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- PDB-8blj: Crystal structure of the ligand-binding domain (LBD) of human iGl... -

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Basic information

Entry
Database: PDB / ID: 8blj
TitleCrystal structure of the ligand-binding domain (LBD) of human iGluR Delta-1 (GluD1), apo state
ComponentsGlutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
KeywordsMEMBRANE PROTEIN / ion channel / ligand binding domain / glutamate receptor / apo state
Function / homology
Function and homology information


glutamate receptor activity / glutamate receptor signaling pathway / regulation of postsynapse organization / social behavior / GABA-ergic synapse / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / glutamatergic synapse ...glutamate receptor activity / glutamate receptor signaling pathway / regulation of postsynapse organization / social behavior / GABA-ergic synapse / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / glutamatergic synapse / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, delta-1 / Isoform 2 of Glutamate receptor ionotropic, delta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsHeroven, C. / Malinauskas, T. / Aricescu, A.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
CitationJournal: Science / Year: 2023
Title: GluD1 binds GABA and controls inhibitory plasticity.
Authors: Piot, L. / Heroven, C. / Bossi, S. / Zamith, J. / Malinauskas, T. / Johnson, C. / Wennagel, D. / Stroebel, D. / Charrier, C. / Aricescu, A.R. / Mony, L. / Paoletti, P.
History
DepositionNov 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
B: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
C: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
D: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
E: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
F: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,09229
Polymers188,0856
Non-polymers2,00723
Water5,224290
1
A: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
B: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,40911
Polymers62,6952
Non-polymers7149
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
D: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,39010
Polymers62,6952
Non-polymers6968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
F: Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2938
Polymers62,6952
Non-polymers5986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.290, 107.569, 98.559
Angle α, β, γ (deg.)90.000, 94.083, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99024126045, 0.139350479792, -0.00192090690038), (0.139004148928, 0.988582013229, 0.0581674281771), (0.0100046330355, 0.0573327733664, -0.998304993685)45.6600086268, -3.38971827634, 3.28754358869
2given(-0.0645356010387, 0.489395714913, 0.869670621801), (0.476873018549, -0.750417205291, 0.457674712195), (0.876599840508, 0.444258767194, -0.184950986462)-2.91206344478, -32.1953650519, 20.195948166
3given(0.174649094491, 0.482342750014, -0.858395692733), (-0.540239821063, -0.681910766801, -0.493090906284), (-0.823188088794, 0.549857415727, 0.141485663013)-6.07081827425, -7.75920708884, 58.0163017745
4given(0.23548563199, 0.587576243007, -0.774145125787), (-0.60715540876, -0.53303761014, -0.589264979266), (-0.758886570404, 0.608789836339, 0.231227395503)36.4503288276, 48.1091905712, 55.0554912574
5given(-0.101588561708, 0.583403572849, 0.805803968293), (0.491189025728, -0.674962451099, 0.550598792781), (0.865108724459, 0.45173660555, -0.21799296794)41.7894715799, 19.951898796, 17.4275635289

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
Glutamate receptor ionotropic, delta-1,Isoform 2 of Glutamate receptor ionotropic, delta-1 / GluD1 / GluR delta-1 subunit


Mass: 31347.420 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRID1, KIAA1220 / Plasmid: pHR-CMV-TetO2 / Details (production host): transient transfection / Cell (production host): epithelial-like / Cell line (production host): HEK293S GnTI-/- / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney; embryo / References: UniProt: Q9ULK0, UniProt: Q9ULK0-2
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 307 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 17% (w/v) polyethylene glycol (PEG) 20000, 100 mM Tris HCl, 100 mM MgCl2
Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.18→98.31 Å / Num. obs: 56271 / % possible obs: 91.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.11 / Net I/σ(I): 4.7
Reflection shellResolution: 2.18→2.39 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1959 / CC1/2: 0.641 / Rpim(I) all: 0.477 / % possible all: 61.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0270refinement
PHENIXdev_4761refinement
autoPROC1.0.5 (20210420)data reduction
autoPROC1.0.5 (20210420)data scaling
PHASER2.8.3phasing
XDSFeb 5, 2021 (BUILT 20210205)data reduction
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V3T

