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- PDB-5dt6: Crystal structure of the Drosophila GluR1A ligand binding domain ... -

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Basic information

Entry
Database: PDB / ID: 5dt6
TitleCrystal structure of the Drosophila GluR1A ligand binding domain 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: 1.598 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
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 1.4Nov 13, 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)30,8984
Polymers30,5671
Non-polymers3313
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.396, 58.351, 100.179
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: 30566.738 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.: 245 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Sample buffer 150 NaCl, 10 Tris pH 8.5, 2 glutamate, 1 EDTA, 10% glycerol Reservoir 13% 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 46081 / % possible obs: 98.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 26.4
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.42 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S50

1s50


Resolution: 1.598→29.176 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 2064 4.97 %Random
Rwork0.1535 ---
obs0.1546 41563 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.598→29.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 22 245 2405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132248
X-RAY DIFFRACTIONf_angle_d1.4483036
X-RAY DIFFRACTIONf_dihedral_angle_d12.936854
X-RAY DIFFRACTIONf_chiral_restr0.063320
X-RAY DIFFRACTIONf_plane_restr0.009394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.598-1.63510.2261280.22232551X-RAY DIFFRACTION97
1.6351-1.6760.21751470.19542652X-RAY DIFFRACTION100
1.676-1.72130.221400.18732637X-RAY DIFFRACTION100
1.7213-1.7720.16561290.17652616X-RAY DIFFRACTION100
1.772-1.82920.1981420.16562649X-RAY DIFFRACTION100
1.8292-1.89450.2051310.16162615X-RAY DIFFRACTION100
1.8945-1.97040.21671570.16282628X-RAY DIFFRACTION99
1.9704-2.060.19831280.15462646X-RAY DIFFRACTION99
2.06-2.16860.17031420.14312621X-RAY DIFFRACTION99
2.1686-2.30440.1721410.14322627X-RAY DIFFRACTION99
2.3044-2.48230.17221360.14862641X-RAY DIFFRACTION99
2.4823-2.73190.16631450.15142622X-RAY DIFFRACTION98
2.7319-3.12680.15511370.1572652X-RAY DIFFRACTION97
3.1268-3.93790.16261350.14582632X-RAY DIFFRACTION97
3.9379-29.18030.16971260.14482710X-RAY DIFFRACTION94
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)
10.3142-0.25850.08860.43140.04080.4266-0.0378-0.16570.1487-0.02640.0514-0.07620.0616-0.03010.00190.1563-0.008-0.01660.20170.00130.169414.9047-9.07659.4984
20.751-0.03580.22490.1943-0.09830.2717-0.0405-0.02230.0186-0.0169-0.0031-0.00570.01270.058800.15510.0037-0.00680.1579-0.00470.154410.0851-9.13443.1486
30.68010.0233-0.05750.257-0.06610.1224-0.03120.0740.0272-0.01970.04290.0049-0.0253-0.0325-00.1694-0.0131-0.00550.15580.02070.15166.5977-4.875-6.9631
40.2238-0.0314-0.19580.0699-0.09030.30580.03210.37860.1282-0.18020.0964-0.04320.0339-0.23490.04940.2347-0.01120.01120.30580.12520.178611.59094.6746-21.507
50.43450.1201-0.24460.6424-0.4330.90610.01320.08160.13140.0204-0.0366-0.0812-0.10610.0122-0.09360.1476-0.0125-0.00730.12790.05250.166215.70423.4424-11.3444
60.0726-0.02060.03860.16160.08740.2031-0.0676-0.04630.2132-0.02360.05380.0999-0.0887-0.115700.1880.0189-0.00090.1568-0.03990.23572.32483.21348.3854
70.00120.003-0.00760.00840.00120.0108-0.03490.12610.1471-0.1911-0.07320.0755-0.0743-0.0204-0.00010.7508-0.29470.0520.6591-0.10370.382118.527913.65265.253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:36)
2X-RAY DIFFRACTION2(chain A and resid 37:72)
3X-RAY DIFFRACTION3(chain A and resid 73:127)
4X-RAY DIFFRACTION4(chain A and resid 128:162)
5X-RAY DIFFRACTION5(chain A and resid 163:236)
6X-RAY DIFFRACTION6(chain A and resid 237:260)
7X-RAY DIFFRACTION7(chain A and resid 261:266)

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