6J5I | pdb_00006j5i

Cryo-EM structure of the mammalian DP-state ATP synthase


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
J [auth I]SCOP2 Familyepsilon subunit of mitochondrial f1f0-atp synthase 8094376 4001544 SCOP2 (2022-06-29)
J [auth I]SCOP2 Superfamilyepsilon subunit of mitochondrial F1F0-ATP synthase 8094377 3001799 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ATetR_Ne6j5iA1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
BTetR_Ne6j5iB1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
CTetR_Ne6j5iC1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
DTetR_Ne6j5iD1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
ETetR_Ne6j5iE1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
FTetR_Ne6j5iF1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
H [auth G]TetR_Ne6j5iG1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
I [auth H]TetR_Ne6j5iH1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
J [auth I]TetR_Ne6j5iI1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
L [auth b]TetR_Ne6j5ib1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
N [auth d]TetR_Ne6j5id1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
U [auth a]7tm_1e6j5ia1 A: alpha bundlesX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: 7tm_1ECOD (develop294)
AA [auth P]TetR_Ne6j5iP1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
BA [auth Q]TetR_Ne6j5iQ1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
CA [auth R]TetR_Ne6j5iR1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
V [auth K]TetR_Ne6j5iK1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
W [auth L]TetR_Ne6j5iL1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
X [auth M]TetR_Ne6j5iM1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
Z [auth O]TetR_Ne6j5iO1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
Y [auth N]TetR_Ne6j5iN1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)
M [auth c]TetR_Ne6j5ic1 A: alpha bundlesX: Ten stranded beta/alpha barrelH: Ten stranded beta/alpha barrelT: Ten stranded beta/alpha barrelF: TetR_NECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A2.40.30.20 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (utative)
A3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
A1.20.150.20 Mainly Alpha Up-down Bundle Lysin ATP synthase alpha/beta chain, C-terminal domainCATH (utative)
B2.40.30.20 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (utative)
B3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
B1.20.150.20 Mainly Alpha Up-down Bundle Lysin ATP synthase alpha/beta chain, C-terminal domainCATH (utative)
C2.40.30.20 Mainly Beta Beta Barrel Elongation Factor Tu (Ef-tu) domain 3CATH (utative)
C3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
C1.20.150.20 Mainly Alpha Up-down Bundle Lysin ATP synthase alpha/beta chain, C-terminal domainCATH (utative)
D2.40.10.170 Mainly Beta Beta Barrel Thrombin, subunit H CATH (utative)
D3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
D1.10.1140.10 Mainly Alpha Orthogonal Bundle Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain Chain D, domain3CATH (utative)
E2.40.10.170 Mainly Beta Beta Barrel Thrombin, subunit H CATH (utative)
E3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
E1.10.1140.10 Mainly Alpha Orthogonal Bundle Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain Chain D, domain3CATH (utative)
F2.40.10.170 Mainly Beta Beta Barrel Thrombin, subunit H CATH (utative)
F3.40.50.300 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold P-loop containing nucleotide triphosphate hydrolasesCATH (utative)
F1.10.1140.10 Mainly Alpha Orthogonal Bundle Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain Chain D, domain3CATH (utative)
H [auth G]1.10.287.80 Mainly Alpha Orthogonal Bundle Helix Hairpins ATP synthase, gamma subunit, helix hairpin domainCATH (utative)
H [auth G]3.40.1380.10 Alpha Beta 3-Layer(aba) Sandwich Pyruvate Kinase Chain: A, domain 1CATH (utative)
I [auth H]2.60.15.10 Mainly Beta Sandwich ATP Synthase domain 1CATH (utative)
