8HJV | pdb_00008hjv

Cryo-EM structure of carotenoid-depleted RC-LH complex from Roseiflexus castenholzii at 10,000 lux

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
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)
Z [auth Q]	Cullin_AB	e8hjvQ1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
X [auth O]	Cullin_AB	e8hjvO1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
T [auth K]	Cullin_AB	e8hjvK1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
R [auth I]	Cullin_AB	e8hjvI1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
P [auth G]	Cullin_AB	e8hjvG1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
N [auth E]	Cullin_AB	e8hjvE1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
L [auth B]	Cullin_AB	e8hjvB1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
I [auth 8]	Cullin_AB	e8hjv81	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
G [auth 6]	Cullin_AB	e8hjv61	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
FA [auth W]	Cullin_AB	e8hjvW1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
E [auth 4]	Cullin_AB	e8hjv41	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
DA [auth U]	Cullin_AB	e8hjvU1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
C [auth 2]	Cullin_AB	e8hjv21	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
BA [auth S]	Cullin_AB	e8hjvS1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
A [auth 0]	Cullin_AB	e8hjv01	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
HA [auth C]	PF02276	Photosynthetic reaction centre cytochrome C subunit (CytoC_RC)	Photosynthetic reaction centre cytochrome C subunit	-	Family
V [auth M]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
U [auth L]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], FA [auth W], G [auth 6], I [auth 8], L [auth B], N [auth E], P [auth G], R [auth I], T [auth K], X [auth O], Z [auth Q]	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
IA [auth Z]	SUBUNIT Z	-	-	-
HA [auth C]	MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN	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	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 cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle
GA [auth Y]	SUBUNIT Y	-	-	-
V [auth M]	Reaction center protein M chain	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-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 endomembrane system 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
U [auth L]	Reaction center protein L chain	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-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 endomembrane system 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 R], B [auth 1], CA [auth T], D [auth 3], EA [auth V], AA [auth R], B [auth 1], CA [auth T], D [auth 3], EA [auth V], F [auth 5], H [auth 7], J [auth 9], K [auth A], M [auth D], O [auth F], Q [auth H], S [auth J], W [auth N], Y [auth P]	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
A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], FA [auth W], G [auth 6], I [auth 8], L [auth B], N [auth E], P [auth G], R [auth I], T [auth K], X [auth O], Z [auth Q]	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
HA [auth C]	IPR036280	Multiheme cytochrome superfamily	Homologous Superfamily
HA [auth C]	IPR023119	Multihaem cytochrome, PRC subunit superfamily	Homologous Superfamily
HA [auth C]	IPR003158	Photosynthetic reaction centre, cytochrome c subunit	Family
V [auth M]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
V [auth M]	IPR000484	Photosynthetic reaction centre, L/M	Family
V [auth M]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
V [auth M]	IPR005871	Photosynthetic reaction centre, L subunit	Family
U [auth L]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
U [auth L]	IPR000484	Photosynthetic reaction centre, L/M	Family
U [auth L]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
U [auth L]	IPR005871	Photosynthetic reaction centre, L subunit	Family
AA [auth R], B [auth 1], CA [auth T], D [auth 3], EA [auth V], AA [auth R], B [auth 1], CA [auth T], D [auth 3], EA [auth V], F [auth 5], H [auth 7], J [auth 9], K [auth A], M [auth D], O [auth F], Q [auth H], S [auth J], W [auth N], Y [auth P]	IPR002361	Antenna complex, alpha subunit conserved site	Conserved Site
AA [auth R], B [auth 1], CA [auth T], D [auth 3], EA [auth V], AA [auth R], B [auth 1], CA [auth T], D [auth 3], EA [auth V], F [auth 5], H [auth 7], J [auth 9], K [auth A], M [auth D], O [auth F], Q [auth H], S [auth J], W [auth N], Y [auth P]	IPR035889	Light-harvesting complex	Homologous Superfamily
A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], FA [auth W], G [auth 6], I [auth 8], L [auth B], N [auth E], P [auth G], R [auth I], T [auth K], X [auth O], Z [auth Q]	IPR000066	Antenna complex, alpha/beta subunit	Domain
A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], FA [auth W], G [auth 6], I [auth 8], L [auth B], N [auth E], P [auth G], R [auth I], T [auth K], X [auth O], Z [auth Q]	IPR023624	Antenna complex, beta domain superfamily	Homologous Superfamily
A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], FA [auth W], G [auth 6], I [auth 8], L [auth B], N [auth E], P [auth G], R [auth I], T [auth K], X [auth O], Z [auth Q]	IPR035889	Light-harvesting complex	Homologous Superfamily
A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], A [auth 0], BA [auth S], C [auth 2], DA [auth U], E [auth 4], FA [auth W], G [auth 6], I [auth 8], L [auth B], N [auth E], P [auth G], R [auth I], T [auth K], X [auth O], Z [auth Q]	IPR002362	Light-harvesting protein B beta chain	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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