8YY9 | pdb_00008yy9

Cryo-EM structure of a tri-heme cytochrome-associated RC-LH1 complex from a marine photoheterotrophic bacterium, purified with magnesium-free solutions.

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
MA [auth C]	Lip_C	e8yy9C01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Lip_C	ECOD (v295)
LA [auth H]	Lip_C	e8yy9H01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Lip_C	ECOD (v295)
KA [auth L]	Lip_C	e8yy9L01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Lip_C	ECOD (v295)
JA [auth M]	Lip_C	e8yy9M01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Lip_C	ECOD (v295)
Z [auth f]		e8yy9f1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
X [auth g]		e8yy9g1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
V [auth i]		e8yy9i1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
T [auth j]		e8yy9j1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
R [auth k]		e8yy9k1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
P [auth n]		e8yy9n1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
N [auth 2]		e8yy921	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
M [auth p]		e8yy9p1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
L [auth q]		e8yy9q1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
J [auth r]		e8yy9r1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
HA [auth a]		e8yy9a1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
H [auth s]		e8yy9s1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
FA [auth b]		e8yy9b1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
F [auth t]		e8yy9t1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
DA [auth d]		e8yy9d1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
D [auth v]	Lip_C	e8yy9v01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Lip_C	ECOD (v295)
BA [auth e]		e8yy9e1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
Y [auth G]		e8yy9G1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
W [auth I]		e8yy9I1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
U [auth J]		e8yy9J1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
S [auth K]		e8yy9K1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
Q [auth N]		e8yy9N1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
O [auth 1]		e8yy911	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
K [auth R]		e8yy9R1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
IA [auth A]		e8yy9A1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
I [auth Q]		e8yy9Q1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
GA [auth B]		e8yy9B1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
G [auth T]		e8yy9T1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
EA [auth D]		e8yy9D1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
E [auth S]		e8yy9S1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
CA [auth E]		e8yy9E1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
C [auth V]		e8yy9V1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
AA [auth F]		e8yy9F1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F:	ECOD (v295)
A [auth P]	Lip_C	e8yy9P01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Lip_C	ECOD (v295)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
MA [auth C]	PF02276	Photosynthetic reaction centre cytochrome C subunit (CytoC_RC)	Photosynthetic reaction centre cytochrome C subunit	-	Family
LA [auth H]	PF03967	Photosynthetic reaction centre, H-chain N-terminal region (PRCH)	Photosynthetic reaction centre, H-chain N-terminal region	-	Family
LA [auth H]	PF05239	PRC-barrel domain (PRC)	PRC-barrel domain	The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, ...	The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain [1].	Domain
KA [auth L]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
JA [auth M]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], H [auth s], HA [auth a], J [auth r], L [auth q], M [auth p], N [auth 2], P [auth n], R [auth k], T [auth j], V [auth i], X [auth g], Z [auth f]	PF00556	Antenna complex alpha/beta subunit (LHC)	Antenna complex alpha/beta subunit		Domain
A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], EA [auth D], G [auth T], GA [auth B], I [auth Q], IA [auth A], K [auth R], O [auth 1], Q [auth N], S [auth K], U [auth J], W [auth I], Y [auth G]	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
MA [auth C]	Photosynthetic reaction center cytochrome c subunit	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
LA [auth H]	Reaction center protein H chain	-	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
KA [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	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
