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- PDB-9upm: Cryo-EM structure of macaque red cone pigment with Q114N mutation -

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Basic information

Entry
Database: PDB / ID: 9upm
TitleCryo-EM structure of macaque red cone pigment with Q114N mutation
ComponentsLW opsin,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / Cone pigment / GPCR / rhodopsin
Function / homology
Function and homology information


positive regulation of cytokinesis / photoreceptor activity / phototransduction / visual perception / electron transport chain / G protein-coupled receptor activity / photoreceptor disc membrane / electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Opsin red/green sensitive / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) ...Opsin red/green sensitive / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
RETINAL / Soluble cytochrome b562 / LW opsin
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsOhashi, S. / Kojima, A. / Fukuda, M. / Kim, S. / Kato, H.E. / Kandori, H. / Katayama, K.
Funding support Japan, 15items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJFR204S Japan
Japan Science and TechnologyJPMJPR19G4 Japan
Japan Science and TechnologyJPMJCR21P3 Japan
Japan Science and TechnologyJPMJCR1753 Japan
Japan Science and TechnologyJPMJCR23B1 Japan
Japan Science and TechnologyJPMJAX222F Japan
Japan Science and TechnologyJPMJSP2112 Japan
Japan Science and TechnologyJPMJPR24OF Japan
Japan Society for the Promotion of Science (JSPS)22H00400 Japan
Japan Society for the Promotion of Science (JSPS)21H04969 Japan
Japan Society for the Promotion of Science (JSPS)22K19265 Japan
Japan Society for the Promotion of Science (JSPS)JP22H04742 Japan
Japan Society for the Promotion of Science (JSPS)JP23K14142 Japan
Japan Society for the Promotion of Science (JSPS)JP24H02262 Japan
Japan Society for the Promotion of Science (JSPS)25K09525 Japan
CitationJournal: Science / Year: 2026
Title: Structural insights into spectral tuning and retinal exchange in cone visual pigments
Authors: Ohashi, S. / Kojima, A. / Yang, X. / Fukuda, M. / Sacchetta, F. / Sugita, Y. / Nuemket, N. / Kim, S. / Kobayashi, K. / Imai, H. / Iwata, S. / Nango, E. / Kobayashi, T. / Noda, T. / Olivucci, ...Authors: Ohashi, S. / Kojima, A. / Yang, X. / Fukuda, M. / Sacchetta, F. / Sugita, Y. / Nuemket, N. / Kim, S. / Kobayashi, K. / Imai, H. / Iwata, S. / Nango, E. / Kobayashi, T. / Noda, T. / Olivucci, M. / Kato, H.E. / Kandori, H.
History
DepositionApr 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LW opsin,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2102
Polymers49,9261
Non-polymers2841
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein LW opsin,Soluble cytochrome b562 / Cytochrome b-562


Mass: 49925.566 Da / Num. of mol.: 1 / Mutation: Q114N,M257W,R331I,H335I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque), (gene. exp.) Escherichia coli (E. coli)
Gene: cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9XSX4, UniProt: P0ABE7
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MR / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Macaca fascicularis (crab-eating macaque)9541
21Escherichia coli (E. coli)562
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: JEC-3000FC / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 46.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 15824

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256022 / Symmetry type: POINT
RefinementResolution: 3.21→3.21 Å / Cor.coef. Fo:Fc: 0.749 / WRfactor Rwork: 0.459 / SU B: 28.58 / SU ML: 0.444 / Average fsc free: 0 / Average fsc overall: 0.6806 / Average fsc work: 0.6806 / ESU R: 0.615
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.4592 22703 -
all0.459 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 81.37 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0050.0122419
ELECTRON MICROSCOPYr_bond_other_d0.0010.0162296
ELECTRON MICROSCOPYr_angle_refined_deg1.4521.7713312
ELECTRON MICROSCOPYr_angle_other_deg0.6231.6925249
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.4815292
ELECTRON MICROSCOPYr_dihedral_angle_2_deg11.8793.57919
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.84110353
ELECTRON MICROSCOPYr_dihedral_angle_6_deg8.031086
ELECTRON MICROSCOPYr_chiral_restr0.0830.2372
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.022817
ELECTRON MICROSCOPYr_gen_planes_other0.0040.02601
ELECTRON MICROSCOPYr_nbd_refined0.2120.2608
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1620.22273
ELECTRON MICROSCOPYr_nbtor_refined0.1820.21241
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0660.21175
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.150.289
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.0410.22
ELECTRON MICROSCOPYr_mcbond_it5.8957.5171174
ELECTRON MICROSCOPYr_mcbond_other5.8977.5061173
ELECTRON MICROSCOPYr_mcangle_it10.03713.5441464
ELECTRON MICROSCOPYr_mcangle_other10.03313.5561465
ELECTRON MICROSCOPYr_scbond_it7.0518.8471245
ELECTRON MICROSCOPYr_scbond_other7.0498.8471246
ELECTRON MICROSCOPYr_scangle_it12.53215.8011848
ELECTRON MICROSCOPYr_scangle_other12.52915.7991849
ELECTRON MICROSCOPYr_lrange_it23.95490.07210478
ELECTRON MICROSCOPYr_lrange_other23.95390.06910479
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.2-3.2831.70416991.70416990.2121.704
3.283-3.3731.01215901.01215900.3051.012
3.373-3.4710.83516340.83516340.3970.835
3.471-3.5770.6715250.6715250.5350.67
3.577-3.6940.51914950.51914950.640.519
3.694-3.8240.40414610.40414610.7270.404
3.824-3.9680.413650.413650.7970.4
3.968-4.1290.42913720.42913720.840.429
4.129-4.3130.44812790.44812790.8660.448
4.313-4.5220.44412310.44412310.8560.444
4.522-4.7660.41611750.41611750.8540.416
4.766-5.0540.39310960.39310960.8430.393
5.054-5.4020.36310730.36310730.8540.363
5.402-5.8330.3579590.3579590.8170.357
5.833-6.3860.3798920.3798920.7940.379
6.386-7.1350.4037950.4037950.7730.403
7.135-8.2280.3917230.3917230.7770.391
8.228-10.0530.3536010.3536010.8670.353
10.053-14.1140.264710.264710.9160.26
14.114-830.7212670.7212670.9550.721

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