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- PDB-4l17: GluA2-L483Y-A665C ligand-binding domain in complex with the antag... -

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Basic information

Entry
Database: PDB / ID: 4l17
TitleGluA2-L483Y-A665C ligand-binding domain in complex with the antagonist DNQX
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / ion channel / neuroreceptor / membrane
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / ionotropic glutamate receptor binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / 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 / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase 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 ...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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6,7-DINITROQUINOXALINE-2,3-DIONE / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLau, A.Y. / Blachowicz, L. / Roux, B.
CitationJournal: Neuron / Year: 2013
Title: A conformational intermediate in glutamate receptor activation.
Authors: Lau, A.Y. / Salazar, H. / Blachowicz, L. / Ghisi, V. / Plested, A.J. / Roux, B.
History
DepositionJun 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2
C: Glutamate receptor 2
E: Glutamate receptor 2
G: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,50411
Polymers117,2154
Non-polymers1,2897
Water2,468137
1
A: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3006
Polymers58,6082
Non-polymers6924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-21 kcal/mol
Surface area23800 Å2
MethodPISA
2
E: Glutamate receptor 2
hetero molecules

E: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3006
Polymers58,6082
Non-polymers6924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area3220 Å2
ΔGint-17 kcal/mol
Surface area23860 Å2
MethodPISA
3
G: Glutamate receptor 2
hetero molecules

G: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1084
Polymers58,6082
Non-polymers5002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area2870 Å2
ΔGint-5 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.850, 96.790, 252.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 151:155 OR RESSEQ 206 OR RESSEQ 261 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
211CHAIN G AND (RESSEQ 151:155 OR RESSEQ 206 OR RESSEQ 261 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
112CHAIN C AND (RESSEQ 151:155 OR RESSEQ 206 OR RESSEQ 261 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
212CHAIN E AND (RESSEQ 151:155 OR RESSEQ 206 OR RESSEQ 261 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)

NCS ensembles :
ID
1
2

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Components

#1: Protein
Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 29303.768 Da / Num. of mol.: 4
Fragment: Ligand binding domain (UNP residues 413-527, 653-796)
Mutation: L94Y, A153C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE3) / References: UniProt: P19491
#2: Chemical
ChemComp-DNQ / 6,7-DINITROQUINOXALINE-2,3-DIONE / DNQX


