1L9H: Bovine rhodopsin

Crystal structure of bovine rhodopsin at 2.6 angstroms RESOLUTION. Determined by X-ray diffraction at 2.6 Å resolution. Released 15 May 2002.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Bos taurus
Chains: 2
Atoms: 5,584
Mol. weight: 86.55 kDa
Ligands: BNG, HG, ZN, HTO
Released: 15 May 2002

Explore 1L9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1L9H contains 31 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	86-90	5
α-helix	91-100	10
α-helix	106-134	29
α-helix	136-139	4
α-helix	150-168	19
α-helix	170-172	3
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	244-277	34
α-helix	285-295	11
α-helix	296-299	4
α-helix	301-309	9
α-helix	311-321	11

Chain B: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	3
β-strand	10-11	2	3
α-helix	34-64	31
α-helix	71-85	15
α-helix	86-91	6
α-helix	92-100	9
α-helix	106-137	32
α-helix	150-168	19
α-helix	170-172	3
β-strand	178-181	4	4
β-strand	186-189	4	4
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-225	12
α-helix	250-277	28
α-helix	285-295	11
α-helix	296-299	4
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

>1L9H_1 rhodopsin (chains A, B)
XMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTL
YVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATL
GGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYI
PEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQE
SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSA
VYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
BNG	nonyl beta-D-glucopyranoside	C15 H30 O6	7
HG	Mercury (II) ion	Hg	6
ZN	Zinc ion	Zn	7
HTO	Heptane-1,2,3-triol	C7 H16 O3	4
PLM	Palmitic acid	C16 H32 O2	5
RET	Retinal	C20 H28 O	2

Primary citation

Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Okada, T., Fujiyoshi, Y., Silow, M. et al. Proc Natl Acad Sci U S A (2002) 99:5982-5987. DOI 10.1073/pnas.082666399 · 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
2G87 2.6 Å, Crystallographic model of bathorhodopsin

Browse structure collections

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