[English] 日本語
Yorodumi
- EMDB-61204: Cryo-EM Structure of calcium sensing receptor in complex gamma-gl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61204
TitleCryo-EM Structure of calcium sensing receptor in complex gamma-glutamyl-valyl-glycine as a kokumi substance
Map data
Sample
  • Complex: extracellular regions of calcium-sensing receptor
    • Protein or peptide: Extracellular calcium-sensing receptor
  • Protein or peptide: gamma-glutamyl-valyl-glycine
Keywordscomplex / agonist / calcium-sensing receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of presynaptic membrane potential / bile acid secretion / chemosensory behavior / cellular response to peptide / response to fibroblast growth factor / cellular response to vitamin D / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / calcium ion import / positive regulation of positive chemotaxis ...regulation of presynaptic membrane potential / bile acid secretion / chemosensory behavior / cellular response to peptide / response to fibroblast growth factor / cellular response to vitamin D / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / calcium ion import / positive regulation of positive chemotaxis / fat pad development / cellular response to hepatocyte growth factor stimulus / branching morphogenesis of an epithelial tube / amino acid binding / positive regulation of calcium ion import / regulation of calcium ion transport / cellular response to low-density lipoprotein particle stimulus / anatomical structure morphogenesis / detection of calcium ion / JNK cascade / positive regulation of vasoconstriction / axon terminus / chloride transmembrane transport / ossification / response to ischemia / cellular response to glucose stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / positive regulation of insulin secretion / intracellular calcium ion homeostasis / vasodilation / integrin binding / presynaptic membrane / G alpha (i) signalling events / basolateral plasma membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / cellular response to hypoxia / G alpha (q) signalling events / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / apical plasma membrane / neuronal cell body / positive regulation of cell population proliferation / calcium ion binding / positive regulation of gene expression / protein kinase binding / glutamatergic synapse / cell surface / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
GPCR, family 3, extracellular calcium-sensing receptor-related / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site / GPCR, family 3 / G-protein coupled receptors family 3 profile. ...GPCR, family 3, extracellular calcium-sensing receptor-related / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Extracellular calcium-sensing receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsYamaguchi H / Kitajima S / Suzuki H / Suzuki S / Nishikawa K / Maruyama Y / Kamegawa A / Kazutoshi T / Tagami U / Kuroda M ...Yamaguchi H / Kitajima S / Suzuki H / Suzuki S / Nishikawa K / Maruyama Y / Kamegawa A / Kazutoshi T / Tagami U / Kuroda M / Fujiyoshi Y / Sugiki M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2025
Title: Cryo-EM structure of the calcium-sensing receptor complexed with the kokumi substance γ-glutamyl-valyl-glycine.
Authors: Hiroki Yamaguchi / Seiji Kitajima / Hiroshi Suzuki / Shota Suzuki / Kouki Nishikawa / Akiko Kamegawa / Yoshinori Fujiyoshi / Kazutoshi Takahashi / Uno Tagami / Yutaka Maruyama / Motonaka ...Authors: Hiroki Yamaguchi / Seiji Kitajima / Hiroshi Suzuki / Shota Suzuki / Kouki Nishikawa / Akiko Kamegawa / Yoshinori Fujiyoshi / Kazutoshi Takahashi / Uno Tagami / Yutaka Maruyama / Motonaka Kuroda / Masayuki Sugiki /
Abstract: Taste is a key element for food palatability and is strongly influenced by the five basic tastes and other taste sensations, such as fatty orosensation, and koku perception, which indicates taste ...Taste is a key element for food palatability and is strongly influenced by the five basic tastes and other taste sensations, such as fatty orosensation, and koku perception, which indicates taste complexity, mouthfulness and lastingness. This study focuses on the taste modifier γ-glutamyl-valyl-glycine (γ-EVG), a potent kokumi substance that enhances taste and koku perception by modulating the calcium-sensing receptor (CaSR). We used cryo-electron microscopy to determine the structure of the CaSR/γ-EVG complex at a resolution of 3.55 Å. Structural analysis revealed important interactions between γ-EVG and the CaSR, involving key residues, such as Pro39, Phe42, Arg66, Ser147, and Glu297. Mutagenesis experiments demonstrated the importance of these residues in peptide binding. Each γ-EVG residue contributed to its binding to the orthosteric ligand binding site of the CaSR. These findings elucidate the molecular basis of kokumi peptide recognition by the CaSR and contribute to a better understanding of positive allosteric modulators of the CaSR. In addition, this research provides valuable insights into the functionality of class C G-protein-coupled receptors in taste perception, potentially informing the development of new taste modifiers and advancing the field of food science.
History
DepositionAug 19, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_61204.png

