7M78 | pdb_00007m78

Room Temperature XFEL Crystallography reveals asymmetry in the vicinity of the two phylloquinones in Photosystem I

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth K]	SCOP2B Superfamily	Photosystem I reaction center subunit X, PsaK	8034288	3000859	SCOP2B (2022-06-29)
H [auth J]	SCOP2B Superfamily	Subunit IX of photosystem I reaction centre, PsaJ	8034287	3000824	SCOP2B (2022-06-29)
G [auth I]	SCOP2B Superfamily	Subunit VIII of photosystem I reaction centre, PsaI	8034286	3000819	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Subunit III of photosystem I reaction centre, PsaF	8034284	3000813	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Electron transport accessory proteins	8034282	3000325	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Photosystem I subunit PsaD	8034279	3000951	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	4Fe-4S ferredoxins	8034277	3000020	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Photosystem I subunits PsaA/PsaB	8034274	3000850	SCOP2B (2022-06-29)
L [auth X]	SCOP2B Superfamily	Subunit PsaX of photosystem I reaction centre	8034292	3000838	SCOP2B (2022-06-29)
K [auth M]	SCOP2B Superfamily	Subunit XII of photosystem I reaction centre, PsaM	8034290	3000829	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	Photosystem I reaction center subunit XI, PsaL	8034291	3000870	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Photosystem I subunits PsaA/PsaB	8034272	3000850	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I [auth K]	e7m78K1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
H [auth J]	e7m78J1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
G [auth I]	e7m78I1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
F	e7m78F1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
E	e7m78E1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
D	e7m78D1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
C	e7m78C1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
B	e7m78B1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
L [auth X]	e7m78X1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
K [auth M]	e7m78M1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
J [auth L]	e7m78L1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)
A	e7m78A1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Secretin_N	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth L]	1.20.1240.10	Mainly Alpha	Up-down Bundle	Photosystem 1 Reaction Centre Subunit Xi	Chain: L	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H [auth J]	PF01701	Photosystem I reaction centre subunit IX / PsaJ (PSI_PsaJ)	Photosystem I reaction centre subunit IX / PsaJ	-	Family
G [auth I]	PF00796	Photosystem I reaction centre subunit VIII (PSI_8)	Photosystem I reaction centre subunit VIII	-	Family
F	PF02507	Photosystem I reaction centre subunit III (PSI_PsaF)	Photosystem I reaction centre subunit III	-	Family
E	PF02427	Photosystem I reaction centre subunit IV / PsaE (PSI_PsaE)	Photosystem I reaction centre subunit IV / PsaE	PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane [1]. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains [1].	Domain
D	PF02531	PsaD (PsaD)	PsaD	-	Family
C	PF12838	4Fe-4S dicluster domain (Fer4_7)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
B	PF00223	Photosystem I psaA/psaB protein (PsaA_PsaB)	Photosystem I psaA/psaB protein	-	Family
K [auth M]	PF07465	Photosystem I protein M (PsaM) (PsaM)	Photosystem I protein M (PsaM)	-	Family
J [auth L]	PF02605	Photosystem I reaction centre subunit XI (PsaL)	Photosystem I reaction centre subunit XI	-	Family
A	PF00223	Photosystem I psaA/psaB protein (PsaA_PsaB)	Photosystem I psaA/psaB protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth K]	Photosystem I reaction center subunit PsaK	-	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex
H [auth J]	Photosystem I reaction center subunit IX	-	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex
G [auth I]	Photosystem I reaction center subunit VIII	-	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex
F	Photosystem I reaction center subunit III	-	photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem I membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane photosystem I reaction center thylakoid
E	Photosystem I reaction center subunit IV	-	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex photosystem I reaction center
D	Photosystem I reaction center subunit II	-	photosynthesis metabolic process cellular process	protein-containing complex photosystem intracellular anatomical structure photosystem I membrane membrane protein complex intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle photosynthetic membrane photosystem I reaction center thylakoid
