7ZBE: Rhodopsin

Dark state crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SwissFEL). 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: 5,497
Mol. weight: 85.36 kDa
Ligands: ACE, NAG, PLM, OLC
Released: 29 Mar 2023

Explore 7ZBE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZBE contains 32 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	4-6	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	214-227	14
α-helix	245-276	32
α-helix	285-294	10
α-helix	295-299	5
α-helix	301-309	9
α-helix	311-321	11

Chain B: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	3
β-strand	9-11	3	3
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	4
β-strand	186-189	4	4
α-helix	196-198	3
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-227	14
α-helix	245-277	33
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	348	Bos taurus	P02699 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7ZBE_1 Rhodopsin (chains A, B)
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
ACE	Acetyl group	C2 H4 O	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2
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
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)
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
2G87 2.6 Å, Crystallographic model of bathorhodopsin

Browse structure collections

About this viewer

MolViewer shows 7ZBE 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.