Mass: 250.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H2N4O6 / Comment: antagonist*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 19% PEG 1450, 0.3M lithium sulfate, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2009
RadiationMonochromator: Double crystal cryo-cooled, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→52.924 Å / Num. all: 30537 / Num. obs: 29223 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5
Reflection shellResolution: 2.8→2.95 Å / % possible all: 92.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→52.92 Å / SU ML: 0.36 / σ(F): 0.04 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1469 5.08 %RANDOM
Rwork0.1949 ---
obs0.1975 28924 94.58 %-
all-29172 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.561 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.8099 Å2-0 Å2-0 Å2
2---5.3218 Å20 Å2
3----4.488 Å2
Refinement stepCycle: LAST / Resolution: 2.8→52.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7904 0 87 137 8128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0018146
X-RAY DIFFRACTIONf_angle_d0.42910996
X-RAY DIFFRACTIONf_dihedral_angle_d10.4512974
X-RAY DIFFRACTIONf_chiral_restr0.0291218
X-RAY DIFFRACTIONf_plane_restr0.0031372
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A46X-RAY DIFFRACTIONPOSITIONAL
12G46X-RAY DIFFRACTIONPOSITIONAL0.147
21C49X-RAY DIFFRACTIONPOSITIONAL
22E49X-RAY DIFFRACTIONPOSITIONAL0.163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.34351330.24982536X-RAY DIFFRACTION89
2.9001-3.01620.30781220.23812577X-RAY DIFFRACTION90
3.0162-3.15340.29361500.21712564X-RAY DIFFRACTION91
3.1534-3.31970.26581460.19862641X-RAY DIFFRACTION92
3.3197-3.52760.23031350.18462649X-RAY DIFFRACTION92
3.5276-3.79990.23581400.18712716X-RAY DIFFRACTION95
3.7999-4.18220.21471620.17172849X-RAY DIFFRACTION99
4.1822-4.7870.20291810.15242858X-RAY DIFFRACTION99
4.787-6.02970.22581660.17642963X-RAY DIFFRACTION100
6.0297-52.93320.23791340.20653102X-RAY DIFFRACTION99
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)
11.49690.47150.25221.92960.46130.2928-0.13530.34280.0022-0.41880.1409-0.0016-0.15950.00870.02990.0684-0.0025-0.05650.02590.02310.0533-2.776351.222445.5576
20.72730.3685-0.08031.44090.38570.3271-0.10660.08990.0432-0.3270.205-0.204-0.1150.07570.18010.1187-0.02550.06120.0349-0.03470.064913.88831.102949.3483
31.08810.699-0.24472.4462-0.87210.311-0.1331-0.1282-0.0367-0.55660.17730.18130.1054-0.0346-0.08790.1568-0.0629-0.07140.05390.01340.0636-7.41144.983355.0945
40.81840.5455-0.03111.39230.05690.35720.211-0.1613-0.00790.4636-0.0706-0.26190.0458-0.03380.09150.15780.0012-0.09830.0646-0.04330.09963.881552.999979.2172
50.5861-0.54450.05472.4587-0.82870.8017-0.0663-0.2153-0.00690.47010.38530.007-0.1568-0.09620.01720.18080.0155-0.04320.02430.1195-0.0274-9.029830.275376.9205
60.5727-0.3580.48331.157-0.93171.14010.11380.0495-0.17460.1345-0.02-0.06750.03780.2322-0.06450.02370.0298-0.06010.0511-0.01370.1339.805246.920470.2595
70.2828-0.3125-0.08360.35110.23061.4553-0.074-0.11-0.16380.2044-0.0908-0.02430.2327-0.0766-0.02350.0955-0.0661-0.05980.3060.16860.062512.291144.001516.5679
81.68670.5785-0.540.6944-0.25370.18150.1372-0.41460.36450.42210.14710.2499-0.4680.4067-0.12740.2932-0.05550.0760.55660.08060.0368-9.049960.247815.1855
90.3829-0.3802-0.34481.190.31841.03980.10520.0508-0.0012-0.2265-0.1303-0.11640.0633-0.4381-0.02590.0525-0.0941-0.01350.43640.11340.04944.437441.64316.9137
101.6837-0.18671.18410.187-0.0451.54990.6693-0.30470.19010.15950.0831-0.01240.8174-0.9031-0.52311.0297-0.2462-0.2210.25980.52890.04648.0557-2.820316.5982
111.8418-0.21280.20540.4866-0.06320.08250.5544-1.05930.2701-0.0698-0.467-0.0970.78380.4848-0.08430.8954-0.05960.27790.9178-0.03710.1564-12.918112.765914.1875
120.65630.1188-0.66560.85220.08032.09360.4627-0.0094-0.05140.3490.1071-0.19730.5827-1.372-0.47390.894-0.3205-0.21520.87010.35630.23131.9161-7.92917.4033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:109)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 110:217)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 218:261)
4X-RAY DIFFRACTION4(CHAIN C AND RESID 4:109)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 110:217)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 218:261)
7X-RAY DIFFRACTION7(CHAIN E AND RESID 3:111)
8X-RAY DIFFRACTION8(CHAIN E AND RESID 112:209)
9X-RAY DIFFRACTION9(CHAIN E AND RESID 210:261)
10X-RAY DIFFRACTION10(CHAIN G AND RESID 4:111)
11X-RAY DIFFRACTION11(CHAIN G AND RESID 112:216)
12X-RAY DIFFRACTION12(CHAIN G AND RESID 217:261)

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