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- PDB-5h8s: Structure of the human GluA2 LBD in complex with GNE3419 -

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Basic information

Entry
Database: PDB / ID: 5h8s
TitleStructure of the human GluA2 LBD in complex with GNE3419
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsTRANSPORT PROTEIN / GluN1 / GluN2A / NMDA / receptor
Function / homology
Function and homology information


Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor complex / Long-term potentiation / asymmetric synapse / excitatory synapse ...Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel 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 / 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 / chemical synaptic transmission / postsynapse / dendritic spine / 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 ...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
Chem-5YC / CACODYLATE ION / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsWallweber, H.J.A. / Lupardus, P.J.
CitationJournal: Neuron / Year: 2016
Title: Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit Function.
Authors: Hackos, D.H. / Lupardus, P.J. / Grand, T. / Chen, Y. / Wang, T.M. / Reynen, P. / Gustafson, A. / Wallweber, H.J. / Volgraf, M. / Sellers, B.D. / Schwarz, J.B. / Paoletti, P. / Sheng, M. / Zhou, Q. / Hanson, J.E.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,20415
Polymers87,6323
Non-polymers1,57212
Water11,998666
1
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,41510
Polymers58,4212
Non-polymers9938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-70 kcal/mol
Surface area23340 Å2
MethodPISA
2
C: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

C: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,57810
Polymers58,4212
Non-polymers1,1578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area2790 Å2
ΔGint-90 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.232, 114.461, 162.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 3 molecules ACB

#1: Protein Glutamate receptor 2,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: 29210.662 Da / Num. of mol.: 3
Fragment: UNP residues 413-527, GT linker, UNP residues 653-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIA2, GLUR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P42262

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Non-polymers , 5 types, 678 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-5YC / 7-[[ethyl(phenyl)amino]methyl]-2-methyl-[1,3,4]thiadiazolo[3,2-a]pyrimidin-5-one


Mass: 300.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16N4OS
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 96862 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 23.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FTJ

1ftj


Resolution: 1.703→46.812 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 4824 4.98 %
Rwork0.1742 --
obs0.1757 96862 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.703→46.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 83 666 6833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076408
X-RAY DIFFRACTIONf_angle_d1.0518635
X-RAY DIFFRACTIONf_dihedral_angle_d12.4932428
X-RAY DIFFRACTIONf_chiral_restr0.043942
X-RAY DIFFRACTIONf_plane_restr0.0051084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7033-1.72260.32081560.27442835X-RAY DIFFRACTION94
1.7226-1.74290.24151530.25153080X-RAY DIFFRACTION100
1.7429-1.76420.26921660.23713036X-RAY DIFFRACTION100
1.7642-1.78650.26811550.22163026X-RAY DIFFRACTION100
1.7865-1.810.25391710.21983070X-RAY DIFFRACTION100
1.81-1.83480.2611580.2053011X-RAY DIFFRACTION100
1.8348-1.8610.23891370.20033079X-RAY DIFFRACTION100
1.861-1.88880.24211710.19943022X-RAY DIFFRACTION99
1.8888-1.91830.23061390.19772922X-RAY DIFFRACTION96
1.9183-1.94980.24581670.19083049X-RAY DIFFRACTION99
1.9498-1.98340.24771580.18433069X-RAY DIFFRACTION100
1.9834-2.01940.18941700.17913022X-RAY DIFFRACTION100
2.0194-2.05830.21721510.17713108X-RAY DIFFRACTION100
2.0583-2.10030.21521370.17943044X-RAY DIFFRACTION100
2.1003-2.1460.23661600.17373118X-RAY DIFFRACTION100
2.146-2.19590.20171730.17563000X-RAY DIFFRACTION100
2.1959-2.25080.19591540.16913133X-RAY DIFFRACTION100
2.2508-2.31160.19391560.17722916X-RAY DIFFRACTION97
2.3116-2.37970.21861620.17763093X-RAY DIFFRACTION99
2.3797-2.45650.21751690.17773071X-RAY DIFFRACTION100
2.4565-2.54430.20811740.17953071X-RAY DIFFRACTION100
2.5443-2.64610.21121900.17193069X-RAY DIFFRACTION100
2.6461-2.76650.20951590.17963099X-RAY DIFFRACTION100
2.7665-2.91240.22221650.18423097X-RAY DIFFRACTION100
2.9124-3.09480.22921540.17893078X-RAY DIFFRACTION99
3.0948-3.33370.19671720.17013088X-RAY DIFFRACTION100
3.3337-3.66910.17741620.16853144X-RAY DIFFRACTION100
3.6691-4.19970.19391640.14923138X-RAY DIFFRACTION100
4.1997-5.290.18071530.1433216X-RAY DIFFRACTION99
5.29-46.82960.17181680.17843334X-RAY DIFFRACTION99

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