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- PDB-3kei: Crystal Structure of the GluA4 Ligand-Binding domain L651V mutant... -

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Basic information

Entry
Database: PDB / ID: 3kei
TitleCrystal Structure of the GluA4 Ligand-Binding domain L651V mutant in complex with glutamate
ComponentsGlutamate receptor 4
KeywordsTRANSPORT PROTEIN / GluA4 / AMPA receptor / ligand-gated ion channel / ligand-binding domain / L651V / Alternative splicing / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...Trafficking of AMPA receptors / kainate selective glutamate receptor complex / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / chemical synaptic transmission / dendritic spine / postsynaptic density / neuronal cell body / synapse / glutamatergic synapse / dendrite / identical protein binding / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGill, A. / Madden, D.R.
CitationJournal: J.Neurosci. / Year: 2010
Title: Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors.
Authors: Birdsey-Benson, A. / Gill, A. / Henderson, L.P. / Madden, D.R.
History
DepositionOct 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 4
B: Glutamate receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7414
Polymers57,4462
Non-polymers2942
Water4,864270
1
A: Glutamate receptor 4
hetero molecules

B: Glutamate receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7414
Polymers57,4462
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area1700 Å2
ΔGint-9 kcal/mol
Surface area23090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 105.100, 66.300
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glutamate receptor 4 / / GluR-4 / GluR4 / GluR-D / Glutamate receptor ionotropic / AMPA 4 / AMPA-selective glutamate receptor 4


Mass: 28723.168 Da / Num. of mol.: 2 / Fragment: ligand binding domain / Mutation: L134V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley / Gene: Glur4, Gria4 / Plasmid: pET16-b / Production host: Escherichia coli (E. coli) / Strain (production host): XJb(DE3) / References: UniProt: P19493
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE MATCHES TO ISOFORM 2 OF UNIPROT ENTRY P19493 (IDENTIFIER: P19493-2).

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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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 24% PEG 4000, 0.1M Na-Acetate, 0.3M Ammonium Sulphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Focusing Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→37 Å / Num. all: 50508 / Num. obs: 45551 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.9→1.99 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3EPE

3epe


Resolution: 1.9→19.69 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2339 5.1 %THIN SHELLS
Rwork0.205 ---
all0.206 ---
obs-43168 --
Displacement parametersBiso mean: 10.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4026 0 20 270 4316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.32
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.758
X-RAY DIFFRACTIONr_chiral_restr0.076
LS refinement shellResolution: 1.9→1.99 Å

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