I [auth H]1.20.5.440 Mainly Alpha Up-down Bundle Single alpha-helices involved in coiled-coils or other helix-helix interfaces ATP synthase delta/epsilon subunit, C-terminal domainCATH (utative)
J [auth I]1.10.1620.20 Mainly Alpha Orthogonal Bundle Atp Synthase Epsilon Chain Chain: ICATH (utative)
AA [auth P]1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
BA [auth Q]1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
CA [auth R]1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
V [auth K]1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
W [auth L]1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
X [auth M]1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
Z [auth O]1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)
Y [auth N]1.20.20.10 Mainly Alpha Up-down Bundle F1FO ATP Synthase F1F0 ATP synthase subunit CCATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C
PF00006ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)ATP synthase alpha/beta family, nucleotide-binding domainThis entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Domain
A, B, C
PF00306ATP synthase alpha/beta chain, C terminal domain (ATP-synt_ab_C)ATP synthase alpha/beta chain, C terminal domainDomain
A, B, C
PF00119ATP synthase A chain (ATP-synt_A)ATP synthase A chainDomain
A, B, C
PF05511Mitochondrial ATP synthase coupling factor 6 (ATP-synt_F6)Mitochondrial ATP synthase coupling factor 6- Family
A, B, C
PF02874ATP synthase alpha/beta family, beta-barrel domain (ATP-synt_ab_N)ATP synthase alpha/beta family, beta-barrel domainThis family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella. Domain
A, B, C
PF05405Mitochondrial ATP synthase B chain precursor (ATP-synt_B) (Mt_ATP-synt_B)Mitochondrial ATP synthase B chain precursor (ATP-synt_B)- Family
D, E, F
PF00006ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)ATP synthase alpha/beta family, nucleotide-binding domainThis entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. Domain
D, E, F
PF22919C-terminal domain of V and A type ATP synthase (ATP-synt_VA_C)C-terminal domain of V and A type ATP synthaseThis entry represents a small alpha helical domain found at the C-terminus of a variety of ATP synthases. Domain
D, E, F
PF05873ATP synthase D chain, mitochondrial (ATP5H) (Mt_ATP-synt_D)ATP synthase D chain, mitochondrial (ATP5H)- Family
D, E, F
PF02874ATP synthase alpha/beta family, beta-barrel domain (ATP-synt_ab_N)ATP synthase alpha/beta family, beta-barrel domainThis family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella. Domain
D, E, F
PF10206Mitochondrial F1F0-ATP synthase, subunit f (WRW)Mitochondrial F1F0-ATP synthase, subunit f- Family
G [auth J]PF04568Mitochondrial ATPase inhibitor, IATP (IATP)Mitochondrial ATPase inhibitor, IATP- Family
I [auth H]PF02823ATP synthase, Delta/Epsilon chain, beta-sandwich domain (ATP-synt_DE_N)ATP synthase, Delta/Epsilon chain, beta-sandwich domainPart of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensit ...Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (Pfam:PF00213).
Domain
I [auth H]PF21335Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain (ATPD_C_metazoa)Metazoan delta subunit of F1F0-ATP synthase, C-terminal domainF-type ATPases consist of two structural domains, F1 containing the extramembraneous catalytic core, and F0 which contains the membrane proton channel. This entry includes ATP synthase subunit delta from animals (called epsilon in bacteria or chlorop ...F-type ATPases consist of two structural domains, F1 containing the extramembraneous catalytic core, and F0 which contains the membrane proton channel. This entry includes ATP synthase subunit delta from animals (called epsilon in bacteria or chloroplast ATPase), which interacts with subunit C from F0 which is important for connecting the rotor of F1 (gamma subunit) to the rotor of F0 C subunit). This entry represents the C-terminal alpha-helical domain which is likely to act as an inhibitor of ATPase activity [1-5].
