9I3T: PDB entry 9I3T

Dark-state structure of human medium-wave-sensitive cone opsin (OPN1MW). Determined by electron microscopy at 3.7 Å resolution. Released 24 Jun 2026.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Escherichia coli, synthetic construct
Chains: 3
Atoms: 4,940
Mol. weight: 102.99 kDa
Ligands: RET
Released: 24 Jun 2026

Explore 9I3T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I3T contains 21 α-helices and 27 β-strands across 3 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: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	51-80	30
α-helix	87-116	30
α-helix	123-155	33
α-helix	166-183	18
α-helix	186-189	4
β-strand	194-197	4	1
β-strand	202-205	4	1
α-helix	216-224	9
α-helix	225-229	5
α-helix	230-243	14
α-helix	902-917	16
α-helix	922-941	20
α-helix	955-979	25
α-helix	984-998	15
α-helix	1003-254	4
α-helix	257-293	37
α-helix	302-311	10
α-helix	314-325	12
α-helix	327-338	12

Chain H: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	2
β-strand	14	1	3
β-strand	20-28	9	2
β-strand	36-42	7	4
β-strand	48-55	8	4
β-strand	60-63	4	4
α-helix	65-67	3
β-strand	71-76	6	2
β-strand	81-87	7	2
α-helix	91-93	3
β-strand	95-102	8	4
α-helix	103-104	2
α-helix	108-111	4
β-strand	114	1	4
β-strand	118	1	2
β-strand	121-123	3	4
β-strand	124	1	3

Chain L: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	5
β-strand	11-12	2	6
β-strand	20-26	7	5
β-strand	30	1	7
β-strand	32	1	7
β-strand	34-39	6	6
β-strand	46-49	4	6
β-strand	63-68	6	5
β-strand	71-76	6	5
β-strand	85-94	10	6
β-strand	97-99	3	6
β-strand	104-106	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Medium-wave-sensitive opsin 1,Soluble cytochrome b562	A	protein	492	Homo sapiens, Escherichia coli	P04001 (AlphaFold model), P0ABE7 (AlphaFold model)
BAG2 Anti-BRIL Fab Heavy Chain	H	protein	231	synthetic construct
BAG2 Anti-BRIL Fab Light Chain	L	protein	215	synthetic construct

Sequence of entity 1 (A), FASTA

>9I3T_1 Medium-wave-sensitive opsin 1,Soluble cytochrome b562 (chains A)
MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
LGHPMCVLEGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
QVWLAIADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPD
SPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLKESESTQK
AEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFHPLMAALPAFFAKSATIYNPVI
YVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSSVSPALEVLFQGPDYKDDDDKG
AGATETSQVAPA

Sequence of entity 2 (H), FASTA

>9I3T_2 BAG2 Anti-BRIL Fab Heavy Chain (chains H)
EISEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGS
TSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (L), FASTA

>9I3T_3 BAG2 Anti-BRIL Fab Light Chain (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
RET	Retinal	C20 H28 O	1

Primary citation

Illuminating the molecular basis of human daylight vision. Schmidt, S.L., Dostal, J., Sen, S. et al. Science (2026) 392:eadz3624-eadz3624. DOI 10.1126/science.adz3624 · 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
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…

Browse structure collections

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