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- EMDB-28167: Cryo-EM map of squid sensory receptor CRB1 -

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Basic information

Entry
Database: EMDB / ID: EMD-28167
TitleCryo-EM map of squid sensory receptor CRB1
Map dataCryo-EM structure of squid sensory receptor CRB1
Sample
  • Complex: Squid sensory receptor CRB1 in complex with denatonium
    • Protein or peptide: Squid sensory receptor CRB1
  • Ligand: N-benzyl-2-(2,6-dimethylanilino)-N,N-diethyl-2-oxoethan-1-aminium
  • Ligand: water
Biological speciesSepioloidea lineolata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsKang G / Kim JJ / Allard CAH / Valencia-Montoya WA / van Giesen L / Kilian PB / Bai X / 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-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28167.png

Downloads & links

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Map

FileDownload / File: emd_28167.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of squid sensory receptor CRB1
Voxel sizeX=Y=Z: 1.069 Å
Density
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.14953451 - 0.2451885
Average (Standard dev.)0.00013427204 (±0.005994424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 277.94 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_28167_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_28167_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 : Squid sensory receptor CRB1 in complex with denatonium

EntireName: Squid sensory receptor CRB1 in complex with denatonium
Components
  • Complex: Squid sensory receptor CRB1 in complex with denatonium
    • Protein or peptide: Squid sensory receptor CRB1
  • Ligand: N-benzyl-2-(2,6-dimethylanilino)-N,N-diethyl-2-oxoethan-1-aminium
  • Ligand: water

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Supramolecule #1: Squid sensory receptor CRB1 in complex with denatonium

SupramoleculeName: Squid sensory receptor CRB1 in complex with denatonium
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sepioloidea lineolata (invertebrata)
Molecular weightTheoretical: 200 kDa/nm

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Macromolecule #1: Squid sensory receptor CRB1

MacromoleculeName: Squid sensory receptor CRB1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Sepioloidea lineolata (invertebrata)
Molecular weightTheoretical: 45.038723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CWTYEEEYYF RSNFLQQYNK DIRPLNDLSK PISVGIHLEI AKMNDFNLAE GRLKIQTYLI LQWYDEKIFW NESTYPIPKL MVSSKKIWS PAISVYYTEN EMDSKDQFQM EIYKNGSVHQ WKSFYFNILC DVNARAFPFD KYTCETMFYF NDYDIQTAIF S SFRCISST ...String:
CWTYEEEYYF RSNFLQQYNK DIRPLNDLSK PISVGIHLEI AKMNDFNLAE GRLKIQTYLI LQWYDEKIFW NESTYPIPKL MVSSKKIWS PAISVYYTEN EMDSKDQFQM EIYKNGSVHQ WKSFYFNILC DVNARAFPFD KYTCETMFYF NDYDIQTAIF S SFRCISST DLSRKAWYVS FSCDTKIGEE GSLGQLSLKL VRKVSLQCLS VLLPLFIFFI LNIMIGYLPI ESGEKVTFAT TV FLSNVIY IDNLSKQLPK ESSEIPLIFL CHIFLAFLSG LSAVGTIITS KIFCKYKSTE SAPSPSPAPA NNKIDVKKNS QIY SISKEG RVEKEANSSD GIKATTTTTT TTITEDLKKI CLSYAKIESA ILYIMTFISI LCALVFTSLF FESFLD

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Macromolecule #3: N-benzyl-2-(2,6-dimethylanilino)-N,N-diethyl-2-oxoethan-1-aminium

MacromoleculeName: N-benzyl-2-(2,6-dimethylanilino)-N,N-diethyl-2-oxoethan-1-aminium
type: ligand / ID: 3 / Number of copies: 5 / Formula: WK3
Molecular weightTheoretical: 325.468 Da
Chemical component information

ChemComp-WK3:
N-benzyl-2-(2,6-dimethylanilino)-N,N-diethyl-2-oxoethan-1-aminium

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 10 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
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:

6pv7

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70869
FSC plot (resolution estimation)

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