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- PDB-4igt: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -

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Basic information

Entry
Database: PDB / ID: 4igt
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the agonist ZA302 at 1.24A resolution
ComponentsGlutamate receptor 2GRIA2
KeywordsMEMBRANE PROTEIN / AMPA receptor ligand-binding domain / GluR2-S1S2J / agonist
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor 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 / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / receptor internalization / terminal bouton / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / 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 / : / 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. ...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 / : / 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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3ZA / : / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsLarsen, A.P. / Venskutonyte, R. / Gajhede, M. / Kastrup, J.S. / Frydenvang, K.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Chemoenzymatic synthesis of new 2,4-syn-functionalized (S)-glutamate analogues and structure-activity relationship studies at ionotropic glutamate receptors and excitatory amino acid transporters.
Authors: Assaf, Z. / Larsen, A.P. / Venskutonyte, R. / Han, L. / Abrahamsen, B. / Nielsen, B. / Gajhede, M. / Kastrup, J.S. / Jensen, A.A. / Pickering, D.S. / Frydenvang, K. / Gefflaut, T. / Bunch, L.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,13310
Polymers29,2221
Non-polymers9129
Water6,125340
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,26720
Polymers58,4432
Non-polymers1,82318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4480 Å2
ΔGint-95 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.613, 95.641, 48.455
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor 2 / GRIA2 / 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: 29221.682 Da / Num. of mol.: 1
Fragment: Ligand-binding domain, UNP RESIDUES 413-527, 653-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: RAT / Gene: Glur2, Gria2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491

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Non-polymers , 5 types, 349 molecules

#2: Chemical ChemComp-3ZA / (4R)-4-{3-[hydroxy(methyl)amino]-3-oxopropyl}-L-glutamic acid


Mass: 248.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N2O6
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTRANSMEMBRANE REGIONS 528-652 WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (651-652)

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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: 47.96 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15.2% PEG 4000, 0.1M Li2SO4, 0.1M phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.24→50.64 Å / Num. obs: 78559 / % possible obs: 99 % / Redundancy: 6.1 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.24-1.315.30.3420.309258660111460.1450.3420.3096.797.7
1.31-1.395.30.2320.213.156771106350.0970.2320.218.798.1
1.39-1.485.40.1740.1584.254347100660.0730.1740.15811.398.8
1.48-1.65.40.1230.1125.95129294480.0510.1230.11214.899.2
1.6-1.755.50.0890.0818.14776387270.0370.0890.08117.999.2
1.75-1.965.50.0730.0669.14346779360.030.0730.06620.899.6
1.96-2.265.50.0780.07183885770760.0330.0780.07123.899.9
2.26-2.777.60.1010.0956.34596860260.0340.1010.09529.4100
2.77-3.9211.10.0620.05810.95287947490.0190.0620.05841.2100
3.92-50.6439.60.0520.04812.32639427500.0170.0520.04840.599.9

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHENIXrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5E

1m5e


Resolution: 1.24→47.821 Å / Occupancy max: 1 / Occupancy min: 0.15 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.37 / Stereochemistry target values: Engh & Huber
Details: REFINEMENT WITH ANISOTROPIC B-VALUES (EXCEPT SOLVENT AND HYDROGEN ATOMS). HYDROGEN ATOMS INCLUDED IN CALCULATED POSITION. HYDROGEN ATOMS ARE NOT INCLUDED IN PDB.
RfactorNum. reflection% reflectionSelection details
Rfree0.1551 3929 -RANDOM
Rwork0.1365 ---
obs0.1374 78315 98.87 %-
Displacement parametersBiso max: 57.79 Å2 / Biso mean: 13.3228 Å2 / Biso min: 4.12 Å2
Refinement stepCycle: LAST / Resolution: 1.24→47.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 57 340 2443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.29
X-RAY DIFFRACTIONf_chiral_restr0.079
X-RAY DIFFRACTIONf_plane_restr0.007
X-RAY DIFFRACTIONf_dihedral_angle_d12.373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.24-1.25510.20311450.149X-RAY DIFFRACTION252798
1.2551-1.2710.19861430.1434X-RAY DIFFRACTION260597
1.271-1.28770.15891380.1361X-RAY DIFFRACTION259698
1.2877-1.30540.13311330.1249X-RAY DIFFRACTION260697
1.3054-1.3240.13911350.1166X-RAY DIFFRACTION262099
1.324-1.34380.15511360.1127X-RAY DIFFRACTION256097
1.3438-1.36480.15261580.1154X-RAY DIFFRACTION259299
1.3648-1.38720.15771280.1142X-RAY DIFFRACTION262297
1.3872-1.41110.1511290.1171X-RAY DIFFRACTION263299
1.4111-1.43670.14421440.1108X-RAY DIFFRACTION258998
1.4367-1.46440.14421440.1099X-RAY DIFFRACTION262098
1.4644-1.49430.13451380.1067X-RAY DIFFRACTION266199
1.4943-1.52680.14681610.1007X-RAY DIFFRACTION258798
1.5268-1.56230.12471380.1065X-RAY DIFFRACTION264699
1.5623-1.60140.14731390.1049X-RAY DIFFRACTION2675100
1.6014-1.64470.14091470.1074X-RAY DIFFRACTION259899
1.6447-1.69310.12381430.1091X-RAY DIFFRACTION264999
1.6931-1.74770.16321370.112X-RAY DIFFRACTION269299
1.7477-1.81020.14331420.117X-RAY DIFFRACTION266899
1.8102-1.88270.12711130.124X-RAY DIFFRACTION2697100
1.8827-1.96830.1221490.1231X-RAY DIFFRACTION2667100
1.9683-2.07210.12961570.1222X-RAY DIFFRACTION2673100
2.0721-2.20190.1481240.1261X-RAY DIFFRACTION2733100
2.2019-2.37190.13791490.1321X-RAY DIFFRACTION2672100
2.3719-2.61060.16321530.1478X-RAY DIFFRACTION2739100
2.6106-2.98830.18441430.1675X-RAY DIFFRACTION2751100
2.9883-3.76480.17211430.1588X-RAY DIFFRACTION2770100
3.7648-47.85610.19441200.1792X-RAY DIFFRACTION2939100

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