1F88: Bovine rhodopsin

Crystal structure of bovine rhodopsin. Determined by X-ray diffraction at 2.8 Å resolution. Released 4 Aug 2000.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Bos taurus
Chains: 2
Atoms: 5,267
Mol. weight: 81.96 kDa
Ligands: HG, ZN, RET
Released: 4 Aug 2000

Explore 1F88 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1F88 contains 32 α-helices and 10 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: 17 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-11	2	1
α-helix	29-31	3
α-helix	34-64	31
α-helix	71-85	15
α-helix	86-90	5
α-helix	91-100	10
α-helix	106-139	34
α-helix	150-168	19
α-helix	170-173	4
β-strand	178-181	4	2
β-strand	186-189	4	2
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-225	12
α-helix	246-254	9
α-helix	256-277	22
α-helix	285-295	11
α-helix	296-299	4
α-helix	301-309	9
α-helix	311-321	11
β-strand	323	1	3
β-strand	325	1	3

Chain B: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	4
β-strand	10-11	2	4
α-helix	34-64	31
α-helix	71-85	15
α-helix	86-90	5
α-helix	91-98	8
α-helix	107-137	31
α-helix	153-168	16
α-helix	170-173	4
β-strand	178-181	4	5
β-strand	186-189	4	5
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-224	11
α-helix	247-277	31
α-helix	285-294	10
α-helix	295-297	3
α-helix	298-308	11
α-helix	311-322	12

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>1F88_1 RHODOPSIN (chains A, B)
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	6
ZN	Zinc ion	Zn	4
RET	Retinal	C20 H28 O	2

Primary citation

Crystal structure of rhodopsin: A G protein-coupled receptor. Palczewski, K., Kumasaka, T., Hori, T. et al. Science (2000) 289:739-745. DOI 10.1126/science.289.5480.739 · 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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