transport, Hydrolase, Ion transport, Nucleotide-binding, Transport; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

3gqb__assembly_2__model_1

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

Download this curve (.dat)

3gqb__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3gqb__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）32.62 Å
Rg (electron density)31.93 Å
Total Rg32.57 Å
Atom count8078
Residues1038
Excluded volume144340 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3gqb__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3gqb__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

▼

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (14 domains)

Domain ID domain_idd3gqba1
Class classb — All beta proteins
Fold Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamilyb.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family familyb.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase
Domain ID domain_idd3gqba2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd3gqba3
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family familyb.84.5.1 — V1 ATP synthase A subunit, bulge domain-like
Domain ID domain_idd3gqba4
Class classa — All alpha proteins
Fold Fold folda.69 — Left-handed superhelix
Superfamily Superfamily superfamilya.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family familya.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase
Domain ID domain_idd3gqbb1
Class classb — All beta proteins
Fold Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamilyb.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family familyb.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase
Domain ID domain_idd3gqbb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd3gqbb3
Class classa — All alpha proteins
Fold Fold folda.69 — Left-handed superhelix
Superfamily Superfamily superfamilya.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family familya.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase
Domain ID domain_idd3gqbc1
Class classb — All beta proteins
Fold Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamilyb.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family familyb.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase
Domain ID domain_idd3gqbc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd3gqbc3
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.5 — V1 ATP synthase A subunit, bulge domain-like
Family Family familyb.84.5.1 — V1 ATP synthase A subunit, bulge domain-like
Domain ID domain_idd3gqbc4
Class classa — All alpha proteins
Fold Fold folda.69 — Left-handed superhelix
Superfamily Superfamily superfamilya.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family familya.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase
Domain ID domain_idd3gqbd1
Class classb — All beta proteins
Fold Fold foldb.49 — Domain of alpha and beta subunits of F1 ATP synthase-like
Superfamily Superfamily superfamilyb.49.1 — N-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family familyb.49.1.2 — N-terminal domain of A and B subunits of V1 ATP synthase
Domain ID domain_idd3gqbd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.11 — RecA protein-like (ATPase-domain)
Domain ID domain_idd3gqbd3
Class classa — All alpha proteins
Fold Fold folda.69 — Left-handed superhelix
Superfamily Superfamily superfamilya.69.1 — C-terminal domain of alpha and beta (or A/B) subunits of rotary ATPases
Family Family familya.69.1.2 — C-terminal domain of A and B subunits of V1 ATP synthase and A1 ATP sythase

CATH v4.4 (10 domains)

Domain ID domain_id3gqbA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3gqbA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3gqbA03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
Domain ID domain_id3gqbA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3
Domain ID domain_id3gqbB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12240 —
Domain ID domain_id3gqbC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3gqbC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id3gqbC03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain
Domain ID domain_id3gqbC04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1140 — Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3
Homologous superfamily homologous superfamily10 — Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3
Domain ID domain_id3gqbD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12240 —
▶

7. Citations (1)