6LM1

The crystal structure of cyanorhodopsin (CyR) N4075R from cyanobacteria Tolypothrix sp. NIES-4075

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d6lm1c1	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	automated matches	automated matches	(Tolypothrix sp. NIES-4075 ) [TaxId: 2005459 ],	SCOPe (2.08)
C	d6lm1c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Tolypothrix sp. NIES-4075 ) [TaxId: 2005459 ],	SCOPe (2.08)
A	d6lm1a1	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	automated matches	automated matches	(Tolypothrix sp. NIES-4075 ) [TaxId: 2005459 ],	SCOPe (2.08)
A	d6lm1a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Tolypothrix sp. NIES-4075 ) [TaxId: 2005459 ],	SCOPe (2.08)
B	d6lm1b1	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	automated matches	automated matches	(Tolypothrix sp. NIES-4075 ) [TaxId: 2005459 ],	SCOPe (2.08)
B	d6lm1b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Tolypothrix sp. NIES-4075 ) [TaxId: 2005459 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	G protein-coupled receptor-like	8101237	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8101237	3000473	SCOP2B (2022-06-29)
B	SCOP2 Family	Bacteriorhodopsin-like	8101236	4001859	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	G protein-coupled receptor-like	8101237	3000473	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)
C	Bac_rhodopsin	e6lm1C1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Bac_rhodopsin	ECOD (1.6)
A	Bac_rhodopsin	e6lm1A1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Bac_rhodopsin	ECOD (1.6)
B	Bac_rhodopsin	e6lm1B1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: Bac_rhodopsin	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01036	Bacteriorhodopsin-like protein (Bac_rhodopsin)	Bacteriorhodopsin-like protein	The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, th ...	The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins. Some fungal examples are: Swiss:O74870, Swiss:P25619, Swiss:P38079, Swiss:Q12117.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Rhodopsin	passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity molecular transducer activity photoreceptor activity signaling receptor activity cation binding ion binding binding metal ion binding small molecule binding	phototransduction cellular response to stimulus detection of light stimulus response to light stimulus detection of external stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation response to external stimulus detection of abiotic stimulus cell communication detection of stimulus phototransduction cellular response to stimulus detection of light stimulus response to light stimulus detection of external stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation response to external stimulus detection of abiotic stimulus cell communication detection of stimulus cellular process response to abiotic stimulus response to radiation signal transduction	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR018229	Rhodopsin, retinal binding site	Binding Site
A, B, C	IPR001425	Archaeal/bacterial/fungal rhodopsins	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	Microbial and algal rhodopsins

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Bacterial, Algal, Viral, and Unusual Rhodopsins	cyanorhodopsin (CyR) N4075R

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.