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6qum

Thermus thermophilus V/A-type ATPase/synthase, rotational state 1

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

V-type ATP synthase alpha chain

OrganismNot specified

UniProt Q56403

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 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 B； PDBConstruct 1–578； UniProt 1–578 Author chain C； PDBConstruct 1–578； UniProt 1–578

V-type ATP synthase beta chain

OrganismNot specified

UniProt Q56404

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 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 D； PDBConstruct 1–478； UniProt 1–478 Author chain E； PDBConstruct 1–478； UniProt 1–478 Author chain F； PDBConstruct 1–478； UniProt 1–478

V-type ATP synthase subunit D

OrganismNot specified

UniProt O87880

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 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 3j0j 3w3a 3w3a 3w3a 3w3a 5y5x 5y5y 5y5z

52 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VATD_THET8
Isoform —
PDB entities 3
Chains and sequence ranges Author chain G； PDBConstruct 1–223； UniProt 1–223

V-type ATP synthase subunit F

OrganismNot specified

UniProt P74903

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
2d00 2d00

2 assemblies

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

55 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VATF_THET8
Isoform —
PDB entities 4
Chains and sequence ranges Author chain H； PDBConstruct 1–104； UniProt 1–104

V-type ATP synthase, subunit (VAPC-THERM)

OrganismNot specified

UniProt Q5SIT5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 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
3j0j 3k5b 3k5b 3v6i 3v6i 5y5x 5y5y 5y5z 5y60 6ly9 6qum 6r0w

39 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q5SIT5_THET8
Isoform —
PDB entities 5
Chains and sequence ranges Author chain I； PDBConstruct 1–103； UniProt 18–120 Author chain K； PDBConstruct 1–103； UniProt 18–120

V-type ATP synthase subunit E

OrganismNot specified

UniProt P74901

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 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
3j0j 3k5b 3k5b 3v6i 3v6i 5gar 5gas 5tsj 5y5x 5y5y 5y5z 5y60

42 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VATE_THET8
Isoform —
PDB entities 6
Chains and sequence ranges Author chain J； PDBConstruct 1–188； UniProt 1–188 Author chain L； PDBConstruct 1–188； UniProt 1–188

V-type ATP synthase subunit C

OrganismNot specified

UniProt P74902

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit I × 1 （Q5SIT6） V-type ATP synthase, subunit K × 12 （Q5SIT7） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1r5z 1r5z 1r5z 1v9m

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3j0j 5gar 5gas 5tsj 5y5x 5y5y 5y5z 5y60 6ly9 6qum 6r0w 6r0y

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VATC_THET8
Isoform —
PDB entities 7
Chains and sequence ranges Author chain M； PDBConstruct 1–323； UniProt 1–323

V-type ATP synthase subunit I

OrganismNot specified

UniProt Q5SIT6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase, subunit K × 12 （Q5SIT7） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 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
5y5x 5y5z 5y60 6ly9 6qum 6r0w 6r0y 6r0z 6r10 8ywt 8yxz 8yy0

23 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q5SIT6_THET8
Isoform —
PDB entities 8
Chains and sequence ranges Author chain N； PDBConstruct 1–652； UniProt 1–652

V-type ATP synthase, subunit K

OrganismNot specified

UniProt Q5SIT7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 26 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） V-type ATP synthase, subunit (VAPC-THERM) × 2 （Q5SIT5） V-type ATP synthase subunit E × 2 （P74901） V-type ATP synthase subunit C × 1 （P74902） V-type ATP synthase subunit I × 1 （Q5SIT6） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 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
5y5x 5y5z 5y60 6ly9 6qum 6r0w 6r0y 6r0z 6r10 8ywt 8yxz 8yy0

23 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q5SIT7_THET8
Isoform —
PDB entities 9
Chains and sequence ranges Author chain O； PDBConstruct 1–74； UniProt 26–99 Author chain P； PDBConstruct 1–74； UniProt 26–99 Author chain Q； PDBConstruct 1–74； UniProt 26–99 Author chain R； PDBConstruct 1–74； UniProt 26–99 Author chain S； PDBConstruct 1–74； UniProt 26–99 Author chain T； PDBConstruct 1–74； UniProt 26–99 Author chain U； PDBConstruct 1–74； UniProt 26–99 Author chain V； PDBConstruct 1–74； UniProt 26–99 Author chain W； PDBConstruct 1–74； UniProt 26–99 Author chain X； PDBConstruct 1–74； UniProt 26–99 Author chain Y； PDBConstruct 1–74； UniProt 26–99 Author chain Z； PDBConstruct 1–74； UniProt 26–99

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_id6qum
Deposition date deposition_date2019-02-27
Structure title titleThermus thermophilus V/A-type ATPase/synthase, rotational state 1
Keywords keywordsATP hydrolysis/synthesis, proton translocation, rotary catalysis, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON 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.

6qum__assembly_1__model_1

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

Download this curve (.dat)

6qum__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6qum__assembly_1__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）71.62 Å
Rg (electron density)73.16 Å
Total Rg73.21 Å
Atom count44900
Residues5874
Excluded volume805960 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6qum__assembly_1__model_1 26-meric （26） 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 (11)

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6. Fold Classification (SCOP + CATH) 31 domains

CATH v4.4 (31 domains)

Domain ID domain_id6qumA02
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_id6qumA03
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_id6qumA04
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_id6qumB02
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_id6qumB03
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_id6qumB04
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_id6qumC02
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_id6qumC03
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_id6qumC04
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_id6qumD00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12240 —
Domain ID domain_id6qumE00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12240 —
Domain ID domain_id6qumF00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12240 —
Domain ID domain_id6qumJ01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily620 — F1F0 ATP synthase subunit B, membrane domain
Domain ID domain_id6qumJ02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily30 — ATP synthase, E subunit, C-terminal
Domain ID domain_id6qumL01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily620 — F1F0 ATP synthase subunit B, membrane domain
Domain ID domain_id6qumL02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2320 — hypothetical protein PF0899 fold
Homologous superfamily homologous superfamily30 — ATP synthase, E subunit, C-terminal
Domain ID domain_id6qumM01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily50 — ATP synthase (C/AC39) subunit, domain 3
Domain ID domain_id6qumM02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1690 — V-type ATP synthase subunit C fold
Homologous superfamily homologous superfamily10 — V-type ATP synthase subunit C domain
Domain ID domain_id6qumM03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1690 — V-type ATP synthase subunit C fold
Homologous superfamily homologous superfamily10 — V-type ATP synthase subunit C domain
Domain ID domain_id6qumO00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumP00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumQ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumR00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumS00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumT00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumU00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumV00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumW00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumX00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumY00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
Domain ID domain_id6qumZ00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology20 — F1FO ATP Synthase
Homologous superfamily homologous superfamily10 — F1F0 ATP synthase subunit C
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7. Citations (1)