2v3t


Resolution: 2.18→62.59 Å / SU ML: 0.2588 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9354
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2437 2698 4.8 %
Rwork0.2056 53536 -
obs0.2075 56234 59.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.11 Å2
Refinement stepCycle: LAST / Resolution: 2.18→62.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12410 0 104 290 12804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001512816
X-RAY DIFFRACTIONf_angle_d0.411217343
X-RAY DIFFRACTIONf_chiral_restr0.04281926
X-RAY DIFFRACTIONf_plane_restr0.00272224
X-RAY DIFFRACTIONf_dihedral_angle_d9.74224746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.220.2955100.2742135X-RAY DIFFRACTION2.99
2.22-2.260.4083130.2666216X-RAY DIFFRACTION4.7
2.26-2.310.3343210.2865340X-RAY DIFFRACTION7.37
2.31-2.360.3601360.2722612X-RAY DIFFRACTION13.22
2.36-2.410.3681370.2779939X-RAY DIFFRACTION19.77
2.41-2.470.2829590.26471240X-RAY DIFFRACTION26.12
2.47-2.540.278830.27691647X-RAY DIFFRACTION35.39
2.54-2.610.30961010.27742297X-RAY DIFFRACTION48.53
2.61-2.70.34021430.26312800X-RAY DIFFRACTION59.49
2.7-2.790.30841740.26663241X-RAY DIFFRACTION69.5
2.79-2.90.30831670.26653676X-RAY DIFFRACTION77.84
2.9-3.040.32121980.2534058X-RAY DIFFRACTION86.49
3.04-3.20.25092390.24864410X-RAY DIFFRACTION93.39
3.2-3.40.2392250.21784656X-RAY DIFFRACTION98.91
3.4-3.660.25442380.21154683X-RAY DIFFRACTION99.41
3.66-4.030.24032430.17144647X-RAY DIFFRACTION98.87
4.03-4.610.20782430.15074638X-RAY DIFFRACTION98.03
4.61-5.810.19712220.16754692X-RAY DIFFRACTION98.14
5.81-62.590.19732460.19164609X-RAY DIFFRACTION95.95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.45844834570.595126978068-0.617415149011.30550213056-0.2831025057251.80229787074-0.0301989975597-0.185244247860.08339476344430.1466574561770.09567056343280.0866891442453-0.07039963888970.148444424397-0.03953538884430.1162873600460.02686876674560.0179601475820.131122931679-0.004448649045420.087825983005130.2429948403-12.866784400612.0186554279
20.968950587708-0.059146105809-0.5203171429490.556685435451-0.1897554157961.286264601380.09724657476870.502502402790.148042931497-0.2640320156290.1782209475280.151287290658-0.230798565385-0.8390106404720.2021755191120.1740378085760.08708312389980.03357507850430.4627573363020.08430250821450.09430071180313.9748213678-11.3539979123-9.20678690317
31.64833765994-0.436220172414-0.1886651068920.733387241724-0.1350950228051.687690604220.118827572046-0.3123634780690.3984986714390.006069366741020.03447286345560.0574826075923-0.272360537307-0.104148340238-0.1027717842940.08070708384220.01809767724990.1124079031880.423225752012-0.1350364408080.143026655106-1.08953590965-2.8462630674538.9755347634
42.06144806611-0.163382412148-0.5606379062530.6858389621370.1807943235160.97174920588-0.2108624036580.0967638139248-0.4444428345150.0467094907637-0.04427773899980.213222724320.374415595254-0.628309576346-0.05937269306670.0678469279328-0.1345188593540.05539665036230.635853251342-0.04044391896870.252325699934-17.4049410421-21.195299438127.8859842321
51.064809477140.321879501298-0.4477269312521.452371525470.08083734141781.22406222566-0.2272016389280.0972163763533-0.428344232556-0.138078136571-0.1636875280280.397276258840.569771611281-0.628882580578-0.2357952861420.219928360537-0.2134165408680.07737758596350.451310314867-0.1279659235890.39150243739327.301970628529.749139409326.8726452215
61.07329785692-0.25184219533-0.1987040832610.8181052552930.09572514476431.482068432180.0861348593383-0.3140986374020.0860070259246-0.0549972257280.04861494499250.236019458965-0.310343533843-0.211488337941-0.0102369304033-0.00037789025310.05094159270880.1510837494980.250649913051-0.009726376736040.0052551678419340.539244853749.833921690635.368785695
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 437 through 815)AA437 - 8151 - 265
22(chain 'B' and resid 437 through 814)BB437 - 8141 - 264
33(chain 'C' and resid 437 through 815)CC437 - 8151 - 260
44(chain 'D' and resid 437 through 816)DD437 - 8161 - 266
55(chain 'E' and resid 437 through 815)EE437 - 8151 - 258
66(chain 'F' and resid 437 through 814)FF437 - 8141 - 258

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