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- PDB-3fat: X-ray structure of iGluR4 flip ligand-binding core (S1S2) in comp... -

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Basic information

Entry
Database: PDB / ID: 3fat
TitleX-ray structure of iGluR4 flip ligand-binding core (S1S2) in complex with (S)-AMPA at 1.90A resolution
ComponentsGlutamate receptor 4
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptors / iGluR4 / flip / ligand-binding core / agonist complex
Function / homology
Function and homology information


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 / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...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 / 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 / glutamate-gated receptor activity / presynaptic active zone membrane / 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 / dendrite / synapse / glutamatergic synapse / 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
ACETIC ACID / Chem-AMQ / Glutamate receptor 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsKasper, C. / Frydenvang, K. / Naur, P. / Gajhede, M. / Kastrup, J.S.
CitationJournal: Febs Lett. / Year: 2008
Title: Molecular mechanism of agonist recognition by the ligand-binding core of the ionotropic glutamate receptor 4
Authors: Kasper, C. / Frydenvang, K. / Naur, P. / Gajhede, M. / Pickering, D.S. / Kastrup, J.S.
History
DepositionNov 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...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 / 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
B: Glutamate receptor 4
C: Glutamate receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,48228
Polymers87,0623
Non-polymers2,42025
Water11,349630
1
A: Glutamate receptor 4
B: Glutamate receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,59418
Polymers58,0412
Non-polymers1,55316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-71 kcal/mol
Surface area23610 Å2
MethodPISA
2
C: Glutamate receptor 4
hetero molecules

C: Glutamate receptor 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,77520
Polymers58,0412
Non-polymers1,73418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5000 Å2
ΔGint-22 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.175, 169.531, 73.883
Angle α, β, γ (deg.)90.000, 120.580, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1060-

HOH

DetailsThis entry contains the crystallographic asymmetric unit which consists of three chains. Chain A and B forms a dimer, whereas chain C forms a dimer with a symmetry related chain C (-x+1,y,-z+1). A complete tetrameric multimer representing the known biologically significant oligomerization state of the molecule cannot be generated by symmetry within the crystal.

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 29020.543 Da / Num. of mol.: 3 / Fragment: iGluR4 flip ligand-binding core (S1S2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET-32a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P19493

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Non-polymers , 5 types, 655 molecules

#2: Chemical ChemComp-AMQ / (S)-ALPHA-AMINO-3-HYDROXY-5-METHYL-4-ISOXAZOLEPROPIONIC ACID / AMPA / AMPA


Mass: 186.165 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H10N2O4 / Comment: neurotransmitter, agonist*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS SEQUENCE IS ISOFORM 2, P19493-2. THE CONFLICT IN 198TH RESIDUE IS FROM REFERENCE 2 IN P19493 DATABASE.

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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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, Acetate, (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0412 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0412 Å / Relative weight: 1
ReflectionResolution: 1.9→84.819 Å / Num. obs: 87196 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.7 / Num. measured all: 46960 / Num. unique all: 12725 / Rsym value: 0.376 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å32.64 Å
Translation1.9 Å32.64 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FAS

3fas


Resolution: 1.9→32.644 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.869 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: Engh & Huber
Details: Chain A: residue 260 was not observed in the electron density map Chain B: residues 256 and 260 were not observed in eletron density map
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4371 5.01 %random
Rwork0.175 ---
all0.177 87195 --
obs0.177 87195 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.02 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 169.06 Å2 / Biso mean: 28.329 Å2 / Biso min: 0.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.396 Å2-0 Å2-1.452 Å2
2---3.486 Å2-0 Å2
3---6.882 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 152 630 6865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056440
X-RAY DIFFRACTIONf_angle_d0.8848664
X-RAY DIFFRACTIONf_chiral_restr0.063952
X-RAY DIFFRACTIONf_plane_restr0.0041080
X-RAY DIFFRACTIONf_dihedral_angle_d14.7272378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9220.2821310.23927752906100
1.922-1.9440.2551440.22127962940100
1.944-1.9680.2341590.20326912850100
1.968-1.9930.2271530.19327922945100
1.993-2.0190.2661350.1927582893100
2.019-2.0470.2411250.18927582883100
2.047-2.0760.2381500.18527782928100
2.076-2.1070.2391490.19227482897100
2.107-2.140.2271560.18227402896100
2.14-2.1750.211370.18127912928100
2.175-2.2120.2331500.18227152865100
2.212-2.2530.2291330.18827752908100
2.253-2.2960.231640.18727542918100
2.296-2.3430.2251570.16927542911100
2.343-2.3940.2391500.16927482898100
2.394-2.4490.21490.17227712920100
2.449-2.5110.2441480.17227442892100
2.511-2.5780.2241380.18127742912100
2.578-2.6540.231400.17227632903100
2.654-2.740.1971570.16427752932100
2.74-2.8380.2011670.17227372904100
2.838-2.9510.231550.17927292884100
2.951-3.0860.2451420.18428012943100
3.086-3.2480.2271280.17627692897100
3.248-3.4510.2151440.16627802924100
3.451-3.7170.1971490.15927592908100
3.717-4.0910.1841350.14427902925100
4.091-4.6810.1541420.12727662908100
4.681-5.8920.1691390.14427952934100
5.892-32.6490.1881450.172698284396

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