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

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Basic information

Entry
Database: PDB / ID: 5dtb
TitleCrystal structure of the Drosophila CG3822 KaiR1D ligand binding domain complex with glutamate
ComponentsCG3822
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
GLUTAMIC ACID / Kainate-type ionotropic glutamate receptor subunit 1D
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.843 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 1.2Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CG3822
B: CG3822
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0597
Polymers59,5582
Non-polymers5015
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-13 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.704, 87.704, 183.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CG3822


Mass: 29778.984 Da / Num. of mol.: 2 / Fragment: unp residues 411-527; unp residues 650-794
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3822, Dmel_CG3822 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q9VDH5
#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Buffer 150 NaCl 10 Tris, 2 Glu, 1 EDTA Reservoir 10% PEG 8K 0.1 Bicine pH 9, 2% Dioxane
PH range: 8-9

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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: Jul 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. obs: 62542 / % possible obs: 97.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 26.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 2.05 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2124)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S50

1s50


Resolution: 1.843→29.801 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.194 3078 5.03 %Random
Rwork0.1616 ---
obs0.1632 61148 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.843→29.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 33 526 4685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124289
X-RAY DIFFRACTIONf_angle_d1.0075773
X-RAY DIFFRACTIONf_dihedral_angle_d11.5882607
X-RAY DIFFRACTIONf_chiral_restr0.054632
X-RAY DIFFRACTIONf_plane_restr0.007737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8434-1.87220.26331450.21392490X-RAY DIFFRACTION94
1.8722-1.90290.23371550.19712566X-RAY DIFFRACTION97
1.9029-1.93570.22281440.18752540X-RAY DIFFRACTION97
1.9357-1.97090.23511400.1722572X-RAY DIFFRACTION97
1.9709-2.00880.23511240.1632594X-RAY DIFFRACTION97
2.0088-2.04980.20321460.15682590X-RAY DIFFRACTION97
2.0498-2.09440.20161110.15782611X-RAY DIFFRACTION97
2.0944-2.14310.17351270.15732606X-RAY DIFFRACTION97
2.1431-2.19670.2161280.14922607X-RAY DIFFRACTION98
2.1967-2.2560.18271280.14982642X-RAY DIFFRACTION98
2.256-2.32240.20761180.14542602X-RAY DIFFRACTION98
2.3224-2.39730.20341440.14972624X-RAY DIFFRACTION98
2.3973-2.4830.18241320.15512656X-RAY DIFFRACTION98
2.483-2.58230.18861370.15632638X-RAY DIFFRACTION98
2.5823-2.69980.18771370.16132639X-RAY DIFFRACTION98
2.6998-2.8420.24211400.17022652X-RAY DIFFRACTION99
2.842-3.01990.2121660.17242664X-RAY DIFFRACTION99
3.0199-3.25280.22731290.17942693X-RAY DIFFRACTION99
3.2528-3.57970.1931410.16822692X-RAY DIFFRACTION99
3.5797-4.09650.18251670.15492705X-RAY DIFFRACTION99
4.0965-5.15680.15811740.13182751X-RAY DIFFRACTION99
5.1568-29.80460.17651450.17992936X-RAY DIFFRACTION99
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)
10.3469-0.1853-0.24970.33380.08950.20580.0375-0.1825-0.01730.1772-0.09010.00660.229-0.0833-0.00030.3433-0.06370.00890.23370.03820.2407-22.35555.94999.2663
20.32610.4626-0.04760.4997-0.24860.85980.1676-0.2788-0.02240.4615-0.24870.0952-0.0685-0.1384-0.0090.3097-0.06080.03050.2953-0.00830.2404-25.159618.939612.0204
30.33340.3486-0.01990.83520.13460.36350.0314-0.03330.0663-0.0369-0.10010.1038-0.0488-0.1112-00.20710.02280.00330.2181-0.02850.2471-29.266621.2289-7.6105
40.21880.02440.03750.1077-0.13430.1102-0.03470.08810.0821-0.0217-0.10610.1696-0.613-0.378-0.00760.33940.1182-0.07130.3387-0.06580.4025-38.943828.855-11.9501
50.47070.10320.45640.37310.16551.07250.0965-0.0601-0.03020.0312-0.0956-0.01630.1016-0.1109-00.2215-0.02840.01210.2076-0.01760.2164-29.889714.483-7.5065
60.83930.2335-0.16620.4343-0.3270.18530.0560.0067-0.01420.0271-0.1514-0.04730.26020.1881-0.00460.28370.04120.02510.24510.03110.2569-12.922910.3634-1.5184
70.4933-0.0599-0.11990.5775-0.64840.720.0829-0.04160.09990.1299-0.08530.0629-0.27270.21010.0010.2701-0.04410.03030.2006-0.01040.2378-3.648143.4277-8.8373
80.0565-0.0351-0.15470.02760.09330.4610.2711-0.2180.00690.2623-0.1194-0.2898-0.21030.18640.02470.3055-0.0405-0.10850.43580.04720.383410.005229.61632.387
90.51190.2385-0.40690.9852-0.44010.7018-0.0067-0.1332-0.0994-0.0596-0.1447-0.03190.13520.1394-0.11260.21070.03320.01810.22320.04480.21720.209323.6931-10.4414
100.2821-0.0339-0.04440.1204-0.12490.2817-0.1306-0.25040.01780.0966-0.0744-0.1620.53360.4517-0.06670.33050.16320.08350.3560.12710.32528.101114.7487-10.5173
110.7528-0.1968-0.48990.455-0.1180.5593-0.0067-0.0195-0.0223-0.107-0.1068-0.04380.15710.1223-0.0190.2320.02790.03280.19870.03790.20040.753925.2573-18.6197
120.74090.1441-0.15810.4676-0.23280.2037-0.0265-0.02250.043-0.0236-0.06360.1374-0.1063-0.04020.00010.26520.0050.00340.22870.01940.2703-14.384835.1561-11.3613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:44)
2X-RAY DIFFRACTION2(chain A and resid 45:87)
3X-RAY DIFFRACTION3(chain A and resid 88:151)
4X-RAY DIFFRACTION4(chain A and resid 152:170)
5X-RAY DIFFRACTION5(chain A and resid 171:232)
6X-RAY DIFFRACTION6(chain A and resid 233:268)
7X-RAY DIFFRACTION7(chain B and resid 6:68)
8X-RAY DIFFRACTION8(chain B and resid 69:80)
9X-RAY DIFFRACTION9(chain B and resid 81:140)
10X-RAY DIFFRACTION10(chain B and resid 141:170)
11X-RAY DIFFRACTION11(chain B and resid 171:229)
12X-RAY DIFFRACTION12(chain B and resid 230:268)

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