5YQ7 | pdb_00005yq7

Cryo-EM structure of the RC-LH core complex from Roseiflexus castenholzii

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth L]	SCOP2 Family	Bacterial photosystem II reaction centre, L and M subunits	8072654	4002035	SCOP2 (2022-06-29)
D [auth L]	SCOP2 Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8072655	3000736	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
R [auth O]	UNK_F_TYPE	e5yq7O1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
Q	UNK_F_TYPE	e5yq7Q1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
P [auth S]	UNK_F_TYPE	e5yq7S1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
N [auth U]	UNK_F_TYPE	e5yq7U1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
M [auth W]	UNK_F_TYPE	e5yq7W1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
L [auth G]	UNK_F_TYPE	e5yq7G1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
K [auth I]	UNK_F_TYPE	e5yq7I1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
I [auth K]	UNK_F_TYPE	e5yq7K1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
H [auth 2]	UNK_F_TYPE	e5yq721	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
G [auth 4]	UNK_F_TYPE	e5yq741	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
F [auth 6]	UNK_F_TYPE	e5yq761	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
E [auth 8]	UNK_F_TYPE	e5yq781	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
C [auth 0]	UNK_F_TYPE	e5yq701	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
B	UNK_F_TYPE	e5yq7B1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)
A [auth E]	UNK_F_TYPE	e5yq7E1	A: extended segments	X: Bacterial light-harvesting complex subunits (From Topology)	H: Bacterial light-harvesting complex subunits (From Topology)	T: Bacterial light-harvesting complex subunits	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth L]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
IA [auth M]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
J [auth C]	PF02276	Photosynthetic reaction centre cytochrome C subunit (CytoC_RC)	Photosynthetic reaction centre cytochrome C subunit	-	Family
A [auth E], B, C [auth 0], E [auth 8], F [auth 6], A [auth E], B, C [auth 0], E [auth 8], F [auth 6], G [auth 4], H [auth 2], I [auth K], K [auth I], L [auth G], M [auth W], N [auth U], P [auth S], Q, R [auth O]	PF00556	Antenna complex alpha/beta subunit (LHC)	Antenna complex alpha/beta subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth L]	Precursor for L subunits of photosynthetic reaction center	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain photosynthetic electron transport in photosystem II metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure endomembrane system membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cellular anatomical structure endomembrane system membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle
AA [auth A], BA [auth 9], CA [auth 7], DA [auth 5], EA [auth 3], AA [auth A], BA [auth 9], CA [auth 7], DA [auth 5], EA [auth 3], FA [auth 1], O [auth T], S [auth V], T [auth R], U [auth P], V [auth N], W [auth J], X [auth H], Y [auth F], Z [auth D]	Alpha subunit of light-harvesting 1	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy	membrane-bounded organelle intracellular organelle organelle envelope organelle inner membrane cellular anatomical structure intracellular anatomical structure organelle membrane organelle membrane cell periphery plasma membrane plasma membrane light-harvesting complex protein-containing complex intracellular vesicle membrane-bounded organelle intracellular organelle organelle envelope organelle inner membrane cellular anatomical structure intracellular anatomical structure organelle membrane organelle membrane cell periphery plasma membrane plasma membrane light-harvesting complex protein-containing complex intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle cytoplasmic vesicle cytoplasm vesicle
GA [auth Y]	Peptide from Precursor for L and M subunits of photosynthetic reaction center	-	-	-
IA [auth M]	Precursor for M subunits of photosynthetic reaction center	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain photosynthetic electron transport in photosystem II metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure endomembrane system membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cellular anatomical structure endomembrane system membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle
HA [auth X]	Subunit X	-	-	-
J [auth C]	Cytochrome subunit of photosynthetic reaction center	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm cellular anatomical structure membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle
