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

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Basic information

Entry
Database: PDB / ID: 3epe
TitleCrystal Structure of the GluR4 Ligand-Binding domain in complex with glutamate
ComponentsGlutamate receptor 4,Glutamate receptor
KeywordsMEMBRANE PROTEIN / GluR4 / AMPA receptor / ligand-gated ion channel / ligand-binding domain / Kainate / Alternative splicing / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Lipoprotein
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: 1.85 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 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Glutamate receptor 4,Glutamate receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7694
Polymers57,4742
Non-polymers2942
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-8 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.374, 105.124, 66.336
Angle α, β, γ (deg.)90.00, 97.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRMETMETAA1 - 1031 - 103
21THRTHRMETMETBB1 - 1031 - 103
12SERSERLYSLYSAA104 - 214104 - 214
22SERSERLYSLYSBB104 - 214104 - 214
13GLYGLYCYSCYSAA215 - 257215 - 257
23GLYGLYCYSCYSBB215 - 257215 - 257

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Glutamate receptor 4,Glutamate receptor


Mass: 28737.195 Da / Num. of mol.: 2
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-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.: 310 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 4000, 0.1M Na-Acetate pH 4.6, 0.2M Ammonium Sulphate, 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 / Date: May 25, 2005
RadiationMonochromator: Focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→19.27 Å / Num. all: 54964 / Num. obs: 52938 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.85→1.93 Å / % possible all: 94.1

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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: 1FTJ

1ftj


Resolution: 1.85→19.27 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22038 2790 5.3 %THIN SHELLS
Rwork0.19061 ---
obs0.19222 50144 100 %-
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 mean: 15.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4028 0 20 310 4358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224118
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.9755548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7015512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4824.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46715772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7331520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023004
X-RAY DIFFRACTIONr_nbd_refined0.1990.21878
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22915
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.227
X-RAY DIFFRACTIONr_mcbond_it0.4141.52556
X-RAY DIFFRACTIONr_mcangle_it0.75724123
X-RAY DIFFRACTIONr_scbond_it1.50831562
X-RAY DIFFRACTIONr_scangle_it2.4754.51425
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1806medium positional0.260.5
2871medium positional0.380.5
3331medium positional0.10.5
1806medium thermal0.422
2871medium thermal0.452
3331medium thermal0.332
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.187 3807 -
Rfree-0 -
obs--100 %

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