3D38

Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.

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: 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)
C [auth L]	d3d38l1	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	(Blastochloris viridis ) [TaxId: 1079 ],	SCOPe (2.08)
A [auth C]	d3d38c1	All alpha proteins	Multiheme cytochromes	Multiheme cytochromes	Photosynthetic reaction centre (cytochrome subunit)	Photosynthetic reaction centre (cytochrome subunit)	(Blastochloris viridis ) [TaxId: 1079 ],	SCOPe (2.08)
B [auth H]	d3d38h1	All beta proteins	PRC-barrel domain	PRC-barrel domain	Photosynthetic reaction centre, H-chain, cytoplasmic domain	Photosynthetic reaction centre	(Blastochloris viridis ) [TaxId: 1079 ],	SCOPe (2.08)
B [auth H]	d3d38h2	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	(Blastochloris viridis ) [TaxId: 1079 ],	SCOPe (2.08)
D [auth M]	d3d38m1	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	(Blastochloris viridis ) [TaxId: 1079 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth L]	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8042558	3000736	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	PRC cytochrome c repeat-like	8042555	3002452	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	PRC cytochrome c repeat-like	8090734	3002452	SCOP2B (2022-06-29)
B [auth H]	SCOP2B Superfamily	Photosystem II reaction centre subunit H, transmembrane region	8037684	3000750	SCOP2B (2022-06-29)
B [auth H]	SCOP2B Superfamily	PRC-barrel domain	8041991	3000637	SCOP2B (2022-06-29)
D [auth M]	SCOP2B Superfamily	Bacterial photosystem II reaction centre, L and M subunits	8042561	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)
C [auth L]	Photo_RC	e3d38L1	A: alpha bundles	X: Bacterial photosystem II reaction centre L and M subunits-like (From Topology)	H: Bacterial photosystem II reaction centre L and M subunits-like (From Topology)	T: Bacterial photosystem II reaction centre L and M subunits-like	F: Photo_RC	ECOD (1.6)
A [auth C]	CytoC_RC	e3d38C1	A: few secondary structure elements	X: Multiheme cytochromes	H: Photosynthetic reaction centre (cytochrome subunit) (From Topology)	T: Photosynthetic reaction centre (cytochrome subunit)	F: CytoC_RC	ECOD (1.6)
B [auth H]	PRCH_C	e3d38H1	A: beta barrels	X: SH3	H: PRC-barrel domain (From Topology)	T: PRC-barrel domain	F: PRCH_C	ECOD (1.6)
B [auth H]	PRCH_N	e3d38H2	A: extended segments	X: Photosystem II reaction centre subunit H, transmembrane region (From Topology)	H: Photosystem II reaction centre subunit H, transmembrane region (From Topology)	T: Photosystem II reaction centre subunit H, transmembrane region	F: PRCH_N	ECOD (1.6)
D [auth M]	Photo_RC	e3d38M1	A: alpha bundles	X: Bacterial photosystem II reaction centre L and M subunits-like (From Topology)	H: Bacterial photosystem II reaction centre L and M subunits-like (From Topology)	T: Bacterial photosystem II reaction centre L and M subunits-like	F: Photo_RC	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth L]	1.20.85.10	Mainly Alpha	Up-down Bundle	Photosynthetic Reaction Center, subunit M	domain 1	CATH (4.3.0)
A [auth C]	1.10.468.10	Mainly Alpha	Orthogonal Bundle	Photosynthetic Reaction Center, subunit C	domain 2	CATH (4.3.0)
B [auth H]	4.10.540.10	Few Secondary Structures	Irregular	Photosynthetic Reaction Center	Chain H, domain 1	CATH (4.3.0)
B [auth H]	3.90.50.10	Alpha Beta	Alpha-Beta Complex	Photosynthetic Reaction Center	Chain H, domain 2	CATH (4.3.0)
D [auth M]	1.20.85.10	Mainly Alpha	Up-down Bundle	Photosynthetic Reaction Center, subunit M	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth L]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family
A [auth C]	PF02276	Photosynthetic reaction centre cytochrome C subunit (CytoC_RC)	Photosynthetic reaction centre cytochrome C subunit	-	Family
B [auth H]	PF03967	Photosynthetic reaction centre, H-chain N-terminal region (PRCH)	Photosynthetic reaction centre, H-chain N-terminal region	-	Family
B [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
