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- PDB-2wjx: Crystal structure of the human ionotropic glutamate receptor GluR... -

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Basic information

Entry
Database: PDB / ID: 2wjx
TitleCrystal structure of the human ionotropic glutamate receptor GluR2 ATD region at 4.1 A resolution
ComponentsGLUTAMATE RECEPTOR 2
KeywordsTRANSPORT PROTEIN / POSTSYNAPTIC CELL MEMBRANE / GLUR2 / SYNAPSE / MEMBRANE / RECEPTOR / PALMITATE / SYNAPTIC PLASTICITY / ALTERNATIVE SPLICING / ION TRANSPORT / CELL JUNCTION / CELL MEMBRANE / TRANSMEMBRANE / PHOSPHOPROTEIN / GLUTAMATE RECEPTORS / POLYMORPHISM / GLYCOPROTEIN / IONIC CHANNEL / TRANSPORT / ION CHANNEL / RNA EDITING / LIPOPROTEIN
Function / homology
Function and homology information


Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / postsynaptic endocytic zone / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / asymmetric synapse / excitatory synapse ...Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / postsynaptic endocytic zone / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / asymmetric synapse / excitatory synapse / glutamate-gated receptor activity / MECP2 regulates neuronal receptors and channels / ionotropic glutamate receptor signaling pathway / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / endocytic vesicle membrane / amyloid-beta binding / dendritic spine / chemical synaptic transmission / postsynapse / postsynaptic density / external side of plasma membrane / neuronal cell body / dendrite / signal transduction / 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 / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsClayton, A. / Siebold, C. / Gilbert, R.J.C. / Sutton, G.C. / Harlos, K. / McIlhinney, R.A.J. / Jones, E.Y. / Aricescu, A.R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal Structure of the Glur2 Amino-Terminal Domain Provides Insights Into the Architecture and Assembly of Ionotropic Glutamate Receptors.
Authors: Clayton, A. / Siebold, C. / Gilbert, R.J.C. / Sutton, G.C. / Harlos, K. / Mcilhinney, R.A.J. / Jones, E.Y. / Aricescu, A.R.
History
DepositionJun 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 2
C: GLUTAMATE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)131,3263
Polymers131,3263
Non-polymers00
Water00
1
A: GLUTAMATE RECEPTOR 2
B: GLUTAMATE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)87,5512
Polymers87,5512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-12.03 kcal/mol
Surface area31920 Å2
MethodPISA
2
C: GLUTAMATE RECEPTOR 2

C: GLUTAMATE RECEPTOR 2


Theoretical massNumber of molelcules
Total (without water)87,5512
Polymers87,5512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2420 Å2
ΔGint-11.87 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.253, 224.253, 76.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 25:130 OR RESSEQ 262:371 )
211CHAIN B AND (RESSEQ 25:130 OR RESSEQ 262:371 )
311CHAIN C AND (RESSEQ 25:130 OR RESSEQ 262:371 )
112CHAIN A AND (RESSEQ 131:261 OR RESSEQ 372:398 )
212CHAIN B AND (RESSEQ 131:261 OR RESSEQ 372:398 )
312CHAIN C AND (RESSEQ 131:261 OR RESSEQ 372:398 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.900245, -0.431759, -0.056061), (-0.435219, 0.89596, 0.088552), (0.011996, 0.104117, -0.994493)-53.5996, -12.5662, 8.6579
2given(-0.508279, -0.860711, -0.028789), (-0.860997, 0.507166, 0.038296), (-0.018361, 0.044253, -0.998852)-26.674, -14.9084, 22.2928

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Components

#1: Protein GLUTAMATE RECEPTOR 2 / IONOTROPIC GLUTAMATE RECEPTOR GLUR2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC\ / AMPA 2 / ...IONOTROPIC GLUTAMATE RECEPTOR GLUR2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC\ / AMPA 2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2 / GLUR-2