Downloads & links

-
Map

FileDownload / File: emd_61204.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 254 pix.
= 255.27 Å		1.01 Å/pix.
x 254 pix.
= 255.27 Å		1.01 Å/pix.
x 254 pix.
= 255.27 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.024
Minimum - Maximum-0.063505046 - 0.09095414
Average (Standard dev.)0.00003827819 (±0.0029651748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions254254254
Spacing254254254
CellA=B=C: 255.27 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_61204_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61204_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61204_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : extracellular regions of calcium-sensing receptor

EntireName: extracellular regions of calcium-sensing receptor
Components
  • Complex: extracellular regions of calcium-sensing receptor
    • Protein or peptide: Extracellular calcium-sensing receptor
  • Protein or peptide: gamma-glutamyl-valyl-glycine

-
Supramolecule #1: extracellular regions of calcium-sensing receptor

SupramoleculeName: extracellular regions of calcium-sensing receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Extracellular calcium-sensing receptor

MacromoleculeName: Extracellular calcium-sensing receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 101.745445 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKAAAYGP DQRAQKKGDI ILGGLFPIHF GVAAKDQDLK SRPESVECIR YNFRGFRWLQ AMIFAIEEI NSSPALLPNL TLGYRIFDTC NTVSKALEAT LSFVAQNKID SLNLDEFCNC SEHIPSTIAV VGATGSGVST A VANLLGLF ...String:
MKTIIALSYI FCLVFADYKD DDDKAAAYGP DQRAQKKGDI ILGGLFPIHF GVAAKDQDLK SRPESVECIR YNFRGFRWLQ AMIFAIEEI NSSPALLPNL TLGYRIFDTC NTVSKALEAT LSFVAQNKID SLNLDEFCNC SEHIPSTIAV VGATGSGVST A VANLLGLF YIPQVSYASS SRLLSNKNQF KSFLRTIPND EHQATAMADI IEYFRWNWVG TIAADDDYGR PGIEKFREEA EE RDICIDF SELISQYSDE EEIQHVVEVI QNSTAKVIVV FSSGPDLEPL IKEIVRRNIT GKIWLASEAW ASSSLIAMPQ YFH VVGGTI GFALKAGQIP GFREFLKKVH PRKSVHNGFA KEFWEETFNC HLQEGAKGPL PVDTFLRGHE ESGDRFSNSS TAFR PLCTG DENISSVETP YIDYTHLRIS YNVYLAVYSI AHALQDIYTC LPGRGLFTNG SCADIKKVEA WQVLKHLRHL NFTNN MGEQ VTFDECGDLV GNYSIINWHL SPEDGSIVFK EVGYYNVYAK KGERLFINEE KILWSGFSRE VPFSNCSRDC LAGTRK GII EGEPTCCFEC VECPDGEYSD ETDASACNKC PDDFWSNENH TSCIAKEIEF LSWTEPFGIA LTLFAVLGIF LTAFVLG VF IKFRNTPIVK ATNRELSYLL LFSLLCCFSS SLFFIGEPQD WTCRLRQPAF GISFVLCISC ILVKTNRVLL VFEAKIPT S FHRKWWGLNL QFLLVFLCTF MQIVICVIWL YTAPPSSYRN QELEDEIIFI TCHEGSLMAL GFLIGYTCLL AAICFFFAF KSRKLPENFN EAKFITFSML IFFIVWISFI PAYASTYGKF VSAVEVIAIL AASFGLLACI FFNKIYIILF KPSRNTIEEV RCSTAAHAF KVAARATLRR SNV

UniProtKB: Extracellular calcium-sensing receptor

-
Macromolecule #2: gamma-glutamyl-valyl-glycine

MacromoleculeName: gamma-glutamyl-valyl-glycine / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 303.312 Da
SequenceString:
(GGL)VG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Average exposure time: 8.0 sec. / Average electron dose: 63.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.4 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

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

7m3g

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 177479
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