9YDA: Active human green cone opsin

Cryo-EM structure of active human green cone opsin in complex with chimeric G protein (miniGist). Determined by electron microscopy at 2.9 Å resolution. Released 24 Dec 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 9,036
Mol. weight: 172.89 kDa
Ligands: RET
Released: 24 Dec 2025

Explore 9YDA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YDA contains 40 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-40	8	15
α-helix	46-48	3
β-strand	175-180	6	15
β-strand	183-189	7	15
α-helix	200-204	5
β-strand	209-215	7	15
α-helix	222-233	12
α-helix	236-238	3
β-strand	242-248	7	15
α-helix	250-259	10
α-helix	264-266	3
α-helix	269-273	5
α-helix	282-283	2
α-helix	288-306	19
β-strand	315-319	5	15
α-helix	327-347	21

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	11-24	14
α-helix	38-39	2
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
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-153	8	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	208-212	5	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	303-308	6	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	54-55	2
α-helix	56-58	3

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	10
β-strand	27-29	3	11
β-strand	35-42	8	10
β-strand	50-56	7	11
β-strand	62-68	7	11
β-strand	75-77	3	11
β-strand	85-90	6	10
α-helix	91-93	3
β-strand	95-100	6	10
α-helix	105-107	3
β-strand	109-116	8	11
β-strand	127-128	2	11
β-strand	132-136	5	11
β-strand	157-159	3	12
β-strand	163-165	3	13
β-strand	172-178	7	12
β-strand	183	1	14
β-strand	189	1	14
β-strand	191-196	6	13
β-strand	203-206	4	13
α-helix	211	1
β-strand	212	1	13
α-helix	213	1
β-strand	220-224	5	12
β-strand	228-233	6	12
α-helix	238-240	3
β-strand	243-248	6	13
α-helix	254	1
β-strand	255-256	2	13
β-strand	260-263	4	13

Chain R: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	51-80	30
α-helix	82-84	3
α-helix	87-89	3
α-helix	90-114	25
α-helix	123-156	34
β-strand	158	1	1
β-strand	160	1	1
α-helix	162-164	3
α-helix	166-183	18
α-helix	186-188	3
β-strand	194-197	4	2
β-strand	202-205	4	2
α-helix	216-224	9
α-helix	225-229	5
α-helix	230-250	21
α-helix	257-293	37
α-helix	303-305	3
α-helix	306-311	6
α-helix	314-322	9
α-helix	327-333	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Medium-wave-sensitive opsin 1	R	protein	364	Homo sapiens	P04001 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	357	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	H	protein	259	Mus musculus
Genome polyprotein,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas	A	protein	509	Homo sapiens

Sequence of entity 1 (R), FASTA

>9YDA_1 Medium-wave-sensitive opsin 1 (chains R)
MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVTETSQ
VAPA

Sequence of entity 2 (B), FASTA

>9YDA_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGSSGTETSQVAPA

Sequence of entity 3 (G), FASTA

>9YDA_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (H), FASTA

>9YDA_4 scFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 5 (A), FASTA

>9YDA_5 Genome polyprotein,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas (chains A)
MLQNELALKLAGLDINKTGGSGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDAT
YGKLTLKFICTTGKLPVPWPTLVTTFGYGLQCFARYPDHMKQHDFFKSAMPEGYVQERTI
FFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQK
NGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHM
VLLEFVTAAGITLGMDELYKGSGSGCTLSAEDKAAVERSKMIEKQLQKDKQVYRATHRLL
LLGADNSGKSTIVKQMRILHGGSGGSGGTSGIFETKFQVDKVNFHMFDVGGQRDERRKWI
QCFNDVTAIIFVVDSSDYNRLQEALNDFKSIWNNRWLRTISVILFLNKQDLLAEKVLAGK
SKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCYPHFTC
AVDTENARRIFNDVTDIIILEDLKSCGLF

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1

Primary citation

Structure of human green cone opsin yields insights into mechanisms underlying the rapid decay of its active, signaling state. Yao, W., Fay, J.F., Farrens, D.L. Proc Natl Acad Sci U S A (2025) 122:e2516318122-e2516318122. DOI 10.1073/pnas.2516318122 · PubMed

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

8Y01 2.48 Å, Cryo-EM structure of Medium-wave-sensitive opsin 1
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)

Browse structure collections

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