Domain
J [auth I]PF14960ATP synthase regulation (ATP_synth_reg)ATP synthase regulation- Family
K [auth S]PF00213ATP synthase delta (OSCP) subunit (OSCP)ATP synthase delta (OSCP) subunit- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C
ATP synthase subunit alpha, mitochondrial
D, E, F
ATP synthase subunit beta
G [auth J]ATPase inhibitor, mitochondrial
H [auth G]ATP synthase subunit gamma---
I [auth H]ATP synthase subunit delta, mitochondrial -
J [auth I]ATP synthase F1 subunit epsilon -
K [auth S]ATP synthase subunit O, mitochondrial
L [auth b]ATP synthase peripheral stalk-membrane subunit b
N [auth d]ATP synthase subunit d, mitochondrial
O [auth e]ATP synthase subunit e---
P [auth f]ATP synthase subunit f, mitochondrial-
Q [auth g]ATP synthase subunit g---
R [auth i]ATP synthase membrane subunit DAPIT- -
S [auth k]subunit k analog---
T [auth 8]ATP synthase protein 8
U [auth a]ATP synthase subunit a
Mitochondrial H+ transporting ATP synthase subunit c isoform 1
DA [auth u]ATP synthase membrane subunit 6.8PL---
M [auth c]ATP synthase-coupling factor 6, mitochondrial

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C
IPR038376ATP synthase, alpha subunit, C-terminal domain superfamilyHomologous Superfamily
A, B, C
IPR004100ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domainDomain
A, B, C
IPR033732ATP synthase, F1 complex, alpha subunit nucleotide-binding domainDomain
A, B, C
IPR036121ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamilyHomologous Superfamily
A, B, C
IPR023366ATP synthase subunit alpha, N-terminal domain-like superfamilyHomologous Superfamily
A, B, C
IPR000793ATP synthase, alpha subunit, C-terminalDomain
A, B, C
IPR020003ATPase, alpha/beta subunit, nucleotide-binding domain, active siteActive Site
A, B, C
IPR000194ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domainDomain
A, B, C
IPR005294ATP synthase, F1 complex, alpha subunitFamily
A, B, C
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
D, E, F
IPR004100ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domainDomain
D, E, F
IPR024034ATPase, F1/V1 complex, beta/alpha subunit, C-terminalHomologous Superfamily
D, E, F
IPR036121ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamilyHomologous Superfamily
D, E, F
IPR020003ATPase, alpha/beta subunit, nucleotide-binding domain, active siteActive Site
D, E, F
IPR050053ATPase alpha/beta chainsFamily
D, E, F
IPR000194ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domainDomain
D, E, F
IPR055190ATP synthase A/B type, C-terminal domainDomain
D, E, F
IPR003593AAA+ ATPase domainDomain
D, E, F
IPR005722ATP synthase, F1 complex, beta subunitFamily
D, E, F
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
G [auth J]IPR007648Mitochondrial ATPase inhibitorFamily
I [auth H]IPR036771F0F1 ATP synthase delta/epsilon subunit, N-terminalHomologous Superfamily
I [auth H]IPR036794ATP synthase delta/epsilon subunit, C-terminal domain superfamilyHomologous Superfamily
I [auth H]IPR020546ATP synthase, F1 complex, delta/epsilon subunit, N-terminalDomain
I [auth H]IPR048937F1F0-ATP synthase delta subunit, C-terminal domain, metazoanDomain
I [auth H]IPR001469ATP synthase, F1 complex, delta/epsilon subunitFamily
J [auth I]IPR036742ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrialHomologous Superfamily
J [auth I]IPR006721ATP synthase, F1 complex, epsilon subunit, mitochondrialFamily
K [auth S]IPR020781ATPase, OSCP/delta subunit, conserved siteConserved Site
K [auth S]IPR000711ATPase, OSCP/delta subunitFamily
K [auth S]IPR026015F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamilyHomologous Superfamily
L [auth b]IPR008688ATP synthase, F0 complex, subunit B/MI25Family
L [auth b]IPR013837ATP synthase, F0 complex, subunit BFamily
N [auth d]IPR036228ATP synthase, F0 complex, subunit D superfamily, mitochondrialHomologous Superfamily
N [auth d]IPR008689ATP synthase, F0 complex, subunit D, mitochondrialFamily
P [auth f]IPR019344Mitochondrial F1-F0 ATP synthase subunit F, predictedFamily
R [auth i]IPR009125ATP synthase membrane subunit KFamily
T [auth 8]IPR039017ATP synthase protein 8, mammalsFamily
T [auth 8]IPR001421ATP synthase protein 8, metazoaFamily
U [auth a]IPR023011ATP synthase, F0 complex, subunit A, active siteActive Site
U [auth a]IPR000568ATP synthase, F0 complex, subunit AFamily
U [auth a]IPR035908ATP synthase, F0 complex, subunit A superfamilyHomologous Superfamily
U [auth a]IPR045083ATP synthase, F0 complex, subunit A, bacterial/mitochondriaFamily
IPR035921F/V-ATP synthase subunit C superfamilyHomologous Superfamily
IPR038662F1F0 ATP synthase subunit C superfamilyHomologous Superfamily
IPR020537ATP synthase, F0 complex, subunit C, DCCD-binding siteBinding Site
IPR000454ATP synthase, F0 complex, subunit CFamily
IPR002379V-ATPase proteolipid subunit C-like domainDomain
M [auth c]IPR036204ATP synthase-coupling factor 6 superfamily, mitochondrialHomologous Superfamily
M [auth c]IPR008387ATP synthase-coupling factor 6, mitochondrialFamily