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- PDB-6ove: Crystal structure of GluN1/GluN2A NMDA receptor agonist binding d... -

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Basic information

Entry
Database: PDB / ID: 6ove
TitleCrystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-propylphenyl-ACEPC
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsPROTEIN TRANSPORT / NMDA RECEPTOR / ANTAGONIST / TRANSPORT PROTEIN / RECEPTOR
Function / homology
Function and homology information


response to ammonium ion / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion ...response to ammonium ion / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / response to other organism / cellular response to magnesium ion / sleep / response to methylmercury / voltage-gated monoatomic cation channel activity / locomotion / response to morphine / cellular response to dsRNA / glutamate-gated calcium ion channel activity / regulation of monoatomic cation transmembrane transport / dendritic spine organization / response to carbohydrate / cellular response to lipid / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / response to manganese ion / protein heterotetramerization / regulation of NMDA receptor activity / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / cellular response to zinc ion / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / male mating behavior / regulation of dendrite morphogenesis / regulation of axonogenesis / dopamine metabolic process / spinal cord development / suckling behavior / startle response / regulation of neuronal synaptic plasticity / response to amine / monoatomic cation transmembrane transport / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / excitatory synapse / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of dendritic spine maintenance / neuron development / glutamate receptor binding / regulation of postsynaptic membrane potential / phosphatase binding / calcium ion homeostasis / cellular response to manganese ion / prepulse inhibition / long-term memory / regulation of neuron apoptotic process / synaptic cleft / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / monoatomic cation channel activity / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / ionotropic glutamate receptor signaling pathway / cell adhesion molecule binding / neurogenesis / regulation of membrane potential / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to cocaine / synaptic membrane / synaptic transmission, glutamatergic / learning / long-term synaptic potentiation / hippocampus development / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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 ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / 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
GLYCINE / Chem-N9D / 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 Å
AuthorsSyrenne, J.T. / Mou, T.C. / Tamborini, L. / Pinto, A. / Sprang, S.R. / Hansen, K.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097536 United States
CitationJournal: To Be Published
Title: Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 3-ethylphenyl-ACEPC
Authors: Syrenne, J.T. / Mou, T.C. / Tamborini, L. / Pinto, A. / Sprang, S.R. / Hansen, K.B.
History
DepositionMay 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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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
B: Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4084
Polymers65,0112
Non-polymers3962
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-5 kcal/mol
Surface area25660 Å2
2
A: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4152
Polymers33,3401
Non-polymers751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9932
Polymers31,6711
Non-polymers3211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.694, 86.987, 121.984
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 ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1


Mass: 33340.031 Da / Num. of mol.: 1
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 / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31671.197 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
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-N9D / (3R,5S)-5-[(2R)-2-amino-2-carboxyethyl]-1-(4-propylphenyl)pyrazolidine-3-carboxylic acid


Mass: 321.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H23N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE CORRESPONDS TO THE NCBI REFERENCE NP_036705.3 FOR GLUN2A. RESIDUE THR242 IN THIS ...THE SEQUENCE CORRESPONDS TO THE NCBI REFERENCE NP_036705.3 FOR GLUN2A. RESIDUE THR242 IN THIS SEQUENCE IS 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: 2.35 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→46.03 Å / Num. obs: 39766 / % possible obs: 99.16 % / Redundancy: 9.8 % / Biso Wilson estimate: 24.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1152 / Rpim(I) all: 0.03666 / Rrim(I) all: 0.1211 / Net I/σ(I): 13.91
Reflection shellResolution: 2→2.072 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.5764 / Mean I/σ(I) obs: 2.75 / Num. unique obs: 3732 / CC1/2: 0.663 / Rpim(I) all: 0.2531 / Rrim(I) all: 0.6334 / % possible all: 94.77

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Processing

Software
NameVersionClassification
PHENIX(1.15_3459)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I57

5i57


Resolution: 2→46.03 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.34
RfactorNum. reflection% reflection
Rfree0.216 2000 5.03 %
Rwork0.1823 --
obs0.1841 39763 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 0 28 379 4814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024525
X-RAY DIFFRACTIONf_angle_d0.4926108
X-RAY DIFFRACTIONf_dihedral_angle_d10.6942702
X-RAY DIFFRACTIONf_chiral_restr0.042674
X-RAY DIFFRACTIONf_plane_restr0.003782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0003-2.05040.33271340.25362525X-RAY DIFFRACTION94
2.0504-2.10580.24421380.24052615X-RAY DIFFRACTION97
2.1058-2.16780.29531400.22322637X-RAY DIFFRACTION100
2.1678-2.23770.26871430.21242700X-RAY DIFFRACTION100
2.2377-2.31770.24571420.20892678X-RAY DIFFRACTION100
2.3177-2.41050.26141420.19732688X-RAY DIFFRACTION100
2.4105-2.52020.2661410.19482658X-RAY DIFFRACTION99
2.5202-2.65310.23681440.19452713X-RAY DIFFRACTION100
2.6531-2.81930.26641420.19522696X-RAY DIFFRACTION100
2.8193-3.03690.22291450.18262730X-RAY DIFFRACTION100
3.0369-3.34250.22721430.17422701X-RAY DIFFRACTION99
3.3425-3.8260.18911440.16462736X-RAY DIFFRACTION100
3.826-4.81980.1561480.142788X-RAY DIFFRACTION100
4.8198-49.95490.1731540.17682898X-RAY DIFFRACTION100

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