2X72: Rhodopsin

Crystal structure of the constitutively active E113Q,D2C,D282C rhodopsin mutant with bound galphact peptide. Determined by X-ray diffraction at 3.0 Å resolution. Released 16 Mar 2011.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: BOS TAURUS
Chains: 2
Atoms: 2,932
Mol. weight: 43.7 kDa
Ligands: PEF, LPP, RET, PLM
Released: 16 Mar 2011

Explore 2X72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2X72 contains 18 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: 17 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	9-11	3	1
α-helix	15-17	3
α-helix	34-64	31
α-helix	66-68	3
α-helix	71-73	3
α-helix	74-85	12
α-helix	86-92	7
α-helix	93-98	6
α-helix	106-140	35
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	214-235	22
α-helix	241-276	36
α-helix	285-296	12
α-helix	298-306	9
α-helix	311-321	11

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	341-347	7

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

>2X72_1 RHODOPSIN (chains A)
XMCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTL
YVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLQGFFATL
GGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYI
PEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQE
SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSA
VYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Sequence of entity 2 (B), FASTA

>2X72_2 GUANINE NUCLEOTIDE-BINDING PROTEIN G(T) SUBUNIT ALPHA-1 (chains B)
ILENLKDCGLF

Ligands and cofactors

ID	Name	Formula	Copies
PEF	Di-palmitoyl-3-sn-phosphatidylethanolamine	C37 H74 N O8 P	1
LPP	2-(hexadecanoyloxy)-1-[(phosphonooxy)methyl]ethyl hexadecanoate	C35 H69 O8 P	1
RET	Retinal	C20 H28 O	1
PLM	Palmitic acid	C16 H32 O2	2
BOG	octyl beta-D-glucopyranoside	C14 H28 O6	1

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

Primary citation

The Structural Basis of Agonist Induced Activation in Constitutively Active Rhodopsin. Standfuss, J., Edwards, P.C., Dantona, A. et al. Nature (2011) 471:656. DOI 10.1038/NATURE09795 · 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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