C	Photosystem I iron-sulfur center	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding electron transfer activity cation binding ion binding metal ion binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain metabolic process cellular process generation of precursor metabolites and energy photosynthetic electron transport in photosystem I	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex
B	Photosystem I P700 chlorophyll a apoprotein A2	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding chlorophyll binding tetrapyrrole binding electron transfer activity	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex
L [auth X]	Photosystem I 4.8K protein	-	-	-
K [auth M]	Photosystem I reaction center subunit XII	-	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex
J [auth L]	Photosystem I reaction center subunit XI	-	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex photosystem I reaction center
A	Photosystem I P700 chlorophyll a apoprotein A1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding chlorophyll binding tetrapyrrole binding electron transfer activity	photosynthesis metabolic process cellular process	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane intracellular membraneless organelle plasma membrane-derived chromatophore thylakoid membrane intracellular organelle cell periphery cellular anatomical structure plasma membrane-derived thylakoid membrane organelle membraneless organelle plasma membrane region bacterial thylakoid cytoplasm photosynthetic membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth K]	IPR037101	Photosystem I reaction centre subunit PsaK	Homologous Superfamily
I [auth K]	IPR000549	Photosystem I reaction center subunit V/PsaK	Family
I [auth K]	IPR035982	Photosystem I reaction centre subunit PsaK superfamily	Homologous Superfamily
I [auth K]	IPR017492	Photosystem I reaction center subunit PsaK	Family
H [auth J]	IPR002615	Photosystem I PsaJ, reaction centre subunit IX	Family
H [auth J]	IPR036062	Photosystem I PsaJ, reaction centre subunit IX superfamily	Homologous Superfamily
G [auth I]	IPR036357	Photosystem I reaction centre subunit VIII superfamily	Homologous Superfamily
G [auth I]	IPR001302	Photosystem I reaction centre subunit VIII	Family
F	IPR036577	Photosystem I PsaF, reaction centre subunit III superfamily	Homologous Superfamily
F	IPR003666	Photosystem I PsaF, reaction centre subunit III	Family
E	IPR008990	Electron transport accessory-like domain superfamily	Homologous Superfamily
E	IPR003375	Photosystem I PsaE, reaction centre subunit IV	Family
D	IPR003685	Photosystem I PsaD	Family
D	IPR036579	Photosystem I, reaction centre subunit PsaD superfamily	Homologous Superfamily
C	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
C	IPR050157	Photosystem I iron-sulfur center	Family
C	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
C	IPR017491	Photosystem I protein PsaC	Family
B	IPR036408	Photosystem I PsaA/PsaB superfamily	Homologous Superfamily
B	IPR001280	Photosystem I PsaA/PsaB	Family
B	IPR006244	Photosystem I PsaB	Family
B	IPR020586	Photosystem I PsaA/PsaB, conserved site	Conserved Site
L [auth X]	IPR036243	Photosystem I PsaX superfamily	Homologous Superfamily
L [auth X]	IPR012986	Photosystem I PsaX	Family
K [auth M]	IPR010010	Photosystem I PsaM, reaction centre	Family
K [auth M]	IPR037279	Photosystem I PsaM, reaction centre superfamily	Homologous Superfamily
J [auth L]	IPR003757	Photosystem I PsaL, reaction centre subunit XI	Domain
J [auth L]	IPR022980	Photosystem I, reaction centre subunit XI	Family
J [auth L]	IPR036592	Photosystem I PsaL, reaction centre subunit XI superfamily	Homologous Superfamily
A	IPR006243	Photosystem I PsaA	Family
A	IPR036408	Photosystem I PsaA/PsaB superfamily	Homologous Superfamily
A	IPR001280	Photosystem I PsaA/PsaB	Family
A	IPR020586	Photosystem I PsaA/PsaB, conserved site	Conserved Site

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, E, F A, B, C, E, F, G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth X]	OPM	Transmembrane	Alpha-helical polytopic	Photosystems	Photosystem I

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, E, F A, B, C, E, F, G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth X]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, E, F A, B, C, E, F, G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth X]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, E, F A, B, C, E, F, G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth X]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Photosystems	Photosystem I. XFEL room temperature structure, dark state, LCLS/SwissFel