5ZGH | pdb_00005zgh

Cryo-EM structure of the red algal PSI-LHCR

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: 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)
A [auth 1]	SCOP2B Superfamily	Chlorophyll a-b binding protein	8098062	3000343	SCOP2B (2022-06-29)
H [auth E]	SCOP2B Superfamily	Electron transport accessory proteins	8074496	3000325	SCOP2B (2022-06-29)
I [auth F]	SCOP2B Superfamily	Subunit III of photosystem I reaction centre, PsaF	8074440	3000813	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	Photosystem I subunit PsaD	8074490	3000951	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Photosystem I subunits PsaA/PsaB	8074464	3000850	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	Photosystem I subunits PsaA/PsaB	8074456	3000850	SCOP2B (2022-06-29)
B [auth 2]	SCOP2B Superfamily	Chlorophyll a-b binding protein	8077006	3000343	SCOP2B (2022-06-29)
N [auth M]	SCOP2B Superfamily	Subunit XII of photosystem I reaction centre, PsaM	8074452	3000829	SCOP2B (2022-06-29)
M [auth L]	SCOP2B Superfamily	Photosystem I reaction center subunit XI, PsaL	8087172	3000870	SCOP2B (2022-06-29)
K [auth J]	SCOP2B Superfamily	Subunit IX of photosystem I reaction centre, PsaJ	8074514	3000824	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth 1]	Diphthamide_syn	e5zgh11	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)
F [auth C]	Diphthamide_syn	e5zghC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)
H [auth E]	UDPGP	e5zghE1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (v294.1)
J [auth I]	UDPGP	e5zghI1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (v294.1)
I [auth F]	Diphthamide_syn	e5zghF1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)
G [auth D]	UDPGP	e5zghD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (v294.1)
E [auth B]	Diphthamide_syn	e5zghB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)
D [auth A]	Diphthamide_syn	e5zghA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)
C [auth 3]	Diphthamide_syn	e5zgh31	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)
B [auth 2]	Diphthamide_syn	e5zgh21	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)
N [auth M]	UDPGP	e5zghM1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (v294.1)
M [auth L]	UDPGP	e5zghL1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (v294.1)
L [auth K]	Diphthamide_syn	e5zghK1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)
K [auth J]	Diphthamide_syn	e5zghJ1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Diphthamide_syn	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth C]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
H [auth E]	2.30.30.50	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I [auth F]	1.10.8.110	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
G [auth D]	3.30.1470.10	Alpha Beta	2-Layer Sandwich	Photosystem 1 Reaction Centre Subunit Ii	Chain: D	CATH (utative)
E [auth B]	1.20.1130.10	Mainly Alpha	Up-down Bundle	Photosystem I p700 chlorophyll A apoprotein A1	Photosystem I PsaA/PsaB	CATH (utative)
D [auth A]	1.20.1130.10	Mainly Alpha	Up-down Bundle	Photosystem I p700 chlorophyll A apoprotein A1	Photosystem I PsaA/PsaB	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 1]	PF00504	Chlorophyll A-B binding protein (Chloroa_b-bind)	Chlorophyll A-B binding protein	-	Family
F [auth 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
H [auth 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
J [auth I]	PF00796	Photosystem I reaction centre subunit VIII (PSI_8)	Photosystem I reaction centre subunit VIII	-	Family
E [auth B]	PF00223	Photosystem I psaA/psaB protein (PsaA_PsaB)	Photosystem I psaA/psaB protein	-	Family
D [auth A]	PF00223	Photosystem I psaA/psaB protein (PsaA_PsaB)	Photosystem I psaA/psaB protein	-	Family
B [auth 2]	PF00504	Chlorophyll A-B binding protein (Chloroa_b-bind)	Chlorophyll A-B binding protein	-	Family
N [auth M]	PF07465	Photosystem I protein M (PsaM) (PsaM)	Photosystem I protein M (PsaM)	-	Family
L [auth K]	PF01241	Photosystem I psaG / psaK (PSI_PSAK)	Photosystem I psaG / psaK	-	Family
K [auth J]	PF01701	Photosystem I reaction centre subunit IX / PsaJ (PSI_PsaJ)	Photosystem I reaction centre subunit IX / PsaJ	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 1]	Lhcr1	chlorophyll binding binding tetrapyrrole binding	photosynthesis photosynthesis, light reaction photosynthesis, light harvesting metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast
F [auth C]	PsaC	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	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast membrane intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane protein-containing complex photosystem photosystem I membrane protein complex
H [auth E]	PsaE	-	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
J [auth I]	PsaI	-	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 thylakoid membrane-bounded organelle 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 thylakoid membrane-bounded organelle plastid membrane plastid intracellular membrane-bounded organelle plastid thylakoid membrane thylakoid membrane plastid thylakoid organelle envelope cytoplasm organelle membrane plastid envelope
O	PsaO	-	-	-
I [auth F]	PsaF	-	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 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 chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
