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- PDB-5ict: Crystal structure of the Drosophila GluR1A ligand binding domain ... -

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Basic information

Entry
Database: PDB / ID: 5ict
TitleCrystal structure of the Drosophila GluR1A ligand binding domain Y792T mutant complex with glutamate
ComponentsGlutamate receptor 1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Cargo concentration in the ER / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / COPII-mediated vesicle transport / glutamate receptor activity / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / monoatomic cation transport ...Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Cargo concentration in the ER / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / COPII-mediated vesicle transport / glutamate receptor activity / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / monoatomic cation transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / plasma membrane
Similarity search - Function
Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II ...Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate receptor 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsDharkar, P. / Mayer, M.L.
CitationJournal: Neuron / Year: 2016
Title: Novel Functional Properties of Drosophila CNS Glutamate Receptors.
Authors: Li, Y. / Dharkar, P. / Han, T.H. / Serpe, M. / Lee, C.H. / Mayer, M.L.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8364
Polymers30,5051
Non-polymers3313
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.208, 58.406, 99.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate receptor 1 / Glutamate receptor I / dGLUR-I / Kainate-selective glutamate receptor


Mass: 30504.668 Da / Num. of mol.: 1 / Fragment: unp residues 474-594; unp residues 739-880
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GluRIA, Glu-RI, CG8442 / Plasmid: pet22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q03445
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Sample buffer 150 NaCl, 10 Tris pH 8.5, 5 Na Glutamate, 1 mM EDTA, 10% glycerol Reservoir 12% PEG 8K, 100 Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→30 Å / Num. obs: 36199 / % possible obs: 98.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 34.2
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.8 / % possible all: 88.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DT6

5dt6


Resolution: 1.68→29.203 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 15.43
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 1722 4.95 %Random
Rwork0.1464 ---
obs0.1476 34798 96.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.68→29.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 22 285 2440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092285
X-RAY DIFFRACTIONf_angle_d1.0183094
X-RAY DIFFRACTIONf_dihedral_angle_d10.9861398
X-RAY DIFFRACTIONf_chiral_restr0.06325
X-RAY DIFFRACTIONf_plane_restr0.007404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6804-1.72980.21321110.17332099X-RAY DIFFRACTION75
1.7298-1.78570.161240.16712423X-RAY DIFFRACTION86
1.7857-1.84950.18871320.16622677X-RAY DIFFRACTION94
1.8495-1.92350.2191580.16962790X-RAY DIFFRACTION99
1.9235-2.0110.2051380.15122835X-RAY DIFFRACTION100
2.011-2.1170.17721520.14062832X-RAY DIFFRACTION100
2.117-2.24960.17661590.1342837X-RAY DIFFRACTION100
2.2496-2.42320.17281390.13872877X-RAY DIFFRACTION100
2.4232-2.6670.17091630.1392841X-RAY DIFFRACTION100
2.667-3.05250.15271550.14322884X-RAY DIFFRACTION100
3.0525-3.84450.15411520.13622922X-RAY DIFFRACTION100
3.8445-29.20740.17071390.15243059X-RAY DIFFRACTION100
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)
10.0471-0.0781-0.00290.13550.01450.01020.0136-0.09810.09860.0139-0.0003-0.09610.0536-0.08120.01010.0796-0.0311-0.01260.1053-0.00730.074913.9024-8.50728.136
20.00520.0012-0.00110.01040.00150.0156-0.0225-0.08430.05420.0193-0.0006-0.0153-0.01610.0177-0.01090.05640.0038-0.00110.0958-0.02390.064412.3669-6.926911.8127
30.0162-0.00780.00760.0033-0.0030.0096-0.02340.0721-0.0285-0.01930.0035-0.00190.00230.0239-0.00760.0704-0.0066-0.00820.0864-0.00290.06338.4012-13.2554-6.1464
40.0015-0.006700.00760.0060.0419-0.00760.00930.0819-0.03280.0142-0.0347-0.0471-0.0522-0.00310.0862-0.0159-0.00030.06460.02370.09976.83172.0848-9.0499
50.0327-0.01530.04960.0729-0.03180.08760.06660.15750.0448-0.13540.0626-0.032-0.0057-0.0830.10590.1332-0.03150.04190.14490.09920.019213.21662.9851-21.8224
60.03540.0007-0.00550.03930.01390.0517-0.00670.00610.0715-0.00650.0006-0.048-0.063-0.0261-0.00580.0772-0.0236-0.00130.0590.0290.111915.02575.0051-7.5367
70.00620.0052-0.00030.0075-0.00020.0031-0.0063-0.01830.040.01710.0123-0.0204-0.0525-0.01360.00610.090.00890.00590.0604-0.06280.1371.01032.23258.884
80.00220.0018-0.00070.0015-0.00150.0089-0.0008-0.00370.00280.00050.0013-0.0026-0.010.0078-0.00130.2052-0.06770.00620.1113-0.07420.172617.366612.67584.6082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:27)
2X-RAY DIFFRACTION2(chain A and resid 28:58)
3X-RAY DIFFRACTION3(chain A and resid 59:100)
4X-RAY DIFFRACTION4(chain A and resid 101:127)
5X-RAY DIFFRACTION5(chain A and resid 128:179)
6X-RAY DIFFRACTION6(chain A and resid 180:236)
7X-RAY DIFFRACTION7(chain A and resid 237:259)
8X-RAY DIFFRACTION8(chain A and resid 260:266)

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