6QNO: Rhodopsin-Gi protein complex

Rhodopsin-Gi protein complex. Determined by electron microscopy at 4.38 Å resolution. Released 10 Jul 2019.

Method: Electron microscopy
Resolution: 4.38 Å
Organisms: Homo sapiens, Bos taurus, Mus musculus
Chains: 6
Atoms: 10,429
Mol. weight: 181.77 kDa
Ligands: RET
Released: 10 Jul 2019

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

Secondary structure: helices and β-sheets

6QNO contains 36 α-helices and 82 β-strands across 6 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, 10 β-strands

Element	Residues	Length	Sheet
α-helix	14-24	11
β-strand	35	1	1
β-strand	37-38	2	2
β-strand	190	1	3
β-strand	195	1	3
β-strand	197	1	1
β-strand	200	1	2
α-helix	208-214	7
β-strand	221-224	4	2
α-helix	244-253	10
β-strand	264-267	4	2
β-strand	268	1	4
α-helix	271-280	10
α-helix	283-285	3
α-helix	297-307	11
β-strand	323	1	4
α-helix	332-348	17

Chain B: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
β-strand	47-51	5	5
β-strand	58-63	6	6
β-strand	69-74	6	6
β-strand	78-83	6	6
β-strand	88-94	7	6
β-strand	103-105	3	7
β-strand	111-114	4	7
β-strand	116	1	8
β-strand	121-125	5	7
β-strand	135-139	5	7
β-strand	146-151	6	8
β-strand	157-161	5	8
β-strand	166-168	3	8
β-strand	178-180	3	8
β-strand	187-192	6	9
β-strand	198-203	6	9
β-strand	207-212	6	9
β-strand	220-222	3	9
α-helix	228	1
β-strand	229-235	7	10
β-strand	240-245	6	10
β-strand	250-254	5	10
β-strand	262-264	3	10
β-strand	273-277	5	11
β-strand	284-289	6	11
β-strand	294-298	5	11
β-strand	304-308	5	11
β-strand	315-320	6	5
β-strand	327-331	5	5
β-strand	336-339	4	5

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	33-44	12
α-helix	45-47	3
α-helix	59-61	3

Chain H: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	19
β-strand	29-31	3	15
β-strand	35-44	10	19
β-strand	52-58	7	15
β-strand	65-70	6	15
α-helix	72-74	3
β-strand	77-79	3	15
β-strand	87-92	6	19
β-strand	97-105	9	19
α-helix	107-109	3
β-strand	111-118	8	15
β-strand	134-138	5	15
β-strand	147-151	5	20
β-strand	162-172	11	20
β-strand	178-181	4	21
β-strand	191-198	8	20
β-strand	201-211	11	20
α-helix	214-217	4
β-strand	221-226	6	21
β-strand	231-236	6	21

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	12
α-helix	31-32	2
β-strand	33	1	13
α-helix	34	1
β-strand	39-45	7	12
β-strand	58-63	6	14
α-helix	69	1
β-strand	70-74	5	14
β-strand	78-79	2	14
β-strand	87-91	5	12
β-strand	95-100	6	12
β-strand	109-115	7	14
β-strand	122	1	15
β-strand	127-129	3	14
β-strand	131	1	13
β-strand	139-143	5	16
α-helix	147-152	6
β-strand	156-162	7	16
β-strand	170-175	6	17
β-strand	178-179	2	17
β-strand	184-188	5	16
β-strand	192	1	18
β-strand	197	1	18
β-strand	199-205	7	16
α-helix	209-212	4
β-strand	216-222	7	17
α-helix	228-229	2
β-strand	230-235	6	17

Chain R: 15 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	22
β-strand	11	1	22
α-helix	34-64	31
α-helix	66-68	3
α-helix	74-86	13
α-helix	87-91	5
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	23
β-strand	186-189	4	23
α-helix	200-208	9
α-helix	209-213	5
α-helix	214-236	23
α-helix	241-277	37
α-helix	285-305	21
α-helix	307-309	3
α-helix	311-318	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	376	Homo sapiens	P63096 (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	74	Bos taurus	P02698 (AlphaFold model)
Fab antibody fragment light chain	L	protein	239	Mus musculus
Fab antibody fragment heavy chain	H	protein	249	Mus musculus
Rhodopsin	R	protein	348	Bos taurus	P02699 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6QNO_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MKKHHHHHHHHHHENLYFQGGSMGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLL
LGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDS
ARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLND
LDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGV
TAIIFCVALSDYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKI
KKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDA
VTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>6QNO_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>6QNO_3 Guanine nucleotide-binding protein G(T) subunit gamma-T1 (chains G)
MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPLVKGIPED
KNPFKELKGGCVIS

Sequence of entity 4 (L), FASTA

>6QNO_4 Fab antibody fragment light chain (chains L)
MRCLAEFLGLLVLWIPGAIGDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYW
FLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYP
LTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSER
QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 5 (H), FASTA

>6QNO_5 Fab antibody fragment heavy chain (chains H)
MDSRLNLVFLVLTLKGVQCDVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAP
EKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIY
YYGSSPFDFWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVT
WNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS
GPISTINPC

Sequence of entity 6 (R), FASTA

>6QNO_6 Rhodopsin (chains R)
MCGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLY
VTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLG
GEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIP
EGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQES
ATTQKAEKEVTRMVIIYVIAFLICWLPYAGVAFYIFTHQGSCFGPIFMTIPAFFAKTSAV
YNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1

Primary citation

Cryo-EM structure of the rhodopsin-G alpha i-beta gamma complex reveals binding of the rhodopsin C-terminal tail to the G beta subunit. Tsai, C.J., Marino, J., Adaixo, R. et al. Elife (2019) 8. DOI 10.7554/eLife.46041 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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