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3vr6

Crystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

V-type sodium ATPase catalytic subunit A

Enterococcus hirae

UniProt Q08636

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 sodium ATPase subunit B × 3 （Q08637） V-type sodium ATPase subunit D × 1 V-type sodium ATPase subunit G × 1 （P43455） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 8 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
3vr2 3vr3 3vr4 3vr5 3vr6 5knb 5knc 5knd 5ze9 5zea 5zea 7coq

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NTPA_ENTHR
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–600； UniProt 1–593 Author chain B； PDBConstruct 8–600； UniProt 1–593 Author chain C； PDBConstruct 8–600； UniProt 1–593

V-type sodium ATPase subunit B

Enterococcus hirae

UniProt Q08637

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 sodium ATPase catalytic subunit A × 3 （Q08636） V-type sodium ATPase subunit D × 1 V-type sodium ATPase subunit G × 1 （P43455） PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 8 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
3vr2 3vr3 3vr4 3vr5 3vr6 5knb 5knc 5knd 5ze9 5zea 5zea 7coq

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NTPB_ENTHR
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 8–465； UniProt 1–458 Author chain E； PDBConstruct 8–465； UniProt 1–458 Author chain F； PDBConstruct 8–465； UniProt 1–458

V-type sodium ATPase subunit G

Enterococcus hirae

UniProt P43455

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 sodium ATPase catalytic subunit A × 3 （Q08636） V-type sodium ATPase subunit B × 3 （Q08637） V-type sodium ATPase subunit D × 1 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MAGNESIUM ION × 2 water × 8 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
3aon 3vr4 3vr5 3vr6 5knb 5knc 5knd

7 assemblies

View Construct and Data Evidence
UniProt name NTPG_ENTHR
Isoform —
PDB entities 4
Chains and sequence ranges Author chain H； PDBConstruct 1–103； UniProt 1–103

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_id3vr6
Deposition date deposition_date2012-04-03
Structure title titleCrystal structure of AMP-PNP bound Enterococcus hirae V1-ATPase [bV1]
Keywords keywordsV-ATPase, Enterococcus hirae, Rotary motor, P-loop, Hydrolase, Na(+)-ATPase, ATP Binding; HYDROLASE
Experimental Method methodX-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.

3vr6__assembly_1__model_1

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

Download this curve (.dat)

3vr6__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.

3vr6__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）45.00 Å
Rg (electron density)44.28 Å
Total Rg44.64 Å
Atom count26561
Residues3397
Excluded volume473550 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3vr6__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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6. Fold Classification (SCOP + CATH) 25 domains

SCOP 2.08 (11 domains)

Domain ID domain_idd3vr6d1
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.49.1.0 — automated matches
Domain ID domain_idd3vr6d2
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.37.1.0 — automated matches
Domain ID domain_idd3vr6d3
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.69.1.0 — automated matches
Domain ID domain_idd3vr6e1
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.49.1.0 — automated matches
Domain ID domain_idd3vr6e2
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.37.1.0 — automated matches
Domain ID domain_idd3vr6e3
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.69.1.0 — automated matches
Domain ID domain_idd3vr6f1
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.49.1.0 — automated matches
Domain ID domain_idd3vr6f2
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.37.1.0 — automated matches
Domain ID domain_idd3vr6f3
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.69.1.0 — automated matches
Domain ID domain_idd3vr6g1
Class classh — Coiled coil proteins
Fold Fold foldh.4 — Antiparallel coiled-coil
Superfamily Superfamily superfamilyh.4.20 — V-type ATPase central rotor subunit D
Family Family familyh.4.20.0 — automated matches
Domain ID domain_idd3vr6g2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (14 domains)

Domain ID domain_id3vr6A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily20 —
Domain ID domain_id3vr6A02
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_id3vr6A03
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_id3vr6A04
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_id3vr6B02
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_id3vr6B03
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_id3vr6B04
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_id3vr6C02
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_id3vr6C03
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_id3vr6C04
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_id3vr6D00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12240 —
Domain ID domain_id3vr6E00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12240 —
Domain ID domain_id3vr6F00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12240 —
Domain ID domain_id3vr6H00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10580 — ATPase, V1 complex, subunit F
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7. Citations (1)