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

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Basic information

Entry
Database: PDB / ID: 2wjw
TitleCrystal structure of the human ionotropic glutamate receptor GluR2 ATD region at 1.8 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 / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse / glutamate-gated receptor activity ...Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / excitatory synapse / asymmetric synapse / glutamate-gated receptor activity / MECP2 regulates neuronal receptors and channels / ionotropic glutamate receptor signaling pathway / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / endocytic vesicle membrane / amyloid-beta binding / postsynapse / chemical synaptic transmission / dendritic spine / postsynaptic density / external side of plasma membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / signal transduction / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Response regulator / 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 ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Glutamate receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1875
Polymers43,7751
Non-polymers4124
Water5,026279
1
A: GLUTAMATE RECEPTOR 2
hetero molecules

A: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,37410
Polymers87,5512
Non-polymers8248
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area4320 Å2
ΔGint-50.03 kcal/mol
Surface area31880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.977, 122.455, 138.852
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-186-

ASP

21A-2053-

HOH

31A-2122-

HOH

41A-2132-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 43775.328 Da / Num. of mol.: 1 / 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
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 282 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 0.08M SODIUM ACETATE, PH 4.6 0.16M AMMONIUM SULPHATE 20 (W/V) PEG4000 20% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 40760 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 19.47 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→39.161 Å / SU ML: 0.23 / σ(F): 0.2 / Phase error: 21.35 / Stereochemistry target values: ML
Details: RESIDUES 322-327 AND 399-412 ARE DISORDERED. RESIDUES 153-159 ARE MODELED IN DOUBLE CONFORMATION.
RfactorNum. reflection% reflection
Rfree0.217 1566 4 %
Rwork0.1814 --
obs0.1829 38999 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.454 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.4107 Å20 Å2-0 Å2
2--0.3614 Å20 Å2
3----7.7721 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 24 279 3243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053078
X-RAY DIFFRACTIONf_angle_d0.8624157
X-RAY DIFFRACTIONf_dihedral_angle_d15.2641109
X-RAY DIFFRACTIONf_chiral_restr0.059458
X-RAY DIFFRACTIONf_plane_restr0.003535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.27731180.22232981X-RAY DIFFRACTION85
1.8581-1.92450.24651230.19623160X-RAY DIFFRACTION89
1.9245-2.00160.21591200.17843290X-RAY DIFFRACTION93
2.0016-2.09270.20411300.16893326X-RAY DIFFRACTION95
2.0927-2.2030.20981580.16723404X-RAY DIFFRACTION97
2.203-2.3410.20441510.16673448X-RAY DIFFRACTION98
2.341-2.52170.19711530.17553442X-RAY DIFFRACTION98
2.5217-2.77550.2391520.1893502X-RAY DIFFRACTION99
2.7755-3.17690.2091420.18433557X-RAY DIFFRACTION99
3.1769-4.00190.17891460.16863604X-RAY DIFFRACTION100
4.0019-39.17050.22761730.18573719X-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)
10.6655-0.06910.01290.63990.23081.8273-0.03920.02060.0504-0.04750.00330.0369-0.3038-0.10650.04080.11240.0188-0.01330.0870.01070.1082-28.7559-19.8748-20.045
20.2604-0.1311-0.09873.2729-1.50922.55570.0042-0.0228-0.00650.2-0.1437-0.4054-0.07610.34610.1270.112-0.0076-0.01290.12550.0140.1742-19.7093-46.8201-13.7358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 25:130 OR RESID 262:371)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 131:261 OR RESID 372:398)

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