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- PDB-3en3: Crystal Structure of the GluR4 Ligand-Binding domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 3en3
TitleCrystal Structure of the GluR4 Ligand-Binding domain in complex with kainate
ComponentsGlutamate receptor 4,Glutamate receptor
KeywordsMEMBRANE PROTEIN / GluR4 / AMPA receptor / ligand-gated ion channel / ligand-binding domain / Kainate / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Lipoprotein
Function / homology
Function and homology information


chemical synaptic transmission, postsynaptic / kainate selective glutamate receptor complex / Trafficking of AMPA receptors / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex ...chemical synaptic transmission, postsynaptic / kainate selective glutamate receptor complex / Trafficking of AMPA receptors / regulation of synapse structure or activity / Synaptic adhesion-like molecules / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / negative regulation of smooth muscle cell apoptotic process / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / glutamate-gated receptor activity / response to fungicide / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / 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 / terminal bouton / monoatomic ion transmembrane transport / chemical synaptic transmission / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / dendrite / synapse / identical protein binding / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / 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 ...Ionotropic glutamate receptor, metazoa / 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.43 Å
AuthorsGill, A. / Madden, D.R.
CitationJournal: Biochemistry / Year: 2008
Title: Correlating AMPA receptor activation and cleft closure across subunits: crystal structures of the GluR4 ligand-binding domain in complex with full and partial agonists
Authors: Gill, A. / Birdsey-Benson, A. / Jones, B.L. / Henderson, L.P. / Madden, D.R.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Jul 26, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,9502
Polymers28,7371
Non-polymers2131
Water1,74797
1
A: Glutamate receptor 4,Glutamate receptor
hetero molecules

A: Glutamate receptor 4,Glutamate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9014
Polymers57,4742
Non-polymers4262
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.906, 48.749, 47.766
Angle α, β, γ (deg.)90.000, 109.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 28737.195 Da / Num. of mol.: 1
Fragment: ligand binding domain (UNP residues 416-528 and 654-958)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: Sprague-Dawley / Gene: Glur4,Glutamate receptor / Plasmid: pET16-b / Production host: Escherichia coli (E. coli) / Strain (production host): XJb(DE3) / References: UniProt: P19493
#2: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


Mass: 213.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25.5% PEG 1500, 0.05M Na-Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 1, 2006
RadiationMonochromator: Focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.43→11.95 Å / Num. all: 10516 / Num. obs: 10025 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.43→2.49 Å / % possible all: 94.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementResolution: 2.43→11.95 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0 / SU B: 15.988 / SU ML: 0.187 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.557 / ESU R Free: 0.256 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 502 5 %RANDOM
Rwork0.156 ---
all0.159 10516 --
obs0.159 10025 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 94.65 Å2 / Biso mean: 43.628 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.08 Å2
2---0.21 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.43→11.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 15 97 2126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222058
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9792774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1495256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02324.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08815380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5471510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021498
X-RAY DIFFRACTIONr_nbd_refined0.1960.2834
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0440.25
X-RAY DIFFRACTIONr_mcbond_it0.3961.51313
X-RAY DIFFRACTIONr_mcangle_it0.69722059
X-RAY DIFFRACTIONr_scbond_it1.0543860
X-RAY DIFFRACTIONr_scangle_it1.7964.5715
LS refinement shellResolution: 2.43→2.491 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 35 -
Rwork0.199 652 -
all-687 -
obs--100 %
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)
14.9532-0.77970.5454.13630.26943.8863-0.1351-0.51-0.06850.51870.1806-0.42110.05240.0678-0.0456-0.20350.044-0.0177-0.21550.0058-0.290910.7615.78510.901
26.21272.86590.40597.05912.07395.6564-0.31660.36550.0487-0.44290.4737-0.6613-0.38420.3855-0.157-0.1948-0.03690.0162-0.1547-0.04-0.151618.12233.582-3.72
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION1A215 - 257
3X-RAY DIFFRACTION2A104 - 214

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