8Y01: Medium-wave-sensitive opsin 1

Cryo-EM structure of Medium-wave-sensitive opsin 1. Determined by electron microscopy at 2.48 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 2.48 Å
Organisms: Homo sapiens, Bos taurus
Chains: 5
Atoms: 8,839
Mol. weight: 155.29 kDa
Ligands: RET
Released: 12 Feb 2025

Explore 8Y01 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y01 contains 35 α-helices and 60 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-40	8	2
α-helix	46-53	8
β-strand	185-191	7	2
β-strand	194-200	7	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	2
α-helix	227-229	3
α-helix	242-254	13
α-helix	257-259	3
β-strand	263-269	7	2
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	2
α-helix	331-350	20

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-25	23
α-helix	30-33	4
α-helix	38-40	3
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	260-264	5	8
α-helix	272	1
β-strand	273-278	6	9
β-strand	285-289	5	9
β-strand	294-297	4	9
β-strand	304-307	4	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	335-339	5	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	6-23	18
α-helix	30-43	14
α-helix	53-55	3

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	50-80	31
α-helix	82-84	3
α-helix	87-89	3
α-helix	90-114	25
α-helix	123-156	34
α-helix	166-184	19
α-helix	186-189	4
β-strand	194-196	3	1
β-strand	203-205	3	1
α-helix	216-224	9
α-helix	225-229	5
α-helix	230-252	23
α-helix	257-280	24
α-helix	282-293	12
α-helix	301-322	22
α-helix	327-337	11

Chain S: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	65	1	10
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	110-111	2	11
β-strand	115-119	5	11
β-strand	140-141	2	12
β-strand	146-148	3	13
β-strand	155-161	7	12
β-strand	166	1	14
β-strand	172	1	14
β-strand	175-179	5	13
β-strand	186-191	6	13
β-strand	194-195	2	13
β-strand	204-208	5	12
β-strand	211-216	6	12
β-strand	226-230	5	13
β-strand	243-246	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Medium-wave-sensitive opsin 2	R	protein	364	Homo sapiens	P04001 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	340	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212 (AlphaFold model)
scFv Recombinant Human Monoclonal Antibody (scFv16)	S	protein	267	Homo sapiens

Sequence of entity 1 (R), FASTA

>8Y01_1 Medium-wave-sensitive opsin 2 (chains R)
MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
LGHPMCVLQGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSS
VSPA

Sequence of entity 2 (A), FASTA

>8Y01_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKCTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVTAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>8Y01_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (G), FASTA

>8Y01_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (S), FASTA

>8Y01_5 scFv Recombinant Human Monoclonal Antibody (scFv16) (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQGPHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1

Primary citation

Cryo-electron microscopy structures of human cone visual pigments. Peng, Q., Li, J., Jiang, H. et al. Science (2026). DOI 10.1126/science.adz8141

Other PDB entries of the same protein (UniProt P04001 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9YDA 2.9 Å, Cryo-EM structure of active human green cone opsin in complex with chimeric G protein…
9YGZ 3.04 Å, Cryo-EM structure of active mutant human green cone opsin (E129Q) in complex with…
9I3T 3.7 Å, Dark-state structure of human medium-wave-sensitive cone opsin (OPN1MW)

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