JA [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	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
BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], H [auth s], HA [auth a], J [auth r], L [auth q], M [auth p], N [auth 2], P [auth n], R [auth k], T [auth j], V [auth i], X [auth g], Z [auth f]	Antenna pigment protein 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
B [auth O]	Reaction center protein O chain	-	-	-
A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], EA [auth D], G [auth T], GA [auth B], I [auth Q], IA [auth A], K [auth R], O [auth 1], Q [auth N], S [auth K], U [auth J], W [auth I], Y [auth G]	Antenna pigment protein 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
MA [auth C]	IPR036280	Multiheme cytochrome superfamily	Homologous Superfamily
MA [auth C]	IPR023119	Multihaem cytochrome, PRC subunit superfamily	Homologous Superfamily
MA [auth C]	IPR003158	Photosynthetic reaction centre, cytochrome c subunit	Family
LA [auth H]	IPR014747	Bacterial photosynthetic reaction centre, H-chain, C-terminal	Homologous Superfamily
LA [auth H]	IPR015810	Photosynthetic reaction centre, H subunit, N-terminal	Domain
LA [auth H]	IPR005652	Photosynthetic reaction centre, H subunit	Family
LA [auth H]	IPR037097	Photosynthetic reaction centre, H subunit, N-terminal domain superfamily	Homologous Superfamily
LA [auth H]	IPR011033	PRC-barrel-like superfamily	Homologous Superfamily
LA [auth H]	IPR027275	PRC-barrel domain	Domain
KA [auth L]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
KA [auth L]	IPR000484	Photosynthetic reaction centre, L/M	Family
KA [auth L]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
KA [auth L]	IPR005871	Photosynthetic reaction centre, L subunit	Family
JA [auth M]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
JA [auth M]	IPR005781	Photosynthetic reaction centre, M subunit	Family
JA [auth M]	IPR000484	Photosynthetic reaction centre, L/M	Family
JA [auth M]	IPR055265	Photosynthetic reaction centre, L/M, conserved site	Conserved Site
BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], H [auth s], HA [auth a], J [auth r], L [auth q], M [auth p], N [auth 2], P [auth n], R [auth k], T [auth j], V [auth i], X [auth g], Z [auth f]	IPR000066	Antenna complex, alpha/beta subunit	Domain
BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], H [auth s], HA [auth a], J [auth r], L [auth q], M [auth p], N [auth 2], P [auth n], R [auth k], T [auth j], V [auth i], X [auth g], Z [auth f]	IPR023624	Antenna complex, beta domain superfamily	Homologous Superfamily
BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], H [auth s], HA [auth a], J [auth r], L [auth q], M [auth p], N [auth 2], P [auth n], R [auth k], T [auth j], V [auth i], X [auth g], Z [auth f]	IPR035889	Light-harvesting complex	Homologous Superfamily
BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], H [auth s], HA [auth a], J [auth r], L [auth q], M [auth p], N [auth 2], P [auth n], R [auth k], T [auth j], V [auth i], X [auth g], Z [auth f]	IPR023623	Antenna complex, beta subunit, conserved site	Conserved Site
BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], BA [auth e], D [auth v], DA [auth d], F [auth t], FA [auth b], H [auth s], HA [auth a], J [auth r], L [auth q], M [auth p], N [auth 2], P [auth n], R [auth k], T [auth j], V [auth i], X [auth g], Z [auth f]	IPR002362	Light-harvesting protein B beta chain	Family
A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], EA [auth D], G [auth T], GA [auth B], I [auth Q], IA [auth A], K [auth R], O [auth 1], Q [auth N], S [auth K], U [auth J], W [auth I], Y [auth G]	IPR000066	Antenna complex, alpha/beta subunit	Domain
A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], EA [auth D], G [auth T], GA [auth B], I [auth Q], IA [auth A], K [auth R], O [auth 1], Q [auth N], S [auth K], U [auth J], W [auth I], Y [auth G]	IPR018332	Antenna complex, alpha subunit	Family
A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], EA [auth D], G [auth T], GA [auth B], I [auth Q], IA [auth A], K [auth R], O [auth 1], Q [auth N], S [auth K], U [auth J], W [auth I], Y [auth G]	IPR002361	Antenna complex, alpha subunit conserved site	Conserved Site
A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], A [auth P], AA [auth F], C [auth V], CA [auth E], E [auth S], EA [auth D], G [auth T], GA [auth B], I [auth Q], IA [auth A], K [auth R], O [auth 1], Q [auth N], S [auth K], U [auth J], W [auth I], Y [auth G]	IPR035889	Light-harvesting complex	Homologous Superfamily

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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.