3OAX: Bovine rhodopsin with beta-ionone

Crystal structure of bovine rhodopsin with beta-ionone. Determined by X-ray diffraction at 2.6 Å resolution. Released 19 Jan 2011.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Bos taurus
Chains: 2
Atoms: 6,015
Mol. weight: 85.71 kDa
Ligands: RET, PLM, HG, ZN
Released: 19 Jan 2011

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

Secondary structure: helices and β-sheets

3OAX 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	4-5	2	1
β-strand	10-11	2	1
α-helix	34-64	31
α-helix	71-85	15
α-helix	86-91	6
α-helix	92-100	9
α-helix	106-139	34
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	214-225	12
α-helix	242-276	35
α-helix	286-295	10
α-helix	296-299	4
α-helix	301-309	9
α-helix	311-321	11

Chain B: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	3
β-strand	10-11	2	3
α-helix	29-31	3
α-helix	34-64	31
α-helix	71-85	15
α-helix	86-91	6
α-helix	92-100	9
α-helix	106-136	31
α-helix	150-168	19
α-helix	170-173	4
β-strand	178-181	4	4
β-strand	186-189	4	4
α-helix	196-198	3
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-221	8
α-helix	242-276	35
α-helix	285-294	10
α-helix	295-299	5
α-helix	301-309	9
α-helix	311-321	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

>3OAX_1 Rhodopsin (chains A, B)
XMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTL
YVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATL
GGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYI
PEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQE
SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSA
VYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	2
PLM	Palmitic acid	C16 H32 O2	4
HG	Mercury (II) ion	Hg	6
ZN	Zinc ion	Zn	7
4E6	(4E,6E)-hexadeca-1,4,6-triene	C16 H28	2
HTO	Heptane-1,2,3-triol	C7 H16 O3	1
ID3	(3E)-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-3-en-2-one	C13 H20 O	2
HTG	heptyl 1-thio-beta-D-glucopyranoside	C13 H26 O5 S	4

Primary citation

Binding of more than one retinoid to visual opsins. Makino, C.L., Riley, C.K., Looney, J. et al. Biophys J (2010) 99:2366-2373. DOI 10.1016/j.bpj.2010.08.003 · 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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