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- PDB-5l1g: AMPA subtype ionotropic glutamate receptor GluA2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5l1g
TitleAMPA subtype ionotropic glutamate receptor GluA2 in complex with GYKI-Br
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN/INHIBITOR / Transporter / MEMBRANE PROTEIN / TRANSPORT PROTEIN / TRANSPORT PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / 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
Chem-GYB / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.507 Å
AuthorsYelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Sobolevsky, A.I.
CitationJournal: Neuron / Year: 2016
Title: Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs.
Authors: Yelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Narangoda, C. / Kurnikova, M. / Sobolevsky, A.I.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Non-polymer description
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / 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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,26413
Polymers359,2234
Non-polymers3,0419
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27370 Å2
ΔGint-210 kcal/mol
Surface area139140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.790, 110.400, 600.140
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 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-2 / AMPA-selective glutamate receptor ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 89805.734 Da / Num. of mol.: 4
Fragment: UNP residues 25-847, with deletions of 397-398, 402-405, 566-587
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pEG BacMam / Cell line (production host): HEK29 GnTI3 / Production host: Homo sapiens (human) / References: UniProt: P19491
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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-GYB / (8R)-5-(4-amino-3-bromophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide


Mass: 431.283 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C19H19BrN4O3
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: 4.36 Å3/Da / Density % sol: 71.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 4.5→48.912 Å / Num. obs: 69606 / % possible obs: 99 % / Redundancy: 8.45 % / Net I/σ(I): 9.17

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KG2

3kg2


Resolution: 4.507→48.912 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 3490 5.01 %
Rwork0.2568 --
obs0.2586 69606 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.507→48.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23896 0 191 0 24087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324573
X-RAY DIFFRACTIONf_angle_d0.57633292
X-RAY DIFFRACTIONf_dihedral_angle_d10.61114457
X-RAY DIFFRACTIONf_chiral_restr0.043749
X-RAY DIFFRACTIONf_plane_restr0.0044210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5074-4.56910.34131140.32752152X-RAY DIFFRACTION82
4.5691-4.63430.30161450.31682753X-RAY DIFFRACTION100
4.6343-4.70350.3321410.30972633X-RAY DIFFRACTION100
4.7035-4.77690.32181370.2862671X-RAY DIFFRACTION100
4.7769-4.85510.25321410.29362648X-RAY DIFFRACTION100
4.8551-4.93880.35441450.2912665X-RAY DIFFRACTION100
4.9388-5.02850.2761400.29042651X-RAY DIFFRACTION100
5.0285-5.12510.25561430.29632700X-RAY DIFFRACTION100
5.1251-5.22960.30181380.27792655X-RAY DIFFRACTION100
5.2296-5.34320.35191390.28532639X-RAY DIFFRACTION100
5.3432-5.46730.33591420.28162714X-RAY DIFFRACTION100
5.4673-5.60390.32591380.26932613X-RAY DIFFRACTION100
5.6039-5.75520.32471440.28552713X-RAY DIFFRACTION100
5.7552-5.92420.29771390.28292628X-RAY DIFFRACTION100
5.9242-6.11510.31811460.27162715X-RAY DIFFRACTION100
6.1151-6.33320.30511390.27812643X-RAY DIFFRACTION100
6.3332-6.58620.36051340.28182689X-RAY DIFFRACTION100
6.5862-6.88520.30551410.27782657X-RAY DIFFRACTION100
6.8852-7.24710.31851430.26962677X-RAY DIFFRACTION100
7.2471-7.69950.27891410.24912664X-RAY DIFFRACTION100
7.6995-8.29140.25661440.22932651X-RAY DIFFRACTION100
8.2914-9.12090.22131430.20062656X-RAY DIFFRACTION100
9.1209-10.42960.31431330.18752654X-RAY DIFFRACTION99
10.4296-13.09830.20971380.19192643X-RAY DIFFRACTION99
13.0983-48.91440.34121420.30862632X-RAY DIFFRACTION99

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