8A6E: Rhodopsin

100 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA). Determined by X-ray diffraction at 1.8 Å resolution. Released 29 Mar 2023.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Bos taurus
Chains: 2
Atoms: 5,477
Mol. weight: 85.32 kDa
Ligands: PLM, OLC, DAO, NAG
Released: 29 Mar 2023

Explore 8A6E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8A6E contains 33 α-helices and 8 β-strands across 2 chains. 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: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	405-406	2	1
β-strand	411-412	2	1
α-helix	435-465	31
α-helix	472-486	15
α-helix	487-492	6
α-helix	493-501	9
α-helix	507-541	35
α-helix	551-569	19
α-helix	571-573	3
β-strand	579-582	4	2
β-strand	587-590	4	2
α-helix	597-599	3
α-helix	601-609	9
α-helix	610-614	5
α-helix	615-628	14
α-helix	647-678	32
α-helix	686-695	10
α-helix	696-700	5
α-helix	702-710	9
α-helix	712-722	11

Chain B: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	405-406	2	3
β-strand	411-412	2	3
α-helix	435-465	31
α-helix	472-486	15
α-helix	487-492	6
α-helix	493-501	9
α-helix	507-536	30
α-helix	537-541	5
α-helix	551-569	19
α-helix	571-573	3
β-strand	579-582	4	4
β-strand	587-590	4	4
α-helix	597-599	3
α-helix	601-609	9
α-helix	610-614	5
α-helix	615-628	14
α-helix	646-678	33
α-helix	686-695	10
α-helix	696-700	5
α-helix	702-710	9
α-helix	712-722	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rhodopsin	A, B	protein	349	Bos taurus	P02699 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8A6E_1 Rhodopsin (chains A, B)
XMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTL
YVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATL
GGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYI
PEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQE
SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSA
VYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
PLM	Palmitic acid	C16 H32 O2	2
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	13
DAO	Lauric acid	C12 H24 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
RET	Retinal	C20 H28 O	2

Primary citation

Ultrafast structural changes direct the first molecular events of vision. Gruhl, T., Weinert, T., Rodrigues, M.J. et al. Nature (2023) 615:939-944. DOI 10.1038/s41586-023-05863-6 · 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
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
2G87 2.6 Å, Crystallographic model of bathorhodopsin

Browse structure collections

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