3C9L: Rhodopsin

Structure of ground-state bovine rhodospin in a hexagonal crystal form. Determined by X-ray diffraction at 2.65 Å resolution. Released 5 Aug 2008.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: Bos taurus
Chains: 1
Atoms: 2,888
Mol. weight: 43.87 kDa
Ligands: C8E, LDA, PEF, PLM
Released: 5 Aug 2008

Explore 3C9L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3C9L contains 17 α-helices and 4 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	9-11	3	1
α-helix	34-64	31
α-helix	71-85	15
α-helix	86-91	6
α-helix	92-100	9
α-helix	106-140	35
α-helix	150-168	19
α-helix	170-172	3
β-strand	178-181	4	2
β-strand	186-189	4	2
α-helix	196-198	3
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-228	15
α-helix	229-233	5
α-helix	241-276	36
α-helix	286-295	10
α-helix	296-299	4
α-helix	301-309	9
α-helix	311-322	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rhodopsin	A	protein	348	Bos taurus	P02699 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3C9L_1 Rhodopsin (chains A)
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
C8E	(hydroxyethyloxy)tri(ethyloxy)octane	C16 H34 O5	6
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	1
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	1
PLM	Palmitic acid	C16 H32 O2	2
RET	Retinal	C20 H28 O	1
ACE	Acetyl group	C2 H4 O	1
ZN	Zinc ion	Zn	1

Primary citation

Alternative models for two crystal structures of bovine rhodopsin. Stenkamp, R.E. Acta Crystallogr D Biol Crystallogr (2008) 64:902-904. DOI 10.1107/S0907444908017162 · PubMed

Other PDB entries of the same protein (UniProt P02699 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7ZBC 1.8 Å, Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA)
7ZBE 1.8 Å, Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL)
8A6C 1.8 Å, 1 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase
8A6D 1.8 Å, 10 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase
8A6E 1.8 Å, 100 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic…
1U19 2.2 Å, Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution
4X1H 2.29 Å, Opsin/G(alpha) peptide complex stabilized by nonyl-glucoside
5DYS 2.3 Å, Crystal Structure of T94I rhodopsin mutant
6FK6 2.36 Å, Crystal structure of N2C/D282C stabilized opsin bound to RS01
6FKC 2.46 Å, Crystal structure of N2C/D282C stabilized opsin bound to RS15
6FKD 2.49 Å, Crystal structure of N2C/D282C stabilized opsin bound to RS16
1L9H 2.6 Å, Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION

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