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- PDB-3o21: High resolution structure of GluA3 N-terminal domain (NTD) -

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Basic information

Entry
Database: PDB / ID: 3o21
TitleHigh resolution structure of GluA3 N-terminal domain (NTD)
ComponentsGlutamate receptor 3
KeywordsTRANSPORT PROTEIN / Periplasmatic binding protein / Oligomerization / Membrane
Function / homology
Function and homology information


chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / monoatomic ion transmembrane transport / dendritic shaft / 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 / presynaptic membrane / amyloid-beta binding / perikaryon / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / dendrite / neuronal cell body / glutamatergic synapse / protein-containing complex / membrane / 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 / : / Response regulator / 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 ...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 / : / Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Glutamate receptor 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsRossmann, M. / Sukumaran, M. / Penn, A.C. / Veprintsev, D.B. / Babu, M.M. / Jensen, M.H. / Greger, I.H.
CitationJournal: Embo J. / Year: 2011
Title: Dynamics and allosteric potential of the AMPA receptor N-terminal domain
Authors: Sukumaran, M. / Rossmann, M. / Shrivastava, I. / Dutta, A. / Bahar, I. / Greger, I.H.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 3
B: Glutamate receptor 3
C: Glutamate receptor 3
D: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,04015
Polymers179,8594
Non-polymers2,18111
Water10,413578
1
A: Glutamate receptor 3
B: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7837
Polymers89,9302
Non-polymers8545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-17 kcal/mol
Surface area31530 Å2
MethodPISA
2
C: Glutamate receptor 3
D: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2578
Polymers89,9302
Non-polymers1,3276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.755, 130.910, 131.085
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 3 / / GluR-3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / AMPA 3 / GluA3 / AMPA-selective ...GluR-3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / AMPA 3 / GluA3 / AMPA-selective glutamate receptor 3


Mass: 44964.773 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria3, Glur3 / Plasmid: pHLsec / Cell (production host): HEK 293 Cell / Production host: Homo sapiens (human) / References: UniProt: P19492
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.36 Å3/Da / Density % sol: 47.78 % / Mosaicity: 0.706 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 18% PEG 3350, 230mM sodium dihydrogen phosphate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 86715 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.085 / Χ2: 0.929 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.2840.36785800.99499.8
2.28-2.374.10.4785410.919100
2.37-2.484.10.28685970.913100
2.48-2.614.20.21885880.899100
2.61-2.774.20.16385840.906100
2.77-2.994.20.11786510.932100
2.99-3.294.10.08286650.923100
3.29-3.764.10.06486920.996100
3.76-4.744.10.06987520.984100
4.74-503.90.03590650.82799.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→41.403 Å / Occupancy max: 1 / Occupancy min: 0.94 / FOM work R set: 0.7994 / SU ML: 0.33 / σ(F): 0.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2583 3444 3.99 %Random
Rwork0.2071 ---
obs0.2092 86270 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.101 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 84.53 Å2 / Biso mean: 34.5782 Å2 / Biso min: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.1469 Å2-0 Å2-0 Å2
2---1.5546 Å2-0 Å2
3----0.5923 Å2
Refinement stepCycle: LAST / Resolution: 2.201→41.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12079 0 136 578 12793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812496
X-RAY DIFFRACTIONf_angle_d1.09816913
X-RAY DIFFRACTIONf_chiral_restr0.0751843
X-RAY DIFFRACTIONf_plane_restr0.0042183
X-RAY DIFFRACTIONf_dihedral_angle_d15.1394550
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2008-2.2310.35181220.2923239336198
2.231-2.26280.34191440.25893271341599
2.2628-2.29660.35681390.29773268340799
2.2966-2.33250.30851280.24793250337899
2.3325-2.37070.28241410.224732673408100
2.3707-2.41160.31191440.216233093453100
2.4116-2.45550.28811120.20532703382100
2.4555-2.50270.26781400.197132703410100
2.5027-2.55380.29951320.209433183450100
2.5538-2.60930.29521170.224333183435100
2.6093-2.670.27651200.220132903410100
2.67-2.73670.32841210.20433373458100
2.7367-2.81070.28061690.208232273396100
2.8107-2.89340.28121420.210533313473100
2.8934-2.98680.27811260.223133023428100
2.9868-3.09350.25331440.217533163460100
3.0935-3.21730.29031590.210132723431100
3.2173-3.36360.25661290.196733233452100
3.3636-3.54090.24281350.195433363471100
3.5409-3.76260.22611430.17943317346099
3.7626-4.05290.21671330.167933303463100
4.0529-4.46030.18781580.150133513509100
4.4603-5.10470.19641300.145433723502100
5.1047-6.42750.22131490.187634203569100
6.4275-41.41020.20561670.19313522368999

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