6OYA: Rhodopsin-Transducin-Nanobody Complex

Structure of the Rhodopsin-Transducin-Nanobody Complex. Determined by electron microscopy at 3.3 Å resolution. Released 24 Jul 2019.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Bos taurus, Lama glama
Chains: 5
Atoms: 8,321
Mol. weight: 142.31 kDa
Ligands: RET
Released: 24 Jul 2019

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

Secondary structure: helices and β-sheets

6OYA contains 29 α-helices and 62 β-strands across 5 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: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-26	20
β-strand	30-31	2	1
β-strand	33-34	2	2
α-helix	42-45	4
β-strand	180-183	4	2
β-strand	186	1	3
β-strand	191	1	3
β-strand	192-193	2	1
β-strand	194-197	4	2
α-helix	208-211	4
β-strand	216-218	3	2
β-strand	222	1	4
α-helix	239-249	11
β-strand	259-261	3	2
β-strand	264	1	5
β-strand	265	1	4
α-helix	267-273	7
α-helix	293-303	11
β-strand	315-316	2	2
β-strand	319	1	5
α-helix	327-347	21

Chain B: 4 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	5-25	21
α-helix	30-33	4
α-helix	45-46	2
β-strand	47-51	5	6
β-strand	58-61	4	7
β-strand	69-74	6	7
β-strand	79-83	5	7
β-strand	88-91	4	7
β-strand	102-105	4	8
β-strand	111-115	5	8
β-strand	121-125	5	8
β-strand	135-139	5	8
β-strand	149-151	3	9
β-strand	156-159	4	9
β-strand	168-170	3	9
β-strand	176	1	9
α-helix	186	1
β-strand	187-192	6	10
β-strand	198-203	6	10
β-strand	207-212	6	10
β-strand	220-223	4	10
β-strand	229	1	11
β-strand	233-234	2	12
β-strand	240-242	3	12
β-strand	245	1	11
β-strand	250-254	5	12
β-strand	260-264	5	12
β-strand	273-277	5	13
β-strand	284	1	14
β-strand	286-289	4	13
β-strand	295	1	13
β-strand	298	1	14
β-strand	303	1	14
β-strand	307	1	13
β-strand	317-320	4	6
β-strand	327-330	4	6
β-strand	336-339	4	6

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	17-24	8
α-helix	33-46	14
α-helix	48-50	3

Chain N: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
β-strand	18-25	8	15
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	68-73	6	15
β-strand	78-83	6	15
β-strand	93-98	6	17
β-strand	118	1	17
β-strand	122-123	2	17
β-strand	125-126	2	16

Chain R: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	18
β-strand	10-11	2	18
α-helix	15-17	3
α-helix	34-64	31
α-helix	74-85	12
α-helix	86-91	6
α-helix	92-100	9
α-helix	107-139	33
α-helix	150-168	19
α-helix	170-173	4
β-strand	180	1	19
β-strand	187	1	19
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-234	21
α-helix	243-262	20
α-helix	266-277	12
α-helix	285-306	22
α-helix	313-321	9

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)
Camelid antibody VHH fragment	N	protein	138	Lama glama
Rhodopsin	R	protein	348	Bos taurus	P02699 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6OYA_1 Gt-alpha/Gi1-alpha chimera (chains A)
MAHHHHHHAMGAGASAEEKHSRELEKKLKEDAEKDARTVKLLLLGAGESGKSTIVKQMKI
IHQDGYSLEECLEFIAIIYGNTLQSILAIVRAMTTLNIQYGDSARQDDARKLMHMADTIE
EGTMPKEMSDIIQRLWKDSGIQACFDRASEYQLNDSAGYYLSDLERLVTPGYVPTEQDVL
RSRVKTTGIIETQFSFKDLNFRMFDVGGQRDERRKWIHCFEGVTAIIFCVALSDYDMVLV
EDNQTNRMQESMNLFKSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTDYYPEYAGSNT
YEEAGNYIKVQFLELNMASDVKEIYSHMTCATDTQNVKFVFDAVTDIIIKENLKDCGLF

Sequence of entity 2 (B), FASTA

>6OYA_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

>6OYA_3 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains G)
MPVINIEDPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPL
VKGIPEDKNPFKELKGGCVIS

Sequence of entity 4 (N), FASTA

>6OYA_4 Camelid antibody VHH fragment (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLQWVSDISQSGASISY
TGSVKGRFTISRDDAKNTLYLQMNSLKPADTAVYYCARCPAPFTRDCFDVTSTAYAYRGQ
GTQVTVSSHHHHHHEPEA

Sequence of entity 5 (R), FASTA

>6OYA_5 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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