6RD8 | pdb_00006rd8

CryoEM structure of Polytomella F-ATP synthase, c-ring position 2, focussed refinement of Fo and peripheral stalk

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
R [auth M]	HNOB	e6rd8M1	A: alpha bundles	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: HNOB	ECOD (develop294)
Q [auth J]	KR	e6rd8J1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
P [auth I]	KR	e6rd8I1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
O [auth H]	KR	e6rd8H1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
N [auth G]	KR	e6rd8G1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
M [auth F]	KR	e6rd8F1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
L [auth E]	KR	e6rd8E1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
K [auth D]	KR	e6rd8D1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
J [auth C]	KR	e6rd8C1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
I [auth B]	KR	e6rd8B1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)
H [auth A]	KR	e6rd8A1	A: alpha bundles	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: KR	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
Q [auth J]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
P [auth I]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
O [auth H]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
N [auth G]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
M [auth F]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
L [auth E]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
K [auth D]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
J [auth C]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
I [auth B]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)
H [auth A]	1.20.20.10	Mainly Alpha	Up-down Bundle	F1FO ATP Synthase	F1F0 ATP synthase subunit C	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
R [auth M]	Mitochondrial ATP synthase subunit 6	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity monoatomic ion channel activity proton channel activity proton-transporting ATP synthase activity, rotational mechanism monoatomic cation channel activity passive transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity catalytic activity ligase activity	-	respiratory chain complex protein-containing complex catalytic complex proton-transporting ATP synthase complex membrane membrane protein complex cation channel complex transporter complex cellular anatomical structure proton-transporting two-sector ATPase complex transmembrane transporter complex monoatomic ion channel complex
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J]	Mitochondrial ATP synthase subunit c	monoatomic cation transmembrane transporter activity proton transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity binding lipid binding	ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process ribose phosphate metabolic process ATP metabolic process ATP biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process purine ribonucleoside triphosphate biosynthetic process proton motive force-driven ATP synthesis nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside triphosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine ribonucleoside triphosphate metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine nucleoside triphosphate metabolic process nucleoside triphosphate biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process ribonucleoside triphosphate biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process nucleoside triphosphate metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex proton-transporting two-sector ATPase complex membrane membrane protein complex proton-transporting two-sector ATPase complex, proton-transporting domain respiratory chain complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex proton-transporting two-sector ATPase complex membrane membrane protein complex proton-transporting two-sector ATPase complex, proton-transporting domain respiratory chain complex catalytic complex proton-transporting ATP synthase complex cation channel complex transporter complex transmembrane transporter complex monoatomic ion channel complex
G [auth 9]	ASA-9: Polytomella F-ATP synthase associated subunit 9	-	-	-
F [auth 8]	Mitochondrial ATP synthase subunit ASA8	-	-	-
E [auth 6]	Mitochondrial ATP synthase subunit ASA6	-	-	-
D [auth 5]	Mitochondrial F1F0 ATP synthase associated 14 kDa protein	-	-	-
C [auth 3]	Mitochondrial F1F0 ATP synthase associated 32 kDa protein	-	-	-
B [auth 1]	ATP synthase associated protein ASA1	-	-	-
A [auth 0]	ASA-10: Polytomella F-ATP synthase associated subunit 10	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
R [auth M]	IPR023011	ATP synthase, F0 complex, subunit A, active site	Active Site
R [auth M]	IPR000568	ATP synthase, F0 complex, subunit A	Family
R [auth M]	IPR035908	ATP synthase, F0 complex, subunit A superfamily	Homologous Superfamily
R [auth M]	IPR045083	ATP synthase, F0 complex, subunit A, bacterial/mitochondria	Family
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J]	IPR035921	F/V-ATP synthase subunit C superfamily	Homologous Superfamily
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J]	IPR038662	F1F0 ATP synthase subunit C superfamily	Homologous Superfamily
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J]	IPR020537	ATP synthase, F0 complex, subunit C, DCCD-binding site	Binding Site
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J]	IPR000454	ATP synthase, F0 complex, subunit C	Family
H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J]	IPR002379	V-ATPase proteolipid subunit C-like domain	Domain
D [auth 5]	IPR054538	F1F0 ATP synthase subunit ASA5	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth 0], F [auth 8], G [auth 9], H [auth A], I [auth B] A [auth 0], F [auth 8], G [auth 9], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth M]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth 0], F [auth 8], G [auth 9], H [auth A], I [auth B] A [auth 0], F [auth 8], G [auth 9], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H], P [auth I], Q [auth J], R [auth M]	MemProtMD	Annotated as membrane protein by MemProtMD

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.