1L9J | pdb_00001l9j

X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H [auth D]	d1l9jd_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	Cytochrome c2	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
D [auth C]	d1l9jc_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	Cytochrome c2	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
G [auth T]	d1l9jt1	All beta proteins	PRC-barrel domain	PRC-barrel domain	Photosynthetic reaction centre, H-chain, cytoplasmic domain	Photosynthetic reaction centre	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
G [auth T]	d1l9jt2	Membrane and cell surface proteins and peptides	Single transmembrane helix	Photosystem II reaction centre subunit H, transmembrane region	Photosystem II reaction centre subunit H, transmembrane region	Photosystem II reaction centre subunit H, transmembrane region	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
C [auth H]	d1l9jh1	All beta proteins	PRC-barrel domain	PRC-barrel domain	Photosynthetic reaction centre, H-chain, cytoplasmic domain	Photosynthetic reaction centre	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
C [auth H]	d1l9jh2	Membrane and cell surface proteins and peptides	Single transmembrane helix	Photosystem II reaction centre subunit H, transmembrane region	Photosystem II reaction centre subunit H, transmembrane region	Photosystem II reaction centre subunit H, transmembrane region	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
F [auth S]	d1l9js_	Membrane and cell surface proteins and peptides	Bacterial photosystem II reaction centre, L and M subunits	Bacterial photosystem II reaction centre, L and M subunits	Bacterial photosystem II reaction centre, L and M subunits	M (medium) subunit	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
B [auth M]	d1l9jm_	Membrane and cell surface proteins and peptides	Bacterial photosystem II reaction centre, L and M subunits	Bacterial photosystem II reaction centre, L and M subunits	Bacterial photosystem II reaction centre, L and M subunits	M (medium) subunit	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
A [auth L]	d1l9jl_	Membrane and cell surface proteins and peptides	Bacterial photosystem II reaction centre, L and M subunits	Bacterial photosystem II reaction centre, L and M subunits	Bacterial photosystem II reaction centre, L and M subunits	L (light) subunit	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)
E [auth R]	d1l9jr_	Membrane and cell surface proteins and peptides	Bacterial photosystem II reaction centre, L and M subunits	Bacterial photosystem II reaction centre, L and M subunits	Bacterial photosystem II reaction centre, L and M subunits	L (light) subunit	(Cereibacter sphaeroides ) [TaxId: 1063 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth D]	SCOP2B Superfamily	Cytochrome c	8036452	3000815	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Cytochrome c	8036452	3000815	SCOP2B (2022-06-29)
G [auth T]	SCOP2B Superfamily	Photosystem II reaction centre subunit H, transmembrane region	8041121	3000750	SCOP2B (2022-06-29)
G [auth T]	SCOP2B Superfamily	PRC-barrel domain	8041120	3000637	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	PRC-barrel domain	8041120	3000637	SCOP2B (2022-06-29)
C [auth H]	SCOP2B Superfamily	Photosystem II reaction centre subunit H, transmembrane region	8041121	3000750	SCOP2B (2022-06-29)
F [auth S]	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8034636	3000736	SCOP2B (2022-06-29)
B [auth M]	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8034636	3000736	SCOP2B (2022-06-29)
A [auth L]	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8034635	3000736	SCOP2B (2022-06-29)
E [auth R]	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8034635	3000736	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)
H [auth D]	MgsA_C	e1l9jD1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: MgsA_C	ECOD (develop294)
D [auth C]	MgsA_C	e1l9jC1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: MgsA_C	ECOD (develop294)
G [auth T]	Chromo	e1l9jT1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Chromo	ECOD (develop294)
G [auth T]	DUF1684	e1l9jT2	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (develop294)
C [auth H]	Chromo	e1l9jH1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Chromo	ECOD (develop294)
C [auth H]	DUF1684	e1l9jH2	A: alpha bundles	X: Lipocalins/Streptavidin	H: SH3	T: Transmembrane protein 14A	F: DUF1684	ECOD (develop294)
