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- PDB-9nyx: Structure of Native Bovine Rhodopsin in Complex with Mb7 in the D... -

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Basic information

Entry
Database: PDB / ID: 9nyx
TitleStructure of Native Bovine Rhodopsin in Complex with Mb7 in the Dark State
Components
  • Megabody 7
  • Rhodopsin
KeywordsISOMERASE/IMMUNE SYSTEM / nanoboy / rhodopsin / native purification / dark state / retinal / ISOMERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / 11-cis retinal binding / podosome assembly ...Opsins / VxPx cargo-targeting to cilium / rod bipolar cell differentiation / sperm head plasma membrane / absorption of visible light / opsin binding / The canonical retinoid cycle in rods (twilight vision) / G protein-coupled opsin signaling pathway / 11-cis retinal binding / podosome assembly / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / cellular response to light stimulus / rod photoreceptor outer segment / G protein-coupled receptor complex / Inactivation, recovery and regulation of the phototransduction cascade / thermotaxis / Activation of the phototransduction cascade / outer membrane / detection of temperature stimulus involved in thermoception / response to light intensity / photoreceptor cell maintenance / arrestin family protein binding / photoreceptor outer segment membrane / G alpha (i) signalling events / response to light stimulus / phototransduction, visible light / phototransduction / G-protein alpha-subunit binding / photoreceptor outer segment / visual perception / guanyl-nucleotide exchange factor activity / sperm midpiece / microtubule cytoskeleton organization / cell-cell junction / photoreceptor disc membrane / gene expression / G protein-coupled receptor signaling pathway / Golgi membrane / zinc ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) ...Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / 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
Biological speciesLama glama (llama)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHuang, W. / Salom-Arbona, D. / Suder, D. / Taylor, D.J. / Palczewski, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RM1 GM142002 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2026
Title: Structure of Native Bovine Rhodopsin in Complex with Mb7 in the Dark State.
Authors: Huang, W. / Salom, D. / Suder, D.S. / Taylor, D.J. / Palczewski, K.
History
DepositionMar 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 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

Downloads & links

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Assembly

Deposited unit
A: Megabody 7
C: Megabody 7
B: Rhodopsin
D: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,59610
Polymers99,0054
Non-polymers2,5916
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: Antibody Megabody 7


Mass: 13035.657 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein Rhodopsin


Mass: 36466.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02699
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Bovin Rhodopsin in complex with Megabody 7 in dark state
Type: COMPLEX / Entity ID: #1 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.5 MDa / Experimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 6000 nm / Nominal defocus min: 10 nm / Calibrated defocus min: 8000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21rc1_5015model refinement
13cryoSPARC3D reconstruction
CTF correctionDetails: C1 / Type: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112705 / Symmetry type: POINT

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