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- PDB-5ehm: Crystal structure of the Drosophila CG3822 KaiR1D ligand binding ... -

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Basic information

Entry
Database: PDB / ID: 5ehm
TitleCrystal structure of the Drosophila CG3822 KaiR1D ligand binding domain complex with NMDA
ComponentsRE06730p,CG3822
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / positive regulation of glutamate secretion, neurotransmission / regulation of synaptic activity / positive regulation of neuromuscular synaptic transmission / glutamate receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone / calcium ion import across plasma membrane / kainate selective glutamate receptor activity ...Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / positive regulation of glutamate secretion, neurotransmission / regulation of synaptic activity / positive regulation of neuromuscular synaptic transmission / glutamate receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone / calcium ion import across plasma membrane / kainate selective glutamate receptor activity / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / presynaptic membrane / 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 ...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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-methyl-D-aspartic acid / RE06730p / Kainate-type ionotropic glutamate receptor subunit 1D
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.281 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
DepositionOct 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Sep 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RE06730p,CG3822
B: RE06730p,CG3822
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9664
Polymers59,6722
Non-polymers2942
Water15,006833
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-10 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.891, 56.891, 143.584
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein RE06730p,CG3822


Mass: 29836.039 Da / Num. of mol.: 2 / Fragment: unp residues 411-529, unp residues 650-794
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3822, CG3822, Dmel_CG3822 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q8MS48, UniProt: Q9VDH5
#2: Chemical ChemComp-OEM / N-methyl-D-aspartic acid / N-Methyl-D-aspartic acid


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Comment: neurotransmitter, agonist*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 833 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Buffer 150 NaCl 10 HEPES pH 7.5 20 mM NMDA 2 mM EDTA Reservoir 22% PEG 6K 0.1 M Na Acetate 0.1M Ammonium Sulfate

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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: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→40 Å / Num. obs: 134785 / % possible obs: 96.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 49.44
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.5 / % possible all: 70.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTB

5dtb


Resolution: 1.281→24.81 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.07 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 12903 4.99 %Random
Rwork0.164 ---
obs0.1655 134785 96.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.281→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 20 833 4916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084303
X-RAY DIFFRACTIONf_angle_d0.9815821
X-RAY DIFFRACTIONf_dihedral_angle_d14.1071623
X-RAY DIFFRACTIONf_chiral_restr0.076641
X-RAY DIFFRACTIONf_plane_restr0.007749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2808-1.29530.24622800.20866196X-RAY DIFFRACTION72
1.2953-1.31050.24983900.2047560X-RAY DIFFRACTION90
1.3105-1.32650.25073760.19288126X-RAY DIFFRACTION95
1.3265-1.34330.23664800.19187962X-RAY DIFFRACTION96
1.3433-1.3610.23653840.18858322X-RAY DIFFRACTION97
1.361-1.37960.23564760.18948098X-RAY DIFFRACTION97
1.3796-1.39930.24954880.18627990X-RAY DIFFRACTION97
1.3993-1.42020.21955080.18178342X-RAY DIFFRACTION97
1.4202-1.44240.21974800.18188067X-RAY DIFFRACTION97
1.4424-1.46610.21283660.17428341X-RAY DIFFRACTION97
1.4661-1.49130.20834280.1738252X-RAY DIFFRACTION97
1.4913-1.51850.19384720.16688228X-RAY DIFFRACTION97
1.5185-1.54770.22914400.16678158X-RAY DIFFRACTION98
1.5477-1.57920.22645080.16428332X-RAY DIFFRACTION98
1.5792-1.61360.20314140.16058234X-RAY DIFFRACTION98
1.6136-1.65110.20324680.1558280X-RAY DIFFRACTION98
1.6511-1.69240.2343160.15698428X-RAY DIFFRACTION98
1.6924-1.73810.20424760.15858268X-RAY DIFFRACTION98
1.7381-1.78930.20543600.15898424X-RAY DIFFRACTION99
1.7893-1.8470.18334840.15378250X-RAY DIFFRACTION99
1.847-1.9130.16674400.15378406X-RAY DIFFRACTION99
1.913-1.98950.17214360.15148336X-RAY DIFFRACTION99
1.9895-2.08010.18764600.16218418X-RAY DIFFRACTION99
2.0801-2.18970.1894280.15928548X-RAY DIFFRACTION99
2.1897-2.32680.19674180.16058306X-RAY DIFFRACTION99
2.3268-2.50620.20334440.16048504X-RAY DIFFRACTION100
2.5062-2.75820.19574880.16518334X-RAY DIFFRACTION100
2.7582-3.15660.19924380.16588488X-RAY DIFFRACTION100
3.1566-3.97430.17254360.15948360X-RAY DIFFRACTION99
3.9743-24.81480.17613210.1647984X-RAY DIFFRACTION93

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