[English] 日本語
Yorodumi
- EMDB-28167: Cryo-EM map of squid sensory receptor CRB1 -

+
Open data


ID or keywords:

Loading...

-
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
Keywordspentameric ligand gated ion channel / squid sensory receptor / cys-loop receptor / STRUCTURAL PROTEIN
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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28167.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 260 pix.
= 277.94 Å		1.07 Å/pix.
x 260 pix.
= 277.94 Å		1.07 Å/pix.
x 260 pix.
= 277.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.069 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
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)

-
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)

-
Sample components

-
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

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

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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

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

6pv7

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more