6RDM | pdb_00006rdm

Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, focussed refinement of F1 head and rotor


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
N [auth S]SCOP2B SuperfamilyATP synthase gamma subunit-like 8099504 3000451 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
K [auth P]OSCPe6rdmP1 A: alpha bundlesX: ATPD N-terminal domain-likeH: N-terminal domain of the delta subunit of the F1F0-ATP synthase (From Topology)T: N-terminal domain of the delta subunit of the F1F0-ATP synthaseF: OSCPECOD (1.6)
L [auth Q]ATP-synt_Epse6rdmQ1 A: extended segmentsX: Epsilon subunit of mitochondrial F1F0-ATP synthase (From Topology)H: Epsilon subunit of mitochondrial F1F0-ATP synthase (From Topology)T: Epsilon subunit of mitochondrial F1F0-ATP synthaseF: ATP-synt_EpsECOD (1.6)
T [auth Z]ATP-synt_ab_Ne6rdmZ2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: ATP-synt_ab_NECOD (1.6)
T [auth Z]ATP-synt_ab,ATP-synt_ab_Ce6rdmZ1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: ATP-synt_ab,ATP-synt_ab_CECOD (1.6)
R [auth X]ATP-synt_ab_Ne6rdmX2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: ATP-synt_ab_NECOD (1.6)
R [auth X]ATP-synt_ab,ATP-synt_ab_Ce6rdmX1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: ATP-synt_ab,ATP-synt_ab_CECOD (1.6)
O [auth T]ATP-synt_ab_Ne6rdmT1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: ATP-synt_ab_NECOD (1.6)
O [auth T]ATP-synt_ab_Ce6rdmT3 A: alpha superhelicesX: C-terminal domain of alpha and beta subunits of F1 ATP synthase (From Topology)H: C-terminal domain of alpha and beta subunits of F1 ATP synthase (From Topology)T: C-terminal domain of alpha and beta subunits of F1 ATP synthaseF: ATP-synt_ab_CECOD (1.6)
O [auth T]ATP-synt_abe6rdmT2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: ATP-synt_abECOD (1.6)
N [auth S]ATP-synte6rdmS1 A: a/b three-layered sandwichesX: ATP synthase (F1-ATPase), gamma subunit (From Topology)H: ATP synthase (F1-ATPase), gamma subunit (From Topology)T: ATP synthase (F1-ATPase), gamma subunitF: ATP-syntECOD (1.6)
AATP-synt_Ce6rdmA1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
BATP-synt_Ce6rdmB1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
CATP-synt_Ce6rdmC1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
EATP-synt_Ce6rdmE1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
FATP-synt_Ce6rdmF1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
GATP-synt_Ce6rdmG1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
HATP-synt_Ce6rdmH1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
IATP-synt_Ce6rdmI1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
JATP-synt_Ce6rdmJ1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)
DATP-synt_Ce6rdmD1 A: extended segmentsX: F1F0 ATP synthase subunit C (From Topology)H: F1F0 ATP synthase subunit C (From Topology)T: F1F0 ATP synthase subunit CF: ATP-synt_CECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
S [auth Y]2.40.10.170 Mainly Beta Beta Barrel Thrombin, subunit H CATH (utative)
S [auth Y]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
S [auth Y]1.10.1140.10 Mainly Alpha Orthogonal Bundle Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain Chain D, domain3CATH (utative)
T [auth Z]2.40.10.170 Mainly Beta Beta Barrel Thrombin, subunit H CATH (utative)
T [auth Z]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
T [auth Z]1.10.1140.10 Mainly Alpha Orthogonal Bundle Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain Chain D, domain3CATH (utative)
R [auth X]2.40.10.170 Mainly Beta Beta Barrel Thrombin, subunit H CATH (utative)
R [auth X]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
R [auth X]1.10.1140.10 Mainly Alpha Orthogonal Bundle Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain Chain D, domain3CATH (utative)
O [auth T]2.40.30.20 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (utative)
O [auth T]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
O [auth T]1.20.150.20 Mainly Alpha Up-down Bundle Lysin ATP synthase alpha/beta chain, C-terminal domainCATH (utative)
P [auth U]2.40.30.20 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (utative)
P [auth U]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
P [auth U]1.20.150.20 Mainly Alpha Up-down Bundle Lysin ATP synthase alpha/beta chain, C-terminal domainCATH (utative)
Q [auth V]2.40.30.20 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (utative)
Q [auth V]3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
Q [auth V]1.20.150.20 Mainly Alpha Up-down Bundle Lysin ATP synthase alpha/beta chain, C-terminal domainCATH (utative)
N [auth S]1.10.287.80 Mainly Alpha Orthogonal Bundle Helix Hairpins ATP synthase, gamma subunit, helix hairpin domainCATH (utative)
A1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
B1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
C1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
E1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
F1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
G1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
H1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
I1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
J1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
D1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
K [auth P]Mitochondrial ATP synthase subunit OSCP -
L [auth Q]epsilon: Polytomella F-ATP synthase epsilon subunit
R [auth X],
S [auth Y],
T [auth Z]
ATP synthase subunit beta
O [auth T],
P [auth U],
Q [auth V]
ATP synthase subunit alpha -
N [auth S]ATP synthase gamma chain, mitochondrial -
M [auth R]Mitochondrial ATP synthase subunit delta -
A, B, C, D, E
Mitochondrial ATP synthase subunit c

