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9u6f

Cryo-EM structure of the V1 domain of V/A-ATPase in liposomes, state1

Method: ELECTRON MICROSCOPY
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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 8 V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 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

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 8 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase subunit D × 1 （O87880） V-type ATP synthase subunit F × 1 （P74903） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 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 1–473； UniProt 2–474 Author chain E； PDBConstruct 1–473； UniProt 2–474 Author chain F； PDBConstruct 1–473； UniProt 2–474

V-type ATP synthase subunit D

Thermus thermophilus HB8

UniProt O87880

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit F × 1 （P74903） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 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 1–206； UniProt 4–209

V-type ATP synthase subunit F

Thermus thermophilus HB8

UniProt P74903

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 8 V-type ATP synthase alpha chain × 3 （Q56403） V-type ATP synthase beta chain × 3 （Q56404） V-type ATP synthase subunit D × 1 （O87880） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 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

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_id9u6f
Deposition date deposition_date2025-03-23
Last revision last_revision2025-10-29
Structure title titleCryo-EM structure of the V1 domain of V/A-ATPase in liposomes, state1
Keywords keywordsATP synthase, V ATPase, V1 ATPase, MOTOR PROTEIN; MOTOR 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.

9u6f__assembly_1__model_1

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

Download this curve (.dat)

9u6f__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.

9u6f__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）45.25 Å
Rg (electron density)44.69 Å
Total Rg45.03 Å
Atom count26946
Residues3453
Excluded volume481590 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9u6f__assembly_1__model_1 octameric （8） 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 (7)

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7. Citations (1)