[English] 日本語
Yorodumi
- EMDB-0347: Apo form metabotropic glutamate receptor 5 with Nanobody 43 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0347
TitleApo form metabotropic glutamate receptor 5 with Nanobody 43
Map dataApo form metabotropic glutamate receptor 5 with Nanobody 43, primary map
Sample
  • Complex: Metabotropic Glutamate Receptor 5 - Nb43 Complex
    • Protein or peptide: Metabotropic Glutamate Receptor 5
    • Protein or peptide: Nanobody 43
Function / homology
Function and homology information


A2A adenosine receptor binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity ...A2A adenosine receptor binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Neurexins and neuroligins / astrocyte projection / protein tyrosine kinase activator activity / regulation of synaptic transmission, glutamatergic / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / dendritic shaft / learning / locomotory behavior / G protein-coupled receptor activity / synapse organization / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cognition / cellular response to amyloid-beta / G alpha (q) signalling events / chemical synaptic transmission / dendritic spine / learning or memory / positive regulation of MAPK cascade / neuronal cell body / dendrite / regulation of DNA-templated transcription / glutamatergic synapse / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 5 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / 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, metabotropic glutamate receptor 5 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / 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 / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Metabotropic glutamate receptor 5
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsKoehl A / Hu H / Feng D / Zhang Y / Sun B / Kobilka TS / Pardon E / Steyaert J / Mathiesen JM / Skiniotis G / Kobilka BK
CitationJournal: Nature / Year: 2019
Title: Structural insights into the activation of metabotropic glutamate receptors.
Authors: Antoine Koehl / Hongli Hu / Dan Feng / Bingfa Sun / Yan Zhang / Michael J Robertson / Matthew Chu / Tong Sun Kobilka / Toon Laeremans / Jan Steyaert / Jeffrey Tarrasch / Somnath Dutta / ...Authors: Antoine Koehl / Hongli Hu / Dan Feng / Bingfa Sun / Yan Zhang / Michael J Robertson / Matthew Chu / Tong Sun Kobilka / Toon Laeremans / Jan Steyaert / Jeffrey Tarrasch / Somnath Dutta / Rasmus Fonseca / William I Weis / Jesper M Mathiesen / Georgios Skiniotis / Brian K Kobilka /
Abstract: Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich ...Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich domains to their 7-transmembrane domains. Spectroscopic studies show that signalling is a dynamic process, in which large-scale conformational changes underlie the transmission of signals from the extracellular Venus flytraps to the G protein-coupling domains-the 7-transmembrane domains-in the membrane. Here, using a combination of X-ray crystallography, cryo-electron microscopy and signalling studies, we present a structural framework for the activation mechanism of metabotropic glutamate receptor subtype 5. Our results show that agonist binding at the Venus flytraps leads to a compaction of the intersubunit dimer interface, thereby bringing the cysteine-rich domains into close proximity. Interactions between the cysteine-rich domains and the second extracellular loops of the receptor enable the rigid-body repositioning of the 7-transmembrane domains, which come into contact with each other to initiate signalling.
History
DepositionNov 20, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseFeb 6, 2019-
UpdateFeb 20, 2019-
Current statusFeb 20, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.054
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.054
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0347.png

Downloads & links

-
Map

FileDownload / File: emd_0347.map.gz / Format: CCP4 / Size: 6.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApo form metabotropic glutamate receptor 5 with Nanobody 43, primary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.58 Å/pix.
x 120 pix.
= 309.6 Å		2.58 Å/pix.
x 120 pix.
= 309.6 Å		2.58 Å/pix.
x 120 pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.054 / Movie #1: 0.054
Minimum - Maximum-0.018538713 - 0.11647756
Average (Standard dev.)0.0010566172 (±0.0109877335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120120120
Spacing120120120
CellA=B=C: 309.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.582.582.58
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z309.600309.600309.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
D min/max/mean-0.0190.1160.001

