9YGZ: Active mutant human green cone opsin
Cryo-EM structure of active mutant human green cone opsin (E129Q) in complex with chimeric G protein (miniGist). Determined by electron microscopy at 3.04 Å resolution. Released 20 May 2026.
- Method
- Electron microscopy
- Resolution
- 3.04 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 5
- Atoms
- 9,043
- Mol. weight
- 173.86 kDa
- Ligands
- RET
- Released
- 20 May 2026
Explore 9YGZ in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9YGZ contains 39 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 | Sheet |
|---|
| 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: 15 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 50-80 | 31 | |
| α-helix | 87-89 | 3 | |
| α-helix | 90-113 | 24 | |
| α-helix | 123-156 | 34 | |
| β-strand | 158 | 1 | 1 |
| β-strand | 160 | 1 | 1 |
| α-helix | 166-183 | 18 | |
| α-helix | 186-189 | 4 | |
| 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 | 257-281 | 25 | |
| α-helix | 284-292 | 9 | |
| α-helix | 303-305 | 3 | |
| α-helix | 306-319 | 14 | |
| α-helix | 320-324 | 5 | |
| α-helix | 327-333 | 7 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Medium-wave-sensitive opsin 1 | R | protein | 365 | 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 | 268 | Mus musculus | |
| Genome polyprotein,Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLas | A | protein | 509 | Homo sapiens | Q5JWF2 (AlphaFold model) |
Sequence of entity 1 (R), FASTA
>9YGZ_1 Medium-wave-sensitive opsin 1 (chains R)
MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWM
IFVVIASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISVVNQVYGYFV
LGHPMCVLQGYTVSLCGITGLWSLAIISWERWMVVCKPFGNVRFDAKLAIVGIAFSWIWA
AVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCITPLSIIVLCYL
QVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMVLAFCFCWGPYAFFACFAAANPGYPFH
PLMAALPAFFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVTETSQ
VAPAX
Sequence of entity 2 (B), FASTA
>9YGZ_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
>9YGZ_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 4 (H), FASTA
>9YGZ_4 scFv16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQGPAAAHHHHHHH
Sequence of entity 5 (A), FASTA
>9YGZ_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
Biophysical and structural analysis of human green cone opsin. Yao, W., Fay, J.F., Farrens, D.L. Biophys J (2026) 125:2448-2462. DOI 10.1016/j.bpj.2026.03.029 · 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…
- 9I3T 3.7 Å, Dark-state structure of human medium-wave-sensitive cone opsin (OPN1MW)
Browse structure collections
About this viewer
MolViewer shows 9YGZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.