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- PDB-6n50: Metabotropic Glutamate Receptor 5 Extracellular Domain in Complex... -

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Basic information

Entry
Database: PDB / ID: 6n50
TitleMetabotropic Glutamate Receptor 5 Extracellular Domain in Complex with Nb43 and L-quisqualic acid
Components
  • Metabotropic glutamate receptor 5
  • Nanobody 43Single-domain antibody
KeywordsSIGNALING PROTEIN / Cell Surface Receptor
Function / homologyGPCR, family 3, conserved site / Homer-binding domain of metabotropic glutamate receptor / Periplasmic binding protein-like I / Metabotropic glutamate receptor, Homer-binding domain / GPCR, family 3, metabotropic glutamate receptor / Receptor family ligand binding region / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, metabotropic glutamate receptor 5 / GPCR, family 3 / Receptor, ligand binding region ...GPCR, family 3, conserved site / Homer-binding domain of metabotropic glutamate receptor / Periplasmic binding protein-like I / Metabotropic glutamate receptor, Homer-binding domain / GPCR, family 3, metabotropic glutamate receptor / Receptor family ligand binding region / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, metabotropic glutamate receptor 5 / GPCR, family 3 / Receptor, ligand binding region / GPCR, family 3, nine cysteines domain / G-protein coupled receptors family 3 signature 1. / GPCR, family 3, nine cysteines domain superfamily / G-protein coupled receptors family 3 signature 2. / GPCR family 3, C-terminal / G-protein coupled receptors family 3 signature 3. / G-protein coupled receptors family 3 profile. / G alpha (q) signalling events / Class C/3 (Metabotropic glutamate/pheromone receptors) / Neurexins and neuroligins / 7 transmembrane sweet-taste receptor of 3 GCPR / regulation of translational elongation / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / protein tyrosine kinase activator activity / postsynaptic modulation of chemical synaptic transmission / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / regulation of intracellular calcium activated chloride channel activity / glutamate receptor activity / G protein-coupled receptor activity / postsynaptic density membrane / modulation of age-related behavioral decline / calcium-mediated signaling using intracellular calcium source / synapse organization / protein tyrosine kinase binding / regulation of synaptic transmission, glutamatergic / locomotory behavior / cognition / regulation of protein phosphorylation / learning / Schaffer collateral - CA1 synapse / positive regulation of protein tyrosine kinase activity / regulation of long-term neuronal synaptic plasticity / cellular response to amyloid-beta / learning or memory / regulation of translation / chemical synaptic transmission / neuron projection / G protein-coupled receptor signaling pathway / integral component of plasma membrane / plasma membrane / cytoplasm / Metabotropic glutamate receptor 5
Function and homology information
Specimen sourceHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 3.751 Å resolution
AuthorsKoehl, A. / Hu, H. / Feng, D. / Sun, B. / Chu, M. / Weis, W.I. / Skiniotis, G. / Mathiesen, J.M. / Kobilka, B.K.
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 / Rasmus Fonseca / William I Weis / Jesper M Mathiesen / Georgios Skiniotis / Brian K Kobilka
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 20, 2018 / Release: Jan 23, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 23, 2019Structure modelrepositoryInitial release
1.1Feb 6, 2019Structure modelData collection / Database referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Feb 20, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 5
B: Metabotropic glutamate receptor 5
C: Metabotropic glutamate receptor 5
E: Nanobody 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,21512
Polyers215,5424
Non-polymers1,6738
Water0
1
A: Metabotropic glutamate receptor 5
E: Nanobody 43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3825
Polyers80,7502
Non-polymers6323
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2290
ΔGint (kcal/M)-8
Surface area (Å2)27410
MethodPISA
2
B: Metabotropic glutamate receptor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8063
Polyers67,3961
Non-polymers4102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)570
ΔGint (kcal/M)-5
Surface area (Å2)18170
MethodPISA
3
C: Metabotropic glutamate receptor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0274
Polyers67,3961
Non-polymers6323
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)750
ΔGint (kcal/M)-2
Surface area (Å2)23010
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)150.433, 157.159, 208.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI 21 21 21

