4BEY: Night blindness causing G90D rhodopsin

Night blindness causing G90D rhodopsin in complex with GaCT2 peptide. Determined by X-ray diffraction at 2.9 Å resolution. Released 8 May 2013.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Bos taurus
Chains: 2
Atoms: 2,810
Mol. weight: 41.81 kDa
Ligands: BOG, PLM
Released: 8 May 2013

Explore 4BEY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BEY contains 17 α-helices and 4 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	15-17	3
α-helix	34-64	31
α-helix	66-68	3
α-helix	71-85	15
α-helix	86-92	7
α-helix	93-98	6
α-helix	106-140	35
α-helix	150-172	23
β-strand	178-181	4	2
β-strand	186-189	4	2
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-236	23
α-helix	241-277	37
α-helix	285-296	12
α-helix	298-303	6
α-helix	304-308	5
α-helix	311-321	11

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	341-346	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rhodopsin	A	protein	349	Bos taurus	P02699 (AlphaFold model)
Guanine nucleotide-binding protein G(t) subunit alpha-1	B	protein	11	Bos taurus	P04695 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4BEY_1 Rhodopsin (chains A)
XMCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTL
YVTVQHKKLRTPLNYILLNLAVADLFMVFGDFTTTLYTSLHGYFVFGPTGCNLEGFFATL
GGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYI
PEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQE
SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSA
VYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Sequence of entity 2 (B), FASTA

>4BEY_2 Guanine nucleotide-binding protein G(t) subunit alpha-1 (chains B)
ILENLKDCGLF

Ligands and cofactors

ID	Name	Formula	Copies
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	1
PLM	Palmitic acid	C16 H32 O2	1

Water and common crystallization additives (ACT, SO4) are not listed.

Primary citation

Insights Into Congenital Stationary Night Blindness Based on the Structure of G90D Rhodopsin. Singhal, A., Ostermaier, M.K., Vishnivetskiy, S.A. et al. EMBO Rep (2013) 14:520. DOI 10.1038/EMBOR.2013.44 · 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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