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- EMDB-47556: octopus sensory receptor CRT1 bound to Lumichrome -

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Basic information

Entry
Database: EMDB / ID: EMD-47556
Titleoctopus sensory receptor CRT1 bound to Lumichrome
Map data
Sample
  • Complex: octopus sensory receptor CRT1 bound to lumichrome
    • Protein or peptide: Chemotactile receptor CRT1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LUMICHROME
Keywordscomplex / membrane protein
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
Neurotransmitter-gated ion-channel ligand-binding domain-containing protein
Similarity search - Component
Biological speciesOctopus bimaculoides (California two-spot octopus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsJiang H / Hibbs RE
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47556.png

Downloads & links

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Map

FileDownload / File: emd_47556.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 343.04 Å		1.07 Å/pix.
x 320 pix.
= 343.04 Å		1.07 Å/pix.
x 320 pix.
= 343.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.25013652 - 0.6611568
Average (Standard dev.)0.0002834756 (±0.015912477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 343.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47556_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47556_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : octopus sensory receptor CRT1 bound to lumichrome

EntireName: octopus sensory receptor CRT1 bound to lumichrome
Components
  • Complex: octopus sensory receptor CRT1 bound to lumichrome
    • Protein or peptide: Chemotactile receptor CRT1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: LUMICHROME

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Supramolecule #1: octopus sensory receptor CRT1 bound to lumichrome

SupramoleculeName: octopus sensory receptor CRT1 bound to lumichrome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Octopus bimaculoides (California two-spot octopus)

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Macromolecule #1: Chemotactile receptor CRT1

MacromoleculeName: Chemotactile receptor CRT1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Octopus bimaculoides (California two-spot octopus)
Molecular weightTheoretical: 47.334262 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIFVIYLVFI LISSIPIVKS TPTYGDERLL REKLLTNYSK SIRPVINLTK VVDVTALLYL QTLYDLDFVN NFIMARYYLG LIWIDEKLT WNPLDYNNIT SIYLPKDKIW TPPIKMCNSM DKSEENDGVG ELMLTYTGWI NMWSFRLLHT YCQINAYTYP F DEHTCEIY ...String:
MIFVIYLVFI LISSIPIVKS TPTYGDERLL REKLLTNYSK SIRPVINLTK VVDVTALLYL QTLYDLDFVN NFIMARYYLG LIWIDEKLT WNPLDYNNIT SIYLPKDKIW TPPIKMCNSM DKSEENDGVG ELMLTYTGWI NMWSFRLLHT YCQINAYTYP F DEHTCEIY LCVALHTINH TRIKELIYED SKFTQNYKWD INVSGKVNGT DELFSYAFAP MYLRRKLTVG IIAMLIPTVM MT ILTIFVF LLPPESGEKV SLATTIFLSN VLYLVQIDKT TPTNTKYPSL LMLYLMLLSM LSGIATLGSV VISKLYVIQS PSL RKSNPS DQNMNKSHTN KVADISTISK VQSDLPIREK PNEKRIYCIS DYIRLDDIFL KLSIATSVII SMIFTCLLFI PLES SAWSH PQFEK

UniProtKB: Neurotransmitter-gated ion-channel ligand-binding domain-containing protein

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 25 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #3: LUMICHROME

MacromoleculeName: LUMICHROME / type: ligand / ID: 3 / Number of copies: 5 / Formula: LUM
Molecular weightTheoretical: 242.233 Da
Chemical component information

ChemComp-LUM:
LUMICHROME

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8eis

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44653
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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