A [auth E], B, C [auth 0], E [auth 8], F [auth 6], A [auth E], B, C [auth 0], E [auth 8], F [auth 6], G [auth 4], H [auth 2], I [auth K], K [auth I], L [auth G], M [auth W], N [auth U], P [auth S], Q, R [auth O]	Beta subunit of light-harvesting 1	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy	cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle cell periphery cellular anatomical structure plasma membrane membrane membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular anatomical structure intracellular vesicle plasma membrane-derived chromatophore light-harvesting complex intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth L]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
D [auth L]	IPR000484	Photosynthetic reaction centre, L/M	Family
D [auth L]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
D [auth L]	IPR005871	Photosynthetic reaction centre, L subunit	Family
AA [auth A], BA [auth 9], CA [auth 7], DA [auth 5], EA [auth 3], AA [auth A], BA [auth 9], CA [auth 7], DA [auth 5], EA [auth 3], FA [auth 1], O [auth T], S [auth V], T [auth R], U [auth P], V [auth N], W [auth J], X [auth H], Y [auth F], Z [auth D]	IPR002361	Antenna complex, alpha subunit conserved site	Conserved Site
AA [auth A], BA [auth 9], CA [auth 7], DA [auth 5], EA [auth 3], AA [auth A], BA [auth 9], CA [auth 7], DA [auth 5], EA [auth 3], FA [auth 1], O [auth T], S [auth V], T [auth R], U [auth P], V [auth N], W [auth J], X [auth H], Y [auth F], Z [auth D]	IPR035889	Light-harvesting complex	Homologous Superfamily
IA [auth M]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
IA [auth M]	IPR000484	Photosynthetic reaction centre, L/M	Family
IA [auth M]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
IA [auth M]	IPR005871	Photosynthetic reaction centre, L subunit	Family
J [auth C]	IPR036280	Multiheme cytochrome superfamily	Homologous Superfamily
J [auth C]	IPR023119	Multihaem cytochrome, PRC subunit superfamily	Homologous Superfamily
J [auth C]	IPR003158	Photosynthetic reaction centre, cytochrome c subunit	Family
A [auth E], B, C [auth 0], E [auth 8], F [auth 6], A [auth E], B, C [auth 0], E [auth 8], F [auth 6], G [auth 4], H [auth 2], I [auth K], K [auth I], L [auth G], M [auth W], N [auth U], P [auth S], Q, R [auth O]	IPR000066	Antenna complex, alpha/beta subunit	Domain
A [auth E], B, C [auth 0], E [auth 8], F [auth 6], A [auth E], B, C [auth 0], E [auth 8], F [auth 6], G [auth 4], H [auth 2], I [auth K], K [auth I], L [auth G], M [auth W], N [auth U], P [auth S], Q, R [auth O]	IPR023624	Antenna complex, beta domain superfamily	Homologous Superfamily
A [auth E], B, C [auth 0], E [auth 8], F [auth 6], A [auth E], B, C [auth 0], E [auth 8], F [auth 6], G [auth 4], H [auth 2], I [auth K], K [auth I], L [auth G], M [auth W], N [auth U], P [auth S], Q, R [auth O]	IPR035889	Light-harvesting complex	Homologous Superfamily
A [auth E], B, C [auth 0], E [auth 8], F [auth 6], A [auth E], B, C [auth 0], E [auth 8], F [auth 6], G [auth 4], H [auth 2], I [auth K], K [auth I], L [auth G], M [auth W], N [auth U], P [auth S], Q, R [auth O]	IPR002362	Light-harvesting protein B beta chain	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth E], AA [auth A], B, BA [auth 9], C [auth 0] A [auth E], AA [auth A], B, BA [auth 9], C [auth 0], CA [auth 7], D [auth L], DA [auth 5], E [auth 8], EA [auth 3], F [auth 6], FA [auth 1], G [auth 4], H [auth 2], I [auth K], IA [auth M], J [auth C], K [auth I], L [auth G], M [auth W], N [auth U], O [auth T], P [auth S], Q, R [auth O], S [auth V], T [auth R], U [auth P], V [auth N], W [auth J], X [auth H], Y [auth F], Z [auth D]	OPM	Transmembrane	Alpha-helical polytopic	Photosystems	Bacterial photosystems

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth E], AA [auth A], B, BA [auth 9], C [auth 0] A [auth E], AA [auth A], B, BA [auth 9], C [auth 0], CA [auth 7], D [auth L], DA [auth 5], E [auth 8], EA [auth 3], F [auth 6], FA [auth 1], G [auth 4], H [auth 2], I [auth K], IA [auth M], J [auth C], K [auth I], L [auth G], M [auth W], N [auth U], O [auth T], P [auth S], Q, R [auth O], S [auth V], T [auth R], U [auth P], V [auth N], W [auth J], X [auth H], Y [auth F], Z [auth D]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth E], AA [auth A], B, BA [auth 9], C [auth 0] A [auth E], AA [auth A], B, BA [auth 9], C [auth 0], CA [auth 7], D [auth L], DA [auth 5], E [auth 8], EA [auth 3], F [auth 6], FA [auth 1], G [auth 4], H [auth 2], I [auth K], IA [auth M], J [auth C], K [auth I], L [auth G], M [auth W], N [auth U], O [auth T], P [auth S], Q, R [auth O], S [auth V], T [auth R], U [auth P], V [auth N], W [auth J], X [auth H], Y [auth F], Z [auth D]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Light-Harvesting+Reaction Center Complexes	RC-LH core complex

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.