1IJD | pdb_00001ijd

Crystallographic Structure of the LH3 Complex from Rhodopseudomonas acidophila strain 7050

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d1ijdf_	Membrane and cell surface proteins and peptides	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	(Rhodoblastus acidophilus ) [TaxId: 1074 ],	SCOPe (2.08)
D	d1ijdd_	Membrane and cell surface proteins and peptides	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	(Rhodoblastus acidophilus ) [TaxId: 1074 ],	SCOPe (2.08)
B	d1ijdb_	Membrane and cell surface proteins and peptides	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	(Rhodoblastus acidophilus ) [TaxId: 1074 ],	SCOPe (2.08)
E	d1ijde_	Membrane and cell surface proteins and peptides	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	(Rhodoblastus acidophilus ) [TaxId: 1074 ],	SCOPe (2.08)
C	d1ijdc_	Membrane and cell surface proteins and peptides	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	(Rhodoblastus acidophilus ) [TaxId: 1074 ],	SCOPe (2.08)
A	d1ijda_	Membrane and cell surface proteins and peptides	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	Light-harvesting complex subunits	(Rhodoblastus acidophilus ) [TaxId: 1074 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Light-harvesting complex subunits	8036617	3000199	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Light-harvesting complex subunits	8036617	3000199	SCOP2B (2022-06-29)
A	SCOP2 Family	Light-harvesting complex subunits	8024238	4003043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Light-harvesting complex subunits	8036617	3000199	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)
F	LHC_like	e1ijdF1	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: LHC_like	ECOD (1.6)
D	LHC_like	e1ijdD1	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: LHC_like	ECOD (1.6)
B	LHC_like	e1ijdB1	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: LHC_like	ECOD (1.6)
E	LHC_like	e1ijdE1	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: LHC_like	ECOD (1.6)
C	LHC_like	e1ijdC1	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: LHC_like	ECOD (1.6)
A	LHC_like	e1ijdA1	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: LHC_like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.20.5.250	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D	1.20.5.250	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.20.5.250	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
E	4.10.220.20	Few Secondary Structures	Irregular	Light-harvesting Protein	Light-harvesting complex	CATH (4.3.0)
C	4.10.220.20	Few Secondary Structures	Irregular	Light-harvesting Protein	Light-harvesting complex	CATH (4.3.0)
A	4.10.220.20	Few Secondary Structures	Irregular	Light-harvesting Protein	Light-harvesting complex	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	PF00556	Antenna complex alpha/beta subunit (LHC)	Antenna complex alpha/beta subunit		Domain
A, C, E	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
B, D, F	LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN	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
A, C, E	LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR000066	Antenna complex, alpha/beta subunit	Domain
B, D, F	IPR023624	Antenna complex, beta domain superfamily	Homologous Superfamily
B, D, F	IPR035889	Light-harvesting complex	Homologous Superfamily
B, D, F	IPR023623	Antenna complex, beta subunit, conserved site	Conserved Site
B, D, F	IPR002362	Light-harvesting protein B beta chain	Family
A, C, E	IPR000066	Antenna complex, alpha/beta subunit	Domain
A, C, E	IPR018332	Antenna complex, alpha subunit	Family
A, C, E	IPR002361	Antenna complex, alpha subunit conserved site	Conserved Site
A, C, E	IPR035889	Light-harvesting complex	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, F	OPM	Transmembrane	Alpha-helical polytopic	Photosystems	Light-harvesting complexes from bacteria

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D, E A, B, C, D, E, F	MemProtMD	Annotated as membrane protein by MemProtMD

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, E	FME	Parent Component: MET RESID: AA0021 , AA0566 PSI-MOD : N-formyl-L-methionine residue MOD:00030 , N-formyl-L-methionine (Met) MOD:00482 , N-[(L-histidin-1'-yl)methyl]-L-methionine (fMet) MOD:01890 , N-[(L-histidin-1'-yl)methyl]-L-methionine (Met) MOD:01891

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.