+Open data
-Basic information
Entry | Database: PDB / ID: 8eiz | ||||||
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Title | Cryo-EM structure of squid sensory receptor CRB1 | ||||||
Components | Squid sensory receptor CRB1 | ||||||
Keywords | STRUCTURAL PROTEIN / pentameric ligand gated ion channel / squid sensory receptor / cys-loop receptor | ||||||
Function / homology | Chem-WK3 Function and homology information | ||||||
Biological species | Sepioloidea lineolata (invertebrata) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.13 Å | ||||||
Authors | Kang, G. / Kim, J.J. / Allard, C.A.H. / Valencia-Montoya, W.A. / van Giesen, L. / Kilian, P.B. / Bai, X. / Bellono, N.W. / Hibbs, R.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eiz.cif.gz | 609.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eiz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8eiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eiz_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8eiz_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8eiz_validation.xml.gz | 56.9 KB | Display | |
Data in CIF | 8eiz_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/8eiz ftp://data.pdbj.org/pub/pdb/validation_reports/ei/8eiz | HTTPS FTP |
-Related structure data
Related structure data | 28167MC 8eisC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 45038.723 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sepioloidea lineolata (invertebrata) / Production host: Homo sapiens (human) #2: 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 Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-WK3 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Squid sensory receptor CRB1 in complex with denatonium Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 200 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Sepioloidea lineolata (invertebrata) |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: CRL-3022 |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70869 / Symmetry type: POINT |