G [auth D]	PsaD	-	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 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 chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
E [auth B]	PsaB	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	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast membrane intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane protein-containing complex photosystem photosystem I membrane protein complex
D [auth A]	PsaA	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	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast membrane intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane protein-containing complex photosystem photosystem I membrane protein complex
C [auth 3]	Lhcr3	-	-	-
B [auth 2]	Lhcr2	chlorophyll binding binding tetrapyrrole binding	photosynthesis photosynthesis, light reaction photosynthesis, light harvesting metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast
N [auth M]	PsaM	-	photosynthesis metabolic process cellular process	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast membrane intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane protein-containing complex photosystem photosystem I membrane protein complex
M [auth L]	PsaL	-	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 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 chloroplast thylakoid membrane membrane-bounded organelle plastid membrane plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid organelle envelope bounding membrane of organelle plastid envelope chloroplast intracellular membrane-bounded organelle thylakoid membrane chloroplast thylakoid outer membrane cytoplasm organelle membrane
L [auth K]	PsaK	-	photosynthesis metabolic process cellular process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membrane membraneless organelle intracellular membraneless organelle photosynthetic membrane thylakoid membrane thylakoid protein-containing complex photosystem photosystem I membrane protein complex
K [auth J]	PsaJ	-	photosynthesis metabolic process cellular process	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope cellular anatomical structure bounding membrane of organelle membraneless organelle plastid envelope thylakoid chloroplast membrane intracellular membraneless organelle intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid outer membrane cytoplasm photosynthetic membrane organelle membrane protein-containing complex photosystem photosystem I membrane protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 1]	IPR001344	Chlorophyll A-B binding protein, plant and chromista	Family
A [auth 1]	IPR022796	Chlorophyll A-B binding protein	Family
F [auth C]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
F [auth C]	IPR050157	Photosystem I iron-sulfur center	Family
F [auth C]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
F [auth C]	IPR017491	Photosystem I protein PsaC	Family
H [auth E]	IPR008990	Electron transport accessory-like domain superfamily	Homologous Superfamily
H [auth E]	IPR003375	Photosystem I PsaE, reaction centre subunit IV	Family
J [auth I]	IPR036357	Photosystem I reaction centre subunit VIII superfamily	Homologous Superfamily
J [auth I]	IPR001302	Photosystem I reaction centre subunit VIII	Family
O	IPR017498	Photosystem I PsaO	Family
I [auth F]	IPR036577	Photosystem I PsaF, reaction centre subunit III superfamily	Homologous Superfamily
I [auth F]	IPR003666	Photosystem I PsaF, reaction centre subunit III	Family
G [auth D]	IPR003685	Photosystem I PsaD	Family
G [auth D]	IPR036579	Photosystem I, reaction centre subunit PsaD superfamily	Homologous Superfamily
E [auth B]	IPR036408	Photosystem I PsaA/PsaB superfamily	Homologous Superfamily
E [auth B]	IPR001280	Photosystem I PsaA/PsaB	Family
E [auth B]	IPR006244	Photosystem I PsaB	Family
E [auth B]	IPR020586	Photosystem I PsaA/PsaB, conserved site	Conserved Site
D [auth A]	IPR006243	Photosystem I PsaA	Family
D [auth A]	IPR036408	Photosystem I PsaA/PsaB superfamily	Homologous Superfamily
D [auth A]	IPR001280	Photosystem I PsaA/PsaB	Family
D [auth A]	IPR020586	Photosystem I PsaA/PsaB, conserved site	Conserved Site
B [auth 2]	IPR001344	Chlorophyll A-B binding protein, plant and chromista	Family
B [auth 2]	IPR022796	Chlorophyll A-B binding protein	Family
N [auth M]	IPR010010	Photosystem I PsaM, reaction centre	Family
N [auth M]	IPR037279	Photosystem I PsaM, reaction centre superfamily	Homologous Superfamily
M [auth L]	IPR003757	Photosystem I PsaL, reaction centre subunit XI	Domain
M [auth L]	IPR022980	Photosystem I, reaction centre subunit XI	Family
M [auth L]	IPR036592	Photosystem I PsaL, reaction centre subunit XI superfamily	Homologous Superfamily
L [auth K]	IPR037101	Photosystem I reaction centre subunit PsaK	Homologous Superfamily
L [auth K]	IPR000549	Photosystem I reaction center subunit V/PsaK	Family
L [auth K]	IPR035982	Photosystem I reaction centre subunit PsaK superfamily	Homologous Superfamily
K [auth J]	IPR002615	Photosystem I PsaJ, reaction centre subunit IX	Family
K [auth J]	IPR036062	Photosystem I PsaJ, reaction centre subunit IX superfamily	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
D [auth A], E [auth B], F [auth C], H [auth E], I [auth F] D [auth A], E [auth B], F [auth C], H [auth E], I [auth F], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Photosystem+Light-Harvesting Complex Supercomplex	Photosystem I-Light harvesting complex supercomplex with 5 Lhcr antennae