[English] 日本語
Yorodumi
- PDB-9y2f: Metabotropic Glutamate Receptor 7 in complex with ecto-domain of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9y2f
TitleMetabotropic Glutamate Receptor 7 in complex with ecto-domain of Extracellular Leucine Rich Repeat and Fibronectin Type III Domain Containing 2
Components
  • Metabotropic glutamate receptor 7
  • Protein phosphatase 1 regulatory subunit 29
KeywordsMEMBRANE PROTEIN / mGluR7 / ELFN2 / GPCR / glutamate / trans-synaptic
Function / homology
Function and homology information


group III metabotropic glutamate receptor activity / negative regulation of glutamate secretion / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / serine binding / synaptic membrane adhesion / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / presynaptic active zone / glutamate binding ...group III metabotropic glutamate receptor activity / negative regulation of glutamate secretion / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / serine binding / synaptic membrane adhesion / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / presynaptic active zone / glutamate binding / protein phosphatase inhibitor activity / axon development / asymmetric synapse / regulation of synaptic transmission, glutamatergic / adenylate cyclase inhibitor activity / sensory perception of sound / dendritic shaft / PDZ domain binding / establishment of protein localization / postsynaptic density membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / signaling receptor activity / chemical synaptic transmission / cell cortex / G alpha (i) signalling events / signaling receptor complex / postsynaptic membrane / protein dimerization activity / axon / calcium ion binding / dendrite / : / membrane / plasma membrane
Similarity search - Function
: / ELFN1/ELFN2, fibronectin type-III domain / GPCR, family 3, metabotropic glutamate receptor 7 / : / GPCR, family 3, metabotropic glutamate receptor / : / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain ...: / ELFN1/ELFN2, fibronectin type-III domain / GPCR, family 3, metabotropic glutamate receptor 7 / : / GPCR, family 3, metabotropic glutamate receptor / : / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 3. / 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 / 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Receptor, ligand binding region / Receptor family ligand binding region / Leucine-rich repeat domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
Metabotropic glutamate receptor 7 / Protein phosphatase 1 regulatory subunit 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsLudlam, W.G. / Chang, C.T. / Liauw, B.W. / Cho, H.J. / Sawh-Gopal, A. / Izard, T. / Bao, H. / Dunn, H.A. / Vafabakhsh, R. / Martemyanov, K.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA056414 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F32NS124758 United States
CitationJournal: To Be Published
Title: Structural basis for modulation of group III mGlu receptors by trans-synaptic interactions
Authors: Ludlam, W.G. / Chang, C.T. / Liauw, B.W. / Cho, H.J. / Sawh-Gopal, A. / Izard, T. / Bao, H. / Dunn, H.A. / Vafabakhsh, R. / Martemyanov, K.A.
History
DepositionSep 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Protein phosphatase 1 regulatory subunit 29
A: Metabotropic glutamate receptor 7
D: Protein phosphatase 1 regulatory subunit 29
B: Metabotropic glutamate receptor 7


Theoretical massNumber of molelcules
Total (without water)280,4224
Polymers280,4224
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Protein phosphatase 1 regulatory subunit 29 / Extracellular leucine-rich repeat and fibronectin type III domain-containing protein 2 / Leucine- ...Extracellular leucine-rich repeat and fibronectin type III domain-containing protein 2 / Leucine-rich repeat and fibronectin type-III domain-containing protein 6 / Leucine-rich repeat-containing protein 62


Mass: 43056.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: M1-A22 is cleaved off signal peptide. D23-G248 is leucine rich repeat domain. S249-T379 is not resolved in the structure. L380-Q385 is human rhinovirus C3 protease cut site sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: ELFN2, KIAA1904, LRRC62, PPP1R29 / Production host: Homo sapiens (human) / References: UniProt: Q5R3F8
#2: Protein Metabotropic glutamate receptor 7 / mGluR7


Mass: 97154.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: M1-G34 is cleaved signal peptide. Q35-M37 is not resolved in structure. Y38-S521 is Venus Flytrap domain. V522-R859 is not resolved in structure. L860-Q865 is human rhinovirus C3 protease cut site sequence.
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM7, GPRC1G, MGLUR7 / Production host: Homo sapiens (human) / References: UniProt: Q14831
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex of mGluR7 and ecto-domain of ELFN2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28023 / Symmetry type: POINT
RefinementHighest resolution: 4.6 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311156
ELECTRON MICROSCOPYf_angle_d0.53315160
ELECTRON MICROSCOPYf_dihedral_angle_d4.3211530
ELECTRON MICROSCOPYf_chiral_restr0.041686
ELECTRON MICROSCOPYf_plane_restr0.0042000

+
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