1GZM: Bovine Rhodopsin in a Trigonal Crystal Form

Structure of Bovine Rhodopsin in a Trigonal Crystal Form. Determined by X-ray diffraction at 2.65 Å resolution. Released 20 Nov 2003.

Method: X-ray diffraction
Resolution: 2.65 Å
Organism: BOS TAURUS
Chains: 2
Atoms: 5,792
Mol. weight: 87.94 kDa
Ligands: PEF, ZN, C8E, LDA
Released: 20 Nov 2003

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

Secondary structure: helices and β-sheets

1GZM contains 34 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.

Chains A and B: 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, B	protein	349	BOS TAURUS	P02699 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1GZM_1 RHODOPSIN (chains A, B)
XMNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTL
YVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATL
GGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYI
PEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQE
SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSA
VYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	2
ZN	Zinc ion	Zn	2
C8E	(hydroxyethyloxy)tri(ethyloxy)octane	C16 H34 O5	12
LDA	Lauryl dimethylamine-N-oxide	C14 H31 N O	3
PLM	Palmitic acid	C16 H32 O2	4
RET	Retinal	C20 H28 O	2

Primary citation

Structure of Bovine Rhodopsin in a Trigonal Crystal Form. Li, J., Edwards, P., Burghammer, M. et al. J Mol Biol (2004) 343:1409. DOI 10.1016/J.JMB.2004.08.090 · 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

Browse structure collections

About this viewer

MolViewer shows 1GZM directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.