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
K [auth P]IPR020781ATPase, OSCP/delta subunit, conserved siteConserved Site
K [auth P]IPR000711ATPase, OSCP/delta subunitFamily
K [auth P]IPR026015F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamilyHomologous Superfamily
L [auth Q]IPR036742ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrialHomologous Superfamily
L [auth Q]IPR006721ATP synthase, F1 complex, epsilon subunit, mitochondrialFamily
R [auth X],
S [auth Y],
T [auth Z]
IPR004100ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domainDomain
R [auth X],
S [auth Y],
T [auth Z]
IPR024034ATPase, F1/V1 complex, beta/alpha subunit, C-terminalHomologous Superfamily
R [auth X],
S [auth Y],
T [auth Z]
IPR036121ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamilyHomologous Superfamily
R [auth X],
S [auth Y],
T [auth Z]
IPR020003ATPase, alpha/beta subunit, nucleotide-binding domain, active siteActive Site
R [auth X],
S [auth Y],
T [auth Z]
IPR050053ATPase alpha/beta chainsFamily
R [auth X],
S [auth Y],
T [auth Z]
IPR000194ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domainDomain
R [auth X],
S [auth Y],
T [auth Z]
IPR055190ATP synthase A/B type, C-terminal domainDomain
R [auth X],
S [auth Y],
T [auth Z]
IPR003593AAA+ ATPase domainDomain
R [auth X],
S [auth Y],
T [auth Z]
IPR005722ATP synthase, F1 complex, beta subunitFamily
R [auth X],
S [auth Y],
T [auth Z]
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
O [auth T],
P [auth U],
Q [auth V]
IPR038376ATP synthase, alpha subunit, C-terminal domain superfamilyHomologous Superfamily
O [auth T],
P [auth U],
Q [auth V]
IPR004100ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domainDomain
O [auth T],
P [auth U],
Q [auth V]
IPR033732ATP synthase, F1 complex, alpha subunit nucleotide-binding domainDomain
O [auth T],
P [auth U],
Q [auth V]
IPR036121ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamilyHomologous Superfamily
O [auth T],
P [auth U],
Q [auth V]
IPR023366ATP synthase subunit alpha, N-terminal domain-like superfamilyHomologous Superfamily
O [auth T],
P [auth U],
Q [auth V]
IPR000793ATP synthase, alpha subunit, C-terminalDomain
O [auth T],
P [auth U],
Q [auth V]
IPR020003ATPase, alpha/beta subunit, nucleotide-binding domain, active siteActive Site
O [auth T],
P [auth U],
Q [auth V]
IPR000194ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domainDomain
O [auth T],
P [auth U],
Q [auth V]
IPR005294ATP synthase, F1 complex, alpha subunitFamily
O [auth T],
P [auth U],
Q [auth V]
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
N [auth S]IPR023632ATP synthase, F1 complex, gamma subunit conserved siteConserved Site
N [auth S]IPR000131ATP synthase, F1 complex, gamma subunitFamily
N [auth S]IPR035968ATP synthase, F1 complex, gamma subunit superfamilyHomologous Superfamily
M [auth R]IPR036771F0F1 ATP synthase delta/epsilon subunit, N-terminalHomologous Superfamily
M [auth R]IPR020546ATP synthase, F1 complex, delta/epsilon subunit, N-terminalDomain
M [auth R]IPR001469ATP synthase, F1 complex, delta/epsilon subunitFamily
A, B, C, D, E
IPR035921F/V-ATP synthase subunit C superfamilyHomologous Superfamily
A, B, C, D, E
IPR038662F1F0 ATP synthase subunit C superfamilyHomologous Superfamily
A, B, C, D, E
IPR020537ATP synthase, F0 complex, subunit C, DCCD-binding siteBinding Site
A, B, C, D, E
IPR000454ATP synthase, F0 complex, subunit CFamily
A, B, C, D, E
IPR002379V-ATPase proteolipid subunit C-like domainDomain