6OY9: Rhodopsin-Transducin Complex

Structure of the Rhodopsin-Transducin Complex. Determined by electron microscopy at 3.9 Å resolution. Released 24 Jul 2019.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Bos taurus
Chains: 4
Atoms: 7,519
Mol. weight: 127.27 kDa
Ligands: RET
Released: 24 Jul 2019

Explore 6OY9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OY9 contains 32 α-helices and 41 β-strands across 4 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-26	20
β-strand	30-34	5	1
α-helix	42-47	6
β-strand	183	1	1
β-strand	186	1	2
β-strand	191	1	2
β-strand	192-195	4	1
α-helix	204-206	3
α-helix	208-211	4
β-strand	217-218	2	1
β-strand	222	1	3
α-helix	238-250	13
β-strand	260-261	2	1
β-strand	265	1	3
α-helix	267-270	4
α-helix	271-273	3
α-helix	292-304	13
α-helix	328-335	8
α-helix	340-347	8

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-22	19
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-50	4	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	79-83	5	5
β-strand	89-93	5	5
β-strand	103-104	2	6
β-strand	112-114	3	6
β-strand	121-124	4	6
α-helix	133-134	2
β-strand	135-139	5	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	167-170	4	7
β-strand	175-179	5	7
β-strand	189-192	4	8
β-strand	198-202	5	8
β-strand	207-212	6	8
β-strand	218-223	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	251-254	4	9
β-strand	260-263	4	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	296-298	3	10
β-strand	304-306	3	10
β-strand	317-320	4	4
β-strand	327-330	4	4
β-strand	336-339	4	4

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	11-25	15
α-helix	33-47	15
α-helix	48-50	3

Chain R: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	11
β-strand	10-11	2	11
α-helix	34-64	31
α-helix	74-88	15
α-helix	92-99	8
α-helix	107-140	34
α-helix	151-166	16
β-strand	180	1	12
β-strand	187	1	12
α-helix	196-198	3
α-helix	200-210	11
α-helix	213-234	22
α-helix	241-265	25
α-helix	267-277	11
α-helix	287-289	3
α-helix	290-296	7
α-helix	297-299	3
α-helix	304-308	5
α-helix	314-317	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gt-alpha/Gi1-alpha chimera	A	protein	359	Bos taurus	P04695 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Bos taurus	P62871 (AlphaFold model)
Guanine nucleotide-binding protein G(T) subunit gamma-T1	G	protein	81	Bos taurus	P02698 (AlphaFold model)
Rhodopsin	R	protein	348	Bos taurus	P02699 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6OY9_1 Gt-alpha/Gi1-alpha chimera (chains A)
MAHHHHHHAMGAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMKI
IHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDDARKLMHMADTIE
EGTMPKEMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLERLVTPGYVPTEQDVL
RSRVKTTGIIETQFSFKDLNFRMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDMVLV
EDDEVNRMHESMHLFNSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLSICFPDYAGSNT
YEEAGNYIKVQFLELNMRRDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF

Sequence of entity 2 (B), FASTA

>6OY9_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLLSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>6OY9_3 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains G)
MPVINIEDPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPL
VKGIPEDKNPFKELKGGCVIS

Sequence of entity 4 (R), FASTA

>6OY9_4 Rhodopsin (chains R)
MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1

Primary citation

Structures of the Rhodopsin-Transducin Complex: Insights into G-Protein Activation. Gao, Y., Hu, H., Ramachandran, S. et al. Mol Cell (2019) 75:781. DOI 10.1016/j.molcel.2019.06.007 · PubMed

Other PDB entries of the same protein (UniProt P04695 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TAD 1.7 Å, Gtpase mechanism of gproteins from the 1.7-Å crystal structure of transducin…
1TAG 1.8 Å, Structural determinants for activation of the alpha-subunit of a heterotrimeric G protein
1GOT 2.0 Å, Heterotrimeric complex of a gt-alpha/gi-alpha chimera and the gt-beta-gamma subunits
1FQJ 2.02 Å, Crystal structure of the heterotrimeric complex of the rgs domain of RGS9, the gamma…
1TND 2.2 Å, The 2.2 Å crystal structure of transducin-alpha complexed with GTP gamma S
1FQK 2.3 Å, Crystal structure of the heterodimeric complex of the rgs domain of RGS9, and the GT/I1…
4J4Q 2.65 Å, Crystal structure of active conformation of GPCR opsin stabilized by octylglucoside
3PQR 2.85 Å, Crystal structure of Metarhodopsin II in complex with a C-terminal peptide derived from…
3V00 2.9 Å, Studies of a constitutively active G-alpha subunit provide insights into the mechanism…
4BEY 2.9 Å, Night blindness causing G90D rhodopsin in complex with GaCT2 peptide
2X72 3.0 Å, Crystal structure of the constitutively active E113Q,D2C,D282C rhodopsin mutant with…
3DQB 3.2 Å, Crystal structure of the active G-protein-coupled receptor opsin in complex with a…

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