Mass: 43775.328 Da / Num. of mol.: 3 / Fragment: AMINO-TERMINAL DOMAIN, RESIDUES 25-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK 293S GNTI- CELLS / Production host: HOMO SAPIENS (human) / References: UniProt: P42262
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: 3.58 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growDetails: 0.2M BIS-TRIS PROPANE, PH 7.5 0.2M POTASSIUM/SODIUM TARTRATE 20% (W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 15949 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 28.5 % / Biso Wilson estimate: 149.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 23.3
Reflection shellResolution: 4.1→4.2 Å / Redundancy: 29.2 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→48.379 Å / SU ML: 0.46 / σ(F): 0.23 / Phase error: 34.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3539 773 5 %
Rwork0.2896 --
obs0.2928 15433 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1656 Å20 Å2-0 Å2
2--7.1656 Å20 Å2
3----14.3312 Å2
Refinement stepCycle: LAST / Resolution: 4.1→48.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8706 0 0 0 8706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118862
X-RAY DIFFRACTIONf_angle_d1.49211982
X-RAY DIFFRACTIONf_dihedral_angle_d15.8073177
X-RAY DIFFRACTIONf_chiral_restr0.0631323
X-RAY DIFFRACTIONf_plane_restr0.0121545
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1667X-RAY DIFFRACTIONPOSITIONAL
12B1667X-RAY DIFFRACTIONPOSITIONAL0.197
13C1667X-RAY DIFFRACTIONPOSITIONAL0.208
21A1227X-RAY DIFFRACTIONPOSITIONAL
22B1227X-RAY DIFFRACTIONPOSITIONAL0.28
23C1227X-RAY DIFFRACTIONPOSITIONAL0.188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1001-4.35680.38021380.31252260X-RAY DIFFRACTION93
4.3568-4.69290.36041420.27892341X-RAY DIFFRACTION95
4.6929-5.16470.35461110.26942422X-RAY DIFFRACTION97
5.1647-5.91090.36671250.28592464X-RAY DIFFRACTION98
5.9109-7.44280.37651210.27132503X-RAY DIFFRACTION98
7.4428-48.38190.31691360.28332670X-RAY DIFFRACTION100
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)
13.42542.10082.93924.9725-0.52153.8679-0.0666-0.13740.15010.1638-0.03430.0671-0.17720.47180.10590.4417-0.18470.05111.1997-0.18580.8682-3.75-86.774419.4427
27.3968-0.78314.52571.0588-0.36465.6816-0.41350.41920.1257-0.87610.0103-0.15520.5002-0.83080.41451.2226-0.13180.21680.972-0.05990.6838-12.4509-86.8882-20.0919
33.20912.53770.65272.0772-0.26272.43190.55020.2641-0.0522-0.6351-0.5965-0.2066-0.1925-0.22520.10071.5841-0.36520.30341.16240.26791.49450.2767-56.3054-0.5659
40.8922-0.9816-0.86191.79612.54423.8561-0.34040.09681.6041-0.15960.00860.17090.24920.39790.24551.5517-0.275-0.36071.0678-0.08222.13626.9421-41.75217.4788
50.50630.30351.33891.9952-1.57865.8617-0.38990.29991.03180.4057-0.67121.15820.217-0.08140.85740.98290.2834-0.30741.279-0.5941.87-4.1718-59.139411.9653
63.6067-1.0225-1.2341.11882.82215.6750.24140.1170.72890.23360.338-0.9661-0.12370.0335-0.40661.5351-0.1485-0.30830.86750.31471.2633-24.5736-62.3121-10.7223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 25:130 OR RESID 262:371)
2X-RAY DIFFRACTION2CHAIN B AND (RESID 25:130 OR RESID 262:371)
3X-RAY DIFFRACTION3CHAIN C AND (RESID 25:130 OR RESID 262:371)
4X-RAY DIFFRACTION4CHAIN C AND (RESID 131:261 OR RESID 372:398)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 131:261 OR RESID 372:398)
6X-RAY DIFFRACTION6CHAIN B AND (RESID 131:261 OR RESID 372:398)

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