-
Supplemental data

-
Sample components

-
Entire : Metabotropic Glutamate Receptor 5 - Nb43 Complex

EntireName: Metabotropic Glutamate Receptor 5 - Nb43 Complex
Components
  • Complex: Metabotropic Glutamate Receptor 5 - Nb43 Complex
    • Protein or peptide: Metabotropic Glutamate Receptor 5
    • Protein or peptide: Nanobody 43

-
Supramolecule #1: Metabotropic Glutamate Receptor 5 - Nb43 Complex

SupramoleculeName: Metabotropic Glutamate Receptor 5 - Nb43 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Complex between metabotropic glutamate receptor 5 and Nb43
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: SF9
Molecular weightTheoretical: 220 KDa

-
Macromolecule #1: Metabotropic Glutamate Receptor 5

MacromoleculeName: Metabotropic Glutamate Receptor 5 / type: protein_or_peptide / ID: 1
Details: Polypeptide encoding metabotropic glutamate receptor 5
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QSSERRVVAH MPGDIIIGAL FSVHHQPTVD KVHERKCGAV REQYGIQRV EAMLHTLERI NSDPTLLPNI TLGCEIRDSC WHSAVALEQS IEFIRDSLIS S EEEEGLVR CVDGSSSSFR SKKPIVGVIG PGSSSVAIQV QNLLQLFNIP QIAYSATSMD LS DKTLFKY ...String:
QSSERRVVAH MPGDIIIGAL FSVHHQPTVD KVHERKCGAV REQYGIQRV EAMLHTLERI NSDPTLLPNI TLGCEIRDSC WHSAVALEQS IEFIRDSLIS S EEEEGLVR CVDGSSSSFR SKKPIVGVIG PGSSSVAIQV QNLLQLFNIP QIAYSATSMD LS DKTLFKY FMRVVPSDAQ QARAMVDIVK RYNWTYVSAV HTEGNYGESG MEAFKDMSAK EGI CIAHSY KIYSNAGEQS FDKLLKKLTS HLPKARVVAC FCEGMTVRGL LMAMRRLGLA GEFL LLGSD GWADRYDVTD GYQREAVGGI TIKLQSPDVK WFDDYYLKLR PETNHRNPWF QEFWQ HRFQ CRLEGFPQEN SKYNKTCNSS LTLKTHHVQD SKMGFVINAI YSMAYGLHNM QMSLCP GYA GLCDAMKPID GRKLLESLMK TNFTGVSGDT ILFDENGDSP GRYEIMNFKE MGKDYFD YI NVGSWDNGEL KMDDDEVWSK KSNIIRSVCS EPCEKGQIKV IRKGEVSCCW TCTPCKEN E YVFDEYTCKA CQLGSWPTDD LTGCDLIPVQ YLRWGDPEPI AAVVFACLGL LATLFVTVV FIIYRDTPVV KSSSRELCYI ILAGICLGYL CTFCLIAKPK QIYCYLQRIG IGLSPAMSYS ALVTKTNRI ARILAGSKKK ICTKKPRFMS ACAQLVIAFI LICIQLGIIV ALFIMEPPDI M HDYPSIRE VYLICNTTNL GVVTPLGYNG LLILSCTFYA FKTRNVPANF NEAKYIAFTM YT TCIIWLA FVPIYFGSNY KIITMCFSVS LSATVALGCM FVPKVYIILA KPERNVRSAF TTS TVVRMH VGDGKSSSAA SRSSSLVNL

-
Macromolecule #2: Nanobody 43

MacromoleculeName: Nanobody 43 / type: protein_or_peptide / ID: 2 / Details: Nanobody 43 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG LVQAGGSLRL SCAASGRTFT SYAMGWFRQA PGKERESVAA ISSSGGSTHY ADSVKGRFTI SRDNSKNTVY LQMNSLKPED TAVYYCAAAM YGSRWPDWEY DYWGQGTQVT VSSAA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMHEPESHEPES
0.02 percentGDNGlyco Disogenin
0.002 percentCHSCholesteryl Hemisuccinate
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE
DetailsSample was mono disperse as assayed by gel filtration and SDS PAGE.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 58139 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: The apo structure was used as starting model.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 44831
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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