F [auth S]		e1l9jS1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
B [auth M]		e1l9jM1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
A [auth L]		e1l9jL1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
E [auth R]		e1l9jR1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth D]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
D [auth C]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
G [auth T]	4.10.540.10	Few Secondary Structures	Irregular	Photosynthetic Reaction Center	Chain H, domain 1	CATH (4.3.0)
G [auth T]	3.90.50.10	Alpha Beta	Alpha-Beta Complex	Photosynthetic Reaction Center	Chain H, domain 2	CATH (4.3.0)
C [auth H]	4.10.540.10	Few Secondary Structures	Irregular	Photosynthetic Reaction Center	Chain H, domain 1	CATH (4.3.0)
C [auth H]	3.90.50.10	Alpha Beta	Alpha-Beta Complex	Photosynthetic Reaction Center	Chain H, domain 2	CATH (4.3.0)
F [auth S]	1.20.85.10	Mainly Alpha	Up-down Bundle	Photosynthetic Reaction Center, subunit M	domain 1	CATH (4.3.0)
B [auth M]	1.20.85.10	Mainly Alpha	Up-down Bundle	Photosynthetic Reaction Center, subunit M	domain 1	CATH (4.3.0)
A [auth L]	1.20.85.10	Mainly Alpha	Up-down Bundle	Photosynthetic Reaction Center, subunit M	domain 1	CATH (4.3.0)
E [auth R]	1.20.85.10	Mainly Alpha	Up-down Bundle	Photosynthetic Reaction Center, subunit M	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth C], H [auth D]	cytochrome c-2	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	photosynthesis metabolic process cellular process	cellular anatomical structure periplasmic space
C [auth H], G [auth T]	REACTION CENTER PROTEIN H CHAIN	chlorophyll binding binding bacteriochlorophyll binding tetrapyrrole binding	photosynthesis photosynthesis, light reaction metabolic process cellular process generation of precursor metabolites and energy	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle light-harvesting complex intracellular membrane-bounded organelle cytoplasmic vesicle vesicle
B [auth M], F [auth S]	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	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle light-harvesting complex intracellular membrane-bounded organelle cytoplasmic vesicle vesicle
A [auth L], E [auth R]	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	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane intracellular membraneless organelle plasma membrane-derived chromatophore intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm photosynthetic membrane thylakoid membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle light-harvesting complex intracellular membrane-bounded organelle cytoplasmic vesicle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth C], H [auth D]	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
D [auth C], H [auth D]	IPR009056	Cytochrome c-like domain	Domain
D [auth C], H [auth D]	IPR002327	Cytochrome c, class IA/ IB	Family
C [auth H], G [auth T]	IPR014747	Bacterial photosynthetic reaction centre, H-chain, C-terminal	Homologous Superfamily
C [auth H], G [auth T]	IPR015810	Photosynthetic reaction centre, H subunit, N-terminal	Domain
C [auth H], G [auth T]	IPR005652	Photosynthetic reaction centre, H subunit	Family
C [auth H], G [auth T]	IPR037097	Photosynthetic reaction centre, H subunit, N-terminal domain superfamily	Homologous Superfamily
C [auth H], G [auth T]	IPR011033	PRC-barrel-like superfamily	Homologous Superfamily
C [auth H], G [auth T]	IPR027275	PRC-barrel domain	Domain
B [auth M], F [auth S]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
B [auth M], F [auth S]	IPR005781	Photosynthetic reaction centre, M subunit	Family
B [auth M], F [auth S]	IPR000484	Photosynthetic reaction centre, L/M	Family
B [auth M], F [auth S]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
A [auth L], E [auth R]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
A [auth L], E [auth R]	IPR000484	Photosynthetic reaction centre, L/M	Family
A [auth L], E [auth R]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
A [auth L], E [auth R]	IPR005871	Photosynthetic reaction centre, L subunit	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth L], B [auth M], C [auth H], E [auth R], F [auth S] A [auth L], B [auth M], C [auth H], E [auth R], F [auth S], G [auth T]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth L], B [auth M], C [auth H], E [auth R], F [auth S] A [auth L], B [auth M], C [auth H], E [auth R], F [auth S], G [auth T]	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.