D [auth M]	PF00124	Photosynthetic reaction centre protein (Photo_RC)	Photosynthetic reaction centre protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth L]	Reaction center protein L chain	electron transfer activity electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity chlorophyll binding binding organic cyclic compound binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain cellular metabolic process 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 plasma membrane-derived chromatophore cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane-derived chromatophore cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle intracellular membrane-bounded organelle light-harvesting complex cytoplasmic vesicle vesicle
A [auth C]	Photosynthetic reaction center cytochrome c subunit	binding organic cyclic compound 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 cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane-derived chromatophore cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane-derived chromatophore cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle intracellular membrane-bounded organelle light-harvesting complex cytoplasmic vesicle vesicle
B [auth H]	Reaction center protein H chain	electron transfer activity electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity chlorophyll binding binding organic cyclic compound binding bacteriochlorophyll binding tetrapyrrole binding	photosynthesis photosynthesis, light reaction cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy	intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane-derived chromatophore cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane-derived chromatophore cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle intracellular membrane-bounded organelle light-harvesting complex cytoplasmic vesicle vesicle
D [auth M]	Reaction center protein M chain	electron transfer activity electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity chlorophyll binding binding organic cyclic compound binding bacteriochlorophyll binding tetrapyrrole binding cation binding ion binding metal ion binding small molecule binding	photosynthesis photosynthesis, light reaction photosynthetic electron transport chain cellular metabolic process 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 plasma membrane-derived chromatophore cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle plasma membrane light-harvesting complex intracellular anatomical structure plasma membrane-derived chromatophore membrane membrane plasma membrane-derived chromatophore cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle cytoplasm photosynthetic membrane thylakoid non-membrane-bounded organelle membrane-bounded organelle plasma membrane light-harvesting complex protein-containing complex intracellular vesicle intracellular membrane-bounded organelle light-harvesting complex cytoplasmic vesicle vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth L]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
C [auth L]	IPR000484	Photosynthetic reaction centre, L/M	Family
C [auth L]	IPR005871	Photosynthetic reaction centre, L subunit	Family
A [auth C]	IPR036280	Multiheme cytochrome superfamily	Homologous Superfamily
A [auth C]	IPR023119	Multihaem cytochrome, PRC subunit superfamily	Homologous Superfamily
A [auth C]	IPR003158	Photosynthetic reaction centre, cytochrome c subunit	Family
B [auth H]	IPR014747	Bacterial photosynthetic reaction centre, H-chain, C-terminal	Homologous Superfamily
B [auth H]	IPR015810	Photosynthetic reaction centre, H subunit, N-terminal	Domain
B [auth H]	IPR005652	Photosynthetic reaction centre, H subunit	Family
B [auth H]	IPR037097	Photosynthetic reaction centre, H subunit, N-terminal domain superfamily	Homologous Superfamily
B [auth H]	IPR011033	PRC-barrel-like superfamily	Homologous Superfamily
B [auth H]	IPR027275	PRC-barrel domain	Domain
D [auth M]	IPR036854	Photosystem II protein D1/D2 superfamily	Homologous Superfamily
D [auth M]	IPR005781	Photosynthetic reaction centre, M subunit	Family
D [auth M]	IPR000484	Photosynthetic reaction centre, L/M	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth C], B [auth H], C [auth L], D [auth M]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth C], B [auth H], C [auth L], D [auth M]	MemProtMD	Annotated as membrane protein by MemProtMD

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth H]	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.