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- PDB-4wxj: Drosophila muscle GluRIIB complex with glutamate -

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Basic information

Entry
Database: PDB / ID: 4wxj
TitleDrosophila muscle GluRIIB complex with glutamate
ComponentsGlutamate receptor IIB,Glutamate receptor IIB
KeywordsMEMBRANE PROTEIN / Glutamate receptor ion channel Ligand binding domain
Function / homology
Function and homology information


Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / muscle cell postsynaptic specialization / regulation of synaptic activity / neuromuscular synaptic transmission / glutamate receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex ...Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / muscle cell postsynaptic specialization / regulation of synaptic activity / neuromuscular synaptic transmission / glutamate receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / glutamate-gated receptor activity / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / modulation of chemical synaptic transmission / neuromuscular junction / calcium ion transport / signaling receptor activity / postsynaptic 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 / Periplasmic binding protein-like II ...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 / Glutamate receptor IIB
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsDharkar, P. / Mayer, M.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Functional reconstitution of Drosophila melanogaster NMJ glutamate receptors.
Authors: Han, T.H. / Dharkar, P. / Mayer, M.L. / Serpe, M.
History
DepositionNov 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor IIB,Glutamate receptor IIB
B: Glutamate receptor IIB,Glutamate receptor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9874
Polymers61,6932
Non-polymers2942
Water4,954275
1
A: Glutamate receptor IIB,Glutamate receptor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9932
Polymers30,8461
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor IIB,Glutamate receptor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9932
Polymers30,8461
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.314, 94.527, 119.538
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 IIB,Glutamate receptor IIB


Mass: 30846.320 Da / Num. of mol.: 2
Fragment: Fragment: Residues 416-537 and 660-802 were connected by a dipeptide GT linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell: Muscle / Gene: GluRIIB, CG7234, Dmel_CG7234 / Plasmid: pET22 modified / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: Q9VMP3
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Reservoir: 18% PEG 2K MME, 0.1 M Tris pH 8.0, 5 mM NiCl2 Protein buffer: 150 mM NaCl, 10 mM Tris pH 8.0, 2 mM Na glutamate, 1 mM EDTA multiple rounds of seeding
PH range: 8

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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: Mar 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 40664 / Num. obs: 40664 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1819)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S50

1s50


Resolution: 2.002→30.054 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 1806 4.94 %Random
Rwork0.1977 ---
obs0.1993 36525 89.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→30.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 20 275 4398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034220
X-RAY DIFFRACTIONf_angle_d0.6475693
X-RAY DIFFRACTIONf_dihedral_angle_d12.2911556
X-RAY DIFFRACTIONf_chiral_restr0.026599
X-RAY DIFFRACTIONf_plane_restr0.003746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0022-2.05630.29391140.2211694X-RAY DIFFRACTION59
2.0563-2.11680.2515800.21531994X-RAY DIFFRACTION67
2.1168-2.18510.25211590.21172123X-RAY DIFFRACTION74
2.1851-2.26320.2455810.21772419X-RAY DIFFRACTION81
2.2632-2.35370.30361770.21732565X-RAY DIFFRACTION88
2.3537-2.46080.2397960.22412878X-RAY DIFFRACTION96
2.4608-2.59050.28141990.21712866X-RAY DIFFRACTION99
2.5905-2.75270.26151000.21443037X-RAY DIFFRACTION100
2.7527-2.96510.23942000.21352910X-RAY DIFFRACTION100
2.9651-3.26310.2671000.20183060X-RAY DIFFRACTION100
3.2631-3.73450.21342000.1872952X-RAY DIFFRACTION100
3.7345-4.70220.17441000.15533095X-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)
10.0057-0.00150.0075-0.00090.00070.00640.0559-0.0259-0.07680.0692-0.0027-0.06860.0530.01430.01240.1871-0.0021-0.44460.13640.13580.196160.0969-9.493548.4074
20.0371-0.0154-0.00780.0567-0.00670.01120.0773-0.0014-0.0450.15760.0096-0.20720.032-0.05970.07620.0898-0.0835-0.16860.1104-0.00310.229556.02718.946343.9372
30.0068-0.009-0.00040.01970.00410.01520.0941-0.06310.01790.0836-0.00870.0185-0.0287-0.0470.03840.2003-0.09570.08130.18670.0230.007345.309516.351346.8314
40.00510.0030.00460.02350.00480.00230.0388-0.0149-0.03340.0821-0.0002-0.03790.0566-0.06110.0060.1114-0.07060.00410.20110.01810.157244.31823.641541.98
50.0019-0.00210.00020.00910.00310.00330.0254-0.00980.01590.01480.0056-0.07080.0795-0.02540.00230.1183-0.0269-0.03140.1507-0.00460.252556.724-7.844335.0425
60.03020.0079-0.02760.0015-0.00540.01810.03580.06020.0415-0.09880.0128-0.0568-0.02440.01880.01250.2637-0.10280.37450.12040.05060.029159.711512.294110.5354
70.0184-0.0187-0.00770.01170.00430.0027-0.03530.0398-0.0239-0.0444-0.0119-0.12060.04810.0309-0.01930.08890.01730.26280.1113-0.07610.297963.4521-2.419717.1954
80.01120.01360.00980.01550.01250.0052-0.01850.0451-0.0537-0.16740.03620.01240.0431-0.0080.00750.242-0.0269-0.01470.1776-0.04030.12842.1836-10.866214.5894
90.00270.0007-0.00110.02420.00590.00880.0084-0.01360.0257-0.0761-0.0255-0.0469-0.0226-0.0070.00020.0952-0.0008-0.05270.1631-0.00610.153744.8431.362118.4125
100.00290.0023-0.00480.00720.00040.00920.02210.0167-0.01850.0007-0.006-0.0931-0.0622-0.0612-0.00310.1147-0.0250.03990.1406-0.01410.205255.946513.463424.7869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 9:58)
2X-RAY DIFFRACTION2(chain A and resid 59:138)
3X-RAY DIFFRACTION3(chain A and resid 139:203)
4X-RAY DIFFRACTION4(chain A and resid 204:231)
5X-RAY DIFFRACTION5(chain A and resid 232:263)
6X-RAY DIFFRACTION6(chain B and resid 9:70)
7X-RAY DIFFRACTION7(chain B and resid 71:115)
8X-RAY DIFFRACTION8(chain B and resid 116:204)
9X-RAY DIFFRACTION9(chain B and resid 205:232)
10X-RAY DIFFRACTION10(chain B and resid 233:263)

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