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- PDB-5i59: Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains... -

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Basic information

Entry
Database: PDB / ID: 5i59
TitleGlutamate- and glycine-bound GluN1/GluN2A agonist binding domains with MPX 007
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / RECEPTOR / NMDA receptor / Antagonist
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / response to other organism / protein localization to postsynaptic membrane / serotonin metabolic process / regulation of ARF protein signal transduction / cellular response to magnesium ion / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / suckling behavior / response to methylmercury / response to manganese ion / response to glycine / propylene metabolic process / sleep / response to carbohydrate / locomotion / dendritic spine organization / regulation of NMDA receptor activity / cellular response to dsRNA / cellular response to lipid / regulation of monoatomic cation transmembrane transport / RAF/MAP kinase cascade / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / voltage-gated monoatomic cation channel activity / response to glycoside / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / response to morphine / regulation of axonogenesis / glutamate receptor signaling pathway / neuromuscular process / regulation of dendrite morphogenesis / calcium ion transmembrane import into cytosol / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / spinal cord development / response to amine / cellular response to zinc ion / startle response / monoatomic cation transmembrane transport / parallel fiber to Purkinje cell synapse / dopamine metabolic process / positive regulation of reactive oxygen species biosynthetic process / response to lithium ion / positive regulation of calcium ion transport into cytosol / response to light stimulus / regulation of postsynaptic membrane potential / cellular response to glycine / modulation of excitatory postsynaptic potential / associative learning / action potential / conditioned place preference / excitatory synapse / positive regulation of dendritic spine maintenance / monoatomic cation transport / social behavior / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of protein targeting to membrane / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / long-term memory / synaptic cleft / neuron development / prepulse inhibition / phosphatase binding / positive regulation of synaptic transmission, glutamatergic / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / cell adhesion molecule binding / regulation of neuron apoptotic process / cellular response to manganese ion / glutamate-gated calcium ion channel activity / presynaptic active zone membrane
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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 / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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-67Q / GLUTAMIC ACID / GLYCINE / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMou, T.-C. / Sprang, S.R. / Hansen, K.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
CitationJournal: Neuron / Year: 2016
Title: Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors.
Authors: Yi, F. / Mou, T.C. / Dorsett, K.N. / Volkmann, R.A. / Menniti, F.S. / Sprang, S.R. / Hansen, K.B.
History
DepositionFeb 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5515
Polymers64,8732
Non-polymers6783
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-7 kcal/mol
Surface area24360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.951, 86.729, 123.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33340.031 Da / Num. of mol.: 1
Fragment: unp residues 415-565, unp residues 684-821 unp residues 6402-539, unp residues 661-800
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31533.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959

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Non-polymers , 4 types, 166 molecules

#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-67Q / 5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-4H-1lambda~4~,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide


Mass: 455.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19F2N5O3S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsThe sequence corresponds to the NCBI Reference Sequence NP_036705.3 for GluN2A. residue Thr242 in ...The sequence corresponds to the NCBI Reference Sequence NP_036705.3 for GluN2A. residue Thr242 in this sequence is a Ser758 in Swiss-Prot Q00959.

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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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate and 16-22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2015 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.11→15.02 Å / Num. obs: 32477 / % possible obs: 95.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 27.39 Å2 / Rsym value: 0.11 / Net I/σ(I): 6.58
Reflection shellResolution: 2.11→2.18 Å / Redundancy: 2.8 % / % possible all: 89.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I57

5i57


Resolution: 2.25→15.02 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 24.95
RfactorNum. reflection% reflection
Rfree0.264 1659 6.16 %
Rwork0.194 --
obs0.198 26931 96.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→15.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4273 0 44 163 4480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094418
X-RAY DIFFRACTIONf_angle_d1.1755956
X-RAY DIFFRACTIONf_dihedral_angle_d15.1911636
X-RAY DIFFRACTIONf_chiral_restr0.045657
X-RAY DIFFRACTIONf_plane_restr0.005758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3160.31681320.27362013X-RAY DIFFRACTION94
2.316-2.39050.33421330.26682027X-RAY DIFFRACTION95
2.3905-2.47560.32841330.26012023X-RAY DIFFRACTION94
2.4756-2.57420.32041350.25482055X-RAY DIFFRACTION95
2.5742-2.69070.27861370.23752072X-RAY DIFFRACTION95
2.6907-2.83170.31591350.22532074X-RAY DIFFRACTION95
2.8317-3.00780.30331370.21032085X-RAY DIFFRACTION96
3.0078-3.23790.27481390.20652115X-RAY DIFFRACTION97
3.2379-3.55980.2731430.17692170X-RAY DIFFRACTION98
3.5598-4.06590.22741410.15912164X-RAY DIFFRACTION98
4.0659-5.08930.23611440.152184X-RAY DIFFRACTION98
5.0893-15.01740.20911500.17062290X-RAY DIFFRACTION98

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