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- PDB-9e6d: octopus sensory receptor CRT1 bound to Lumichrome -

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Basic information

Entry
Database: PDB / ID: 9e6d
Titleoctopus sensory receptor CRT1 bound to Lumichrome
ComponentsChemotactile receptor CRT1
KeywordsMEMBRANE PROTEIN / complex
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
LUMICHROME / Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
Similarity search - Component
Biological speciesOctopus bimaculoides (California two-spot octopus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsJiang, H. / Hibbs, R.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Cell / Year: 2025
Title: Environmental microbiomes drive chemotactile sensation in octopus.
Authors: Rebecka J Sepela / Hao Jiang / Yern-Hyerk Shin / Tessa L Hautala / Jon Clardy / Ryan E Hibbs / Nicholas W Bellono /
Abstract: Microbial communities coat nearly every surface in the environment and have co-existed with animals throughout evolution. Whether animals exploit omnipresent microbial cues to navigate their ...Microbial communities coat nearly every surface in the environment and have co-existed with animals throughout evolution. Whether animals exploit omnipresent microbial cues to navigate their surroundings is not well understood. Octopuses use "taste-by-touch" chemotactile receptors (CRs) to explore the seafloor, but how they distinguish meaningful surfaces from the rocks and crevices they encounter is unknown. Here, we report that secreted signals from microbiomes of ecologically relevant surfaces activate CRs to guide octopus behavior. Distinct molecules isolated from individual bacterial strains located on prey or eggs bind single CRs in subtly different structural conformations to elicit specific mechanisms of receptor activation, ion permeation and signal transduction, and maternal care and predation behavior. Thus, microbiomes on ecological surfaces act at the level of primary sensory receptors to inform behavior. Our study demonstrates that uncovering interkingdom interactions is essential to understanding how animal sensory systems evolved in a microbe-rich world.
History
DepositionOct 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chemotactile receptor CRT1
B: Chemotactile receptor CRT1
C: Chemotactile receptor CRT1
D: Chemotactile receptor CRT1
E: Chemotactile receptor CRT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,41335
Polymers236,6715
Non-polymers6,74130
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
Chemotactile receptor CRT1


Mass: 47334.262 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Octopus bimaculoides (California two-spot octopus)
Gene: OCBIM_22006518mg / Production host: Homo sapiens (human) / References: UniProt: A0A0L8FVQ9
#2: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 25
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-LUM / LUMICHROME / 7,8-DIMETHYLALLOXAZINE / 6,7-DIMETHYLALLOXAZINE


Mass: 242.233 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H10N4O2 / 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: octopus sensory receptor CRT1 bound to lumichrome / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Octopus bimaculoides (California two-spot octopus)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44653 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612620
ELECTRON MICROSCOPYf_angle_d0.8917215
ELECTRON MICROSCOPYf_dihedral_angle_d12.7924670
ELECTRON MICROSCOPYf_chiral_restr0.0472095
ELECTRON MICROSCOPYf_plane_restr0.0072080

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