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- EMDB-28163: Cryo-EM map of octopus sensory receptor CRT1 -

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Basic information

Entry
Database: EMDB / ID: EMD-28163
TitleCryo-EM map of octopus sensory receptor CRT1
Map dataCryo-EM structure of octopus sensory receptor
Sample
  • Complex: Octopus sensory receptor CRT1 in complex with diosgenin
    • Protein or peptide: Octopus sensory receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
Keywordspentameric ligand gated ion channel / octopus sensory receptor / cys-loop receptor / STRUCTURAL PROTEIN
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / 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: 2.62 Å
AuthorsKang G / Kim JJ / Allard CAH / Valencia-Montoya WA / Bellono NW / 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: Nature / Year: 2023
Title: Sensory specializations drive octopus and squid behaviour.
Authors: Guipeun Kang / Corey A H Allard / Wendy A Valencia-Montoya / Lena van Giesen / Jeong Joo Kim / Peter B Kilian / Xiaochen Bai / Nicholas W Bellono / Ryan E Hibbs /
Abstract: The evolution of new traits enables expansion into new ecological and behavioural niches. Nonetheless, demonstrated connections between divergence in protein structure, function and lineage-specific ...The evolution of new traits enables expansion into new ecological and behavioural niches. Nonetheless, demonstrated connections between divergence in protein structure, function and lineage-specific behaviours remain rare. Here we show that both octopus and squid use cephalopod-specific chemotactile receptors (CRs) to sense their respective marine environments, but structural adaptations in these receptors support the sensation of specific molecules suited to distinct physiological roles. We find that squid express ancient CRs that more closely resemble related nicotinic acetylcholine receptors, whereas octopuses exhibit a more recent expansion in CRs consistent with their elaborated 'taste by touch' sensory system. Using a combination of genetic profiling, physiology and behavioural analyses, we identify the founding member of squid CRs that detects soluble bitter molecules that are relevant in ambush predation. We present the cryo-electron microscopy structure of a squid CR and compare this with octopus CRs and nicotinic receptors. These analyses demonstrate an evolutionary transition from an ancestral aromatic 'cage' that coordinates soluble neurotransmitters or tastants to a more recent octopus CR hydrophobic binding pocket that traps insoluble molecules to mediate contact-dependent chemosensation. Thus, our study provides a foundation for understanding how adaptation of protein structure drives the diversification of organismal traits and behaviour.
History
DepositionSep 15, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28163.png

Downloads & links

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Map

FileDownload / File: emd_28163.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of octopus sensory receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 260 pix.
= 274.56 Å		1.06 Å/pix.
x 260 pix.
= 274.56 Å		1.06 Å/pix.
x 260 pix.
= 274.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.2748234 - 0.46551418
Average (Standard dev.)0.00017716142 (±0.00917673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 274.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_28163_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_28163_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Octopus sensory receptor CRT1 in complex with diosgenin

EntireName: Octopus sensory receptor CRT1 in complex with diosgenin
Components
  • Complex: Octopus sensory receptor CRT1 in complex with diosgenin
    • Protein or peptide: Octopus sensory receptor
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol

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Supramolecule #1: Octopus sensory receptor CRT1 in complex with diosgenin

SupramoleculeName: Octopus sensory receptor CRT1 in complex with diosgenin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Octopus bimaculoides (California two-spot octopus)
Molecular weightTheoretical: 200 kDa/nm

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Macromolecule #1: Octopus sensory receptor

MacromoleculeName: Octopus sensory receptor / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Octopus bimaculoides (California two-spot octopus)
Molecular weightTheoretical: 43.768008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TPTYGDERLL REKLLTNYSK SIRPVINLTK VVDVTALLYL QTLYDLDFVN NFIMARYYLG LIWIDEKLTW NPLDYNNITS IYLPKDKIW TPPIKMCNSM DKSEENDGVG ELMLTYTGWI NMWSFRLLHT YCQINAYTYP FDEHTCEIYL CVALHTINHT R IKELIYED ...String:
TPTYGDERLL REKLLTNYSK SIRPVINLTK VVDVTALLYL QTLYDLDFVN NFIMARYYLG LIWIDEKLTW NPLDYNNITS IYLPKDKIW TPPIKMCNSM DKSEENDGVG ELMLTYTGWI NMWSFRLLHT YCQINAYTYP FDEHTCEIYL CVALHTINHT R IKELIYED SKFTQNYKWD INVSGKVNGT DELFSYAFAP MYLRRKLTVG IIAMLIPTVM MTILTIFVFL LPPESGEKVS LA TTIFLSN VLYLVQIDKT TPTNTKYPSL LMLYLMLLSM LSGIATLGSV VISKLYVIQS PSLRKSNPSD QNMNKSHTNK VAD ISTISK VQSDLPIREK PNEKRIYCIS DYIRLDDIFL KLSIATSVII SMIFTCLLFI PLE

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: 20 / 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: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13...

MacromoleculeName: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
type: ligand / ID: 3 / Number of copies: 5 / Formula: DU0
Molecular weightTheoretical: 516.752 Da
Chemical component information

ChemComp-DU0:
2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol

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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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5kxi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157691
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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