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Components

#1: Protein/peptide Metabotropic glutamate receptor 5 / / mGluR5


Mass: 67395.633 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Gene: GRM5, GPRC1E, MGLUR5 / Plasmid name: pACGP67 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P41594
#2: Protein/peptide Nanobody 43 / Single-domain antibody


Mass: 13354.672 Da / Num. of mol.: 1 / Source: (gene. exp.) Lama glama (llama) / Plasmid name: PE SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 5 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-QUS / (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID / QUISQUALATE


Mass: 189.126 Da / Num. of mol.: 3 / Formula: C5H7N3O5 / Quisqualic acid

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 / Density percent sol: 60.37 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM NaCl 50 mM ADA pH 7.0 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 kelvins / Serial crystal experiment: N
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL12-2 / Synchrotron site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Collection date: May 9, 2018
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionD resolution high: 3.75 Å / D resolution low: 39.29 Å / Number obs: 25207 / CC half: 0.916 / Rmerge I obs: 0.123 / Rpim I all: 0.08 / Rrim I all: 0.147 / NetI over sigmaI: 8.8 / Redundancy: 3.4 % / Percent possible obs: 98.6
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique obsCC halfRpim I allRrim I allRedundancyPercent possible all
0.8483.7504.01044870.7860.5401.0103.40098.100
0.02610.61039.29011730.9970.0180.0323.10096.500

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LMK
Overall SU ML: 0.59 / Cross valid method: THROUGHOUT / Sigma F: 1.34 / Overall phase error: 34.03
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 249.2 Å2 / B iso mean: 151.3731 Å2 / B iso min: 85.83 Å2
Least-squares processR factor R free: 0.3001 / R factor R work: 0.2657 / R factor obs: 0.2683 / Highest resolution: 3.751 Å / Lowest resolution: 39.29 Å / Number reflection R free: 1996 / Number reflection obs: 25151 / Percent reflection R free: 7.94 / Percent reflection obs: 98.27
Refine hist #finalHighest resolution: 3.751 Å / Lowest resolution: 39.29 Å / B iso mean ligand: 175.75 / Number residues total: 1596
Number of atoms included #finalProtein: 12039 / Nucleic acid: 0 / Ligand: 109 / Solvent: 0 / Total: 12148
Refine LS restraints ncs

Ens ID: 1 / Number: 4514 / Refine ID: X-RAY DIFFRACTION / Rms: 7.228 / Type: TORSIONAL

Dom IDAuth asym ID
1A
2C
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 14

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.75150.42830.36593.84521451577172296.0000
3.84520.38500.33443.94911371654179199.0000
3.94910.34480.31544.06521491634178399.0000
4.06520.32630.29874.19621261660178699.0000
4.19620.32570.27444.34601351649178499.0000
4.34600.27210.25244.51981451648179399.0000
4.51980.31370.24474.72521391648178798.0000
4.72520.27280.25304.97381451600174597.0000
4.97380.31380.24955.28481341653178799.0000
5.28480.26890.27035.691715216821834100.0000
5.69170.29400.26816.26241581663182199.0000
6.26240.30450.27877.16381461659180598.0000
7.16380.26290.23489.00771291685181498.0000
9.00770.29020.252039.29191561743189997.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
13.5520-0.0291-0.66180.68850.00110.6072-0.14420.13540.2313-0.13570.1621-0.13300.0437-0.1246-0.0179-0.1313-0.06850.1174-0.0221-0.0747-0.127911.189621.3282-15.0843
22.26260.11960.80802.6513-0.07580.3399-0.0583-0.03780.33730.25400.0064-0.2089-0.1477-0.36890.05190.26250.15200.0016-0.30400.1512-0.1217-1.496918.834154.3304
31.5334-0.2723-0.07071.54610.38070.3443-0.1149-0.0240-0.53800.12160.1089-0.23850.47060.18690.0060-0.0300-0.07230.1520-0.2673-0.09960.290319.3552-14.0667-20.3686
44.10651.9829-0.89384.2285-2.04181.1487-0.0218-0.0593-0.01140.0332-0.0043-0.01220.1226-0.03610.0262-0.21370.06820.11480.07320.14860.1218-29.163412.71549.7051
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A25A5691{ A|* }
2B23B4962{ B|* }
3C25C5693{ C|* }
4E3E1254{ E|* }

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