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

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Basic information

Entry
Database: PDB / ID: 6ovd
TitleCrystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 3-ethylphenyl-ACEPC
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsPROTEIN TRANSPORT / ANTAGONIST / TRANSPORT PROTEIN / RECEPTOR
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / response to environmental enrichment / directional locomotion / positive regulation of Schwann cell migration / pons maturation / 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 / response to environmental enrichment / directional locomotion / positive regulation of Schwann cell migration / pons maturation / 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 / regulation of ARF protein signal transduction / response to other organism / protein localization to postsynaptic membrane / cellular response to magnesium ion / serotonin metabolic process / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / response to methylmercury / suckling behavior / response to manganese ion / response to glycine / response to carbohydrate / propylene metabolic process / sleep / dendritic spine organization / cellular response to dsRNA / locomotion / regulation of NMDA receptor activity / cellular response to lipid / RAF/MAP kinase cascade / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / response to glycoside / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / glutamate binding / neurotransmitter receptor complex / ligand-gated sodium channel activity / response to morphine / glutamate receptor signaling pathway / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / spinal cord development / response to amine / glycine binding / cellular response to zinc ion / startle response / positive regulation of reactive oxygen species biosynthetic process / dopamine metabolic process / parallel fiber to Purkinje cell synapse / response to lithium ion / monoatomic cation transmembrane transport / positive regulation of calcium ion transport into cytosol / cellular response to glycine / regulation of postsynaptic membrane potential / response to light stimulus / modulation of excitatory postsynaptic potential / action potential / associative learning / conditioned place preference / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / regulation of neuronal synaptic plasticity / monoatomic cation transport / social behavior / positive regulation of protein targeting to membrane / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / synaptic cleft / neuron development / phosphatase binding / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / calcium ion homeostasis / glutamate-gated receptor activity / regulation of neuron apoptotic process / cell adhesion molecule binding / cellular response to manganese ion / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / neurogenesis / dendrite 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
GLYCINE / Chem-N9A / 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: 2.102 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
Revision 1.2Nov 20, 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
B: Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5084
Polymers65,1252
Non-polymers3822
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-3 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.666, 87.237, 122.597
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 / NMD-R1


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: 31785.299 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


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-N9A / (3S,5S)-5-[(2R)-2-amino-2-carboxyethyl]-1-(3-ethylphenyl)pyrazolidine-3-carboxylic acid


Mass: 307.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N3O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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, hanging drop / 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: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→32.85 Å / Num. obs: 34185 / % possible obs: 98.04 % / Redundancy: 4.6 % / Biso Wilson estimate: 28.17 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1195 / Rpim(I) all: 0.05773 / Rrim(I) all: 0.1333 / Net I/σ(I): 8.59
Reflection shellResolution: 2.1→2.177 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5172 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 3090 / CC1/2: 0.521 / Rpim(I) all: 0.3004 / Rrim(I) all: 0.6019 / % possible all: 90.59

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I57

5i57


Resolution: 2.102→32.85 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.96
RfactorNum. reflection% reflection
Rfree0.2402 1999 5.85 %
Rwork0.194 --
obs0.1967 34185 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.102→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4414 0 22 312 4748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024536
X-RAY DIFFRACTIONf_angle_d0.4816131
X-RAY DIFFRACTIONf_dihedral_angle_d9.383240
X-RAY DIFFRACTIONf_chiral_restr0.043678
X-RAY DIFFRACTIONf_plane_restr0.003785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.102-2.15450.30441230.26651994X-RAY DIFFRACTION87
2.1545-2.21270.30551400.26622233X-RAY DIFFRACTION97
2.2127-2.27780.29711410.25432269X-RAY DIFFRACTION97
2.2778-2.35130.31021410.23382272X-RAY DIFFRACTION98
2.3513-2.43540.26681390.22572255X-RAY DIFFRACTION99
2.4354-2.53280.2561450.21682308X-RAY DIFFRACTION99
2.5328-2.64810.28531430.21232313X-RAY DIFFRACTION99
2.6481-2.78760.26791430.20892301X-RAY DIFFRACTION99
2.7876-2.96220.26081430.20322306X-RAY DIFFRACTION99
2.9622-3.19070.25081450.19792335X-RAY DIFFRACTION99
3.1907-3.51150.22951460.17962344X-RAY DIFFRACTION100
3.5115-4.0190.20441470.16782360X-RAY DIFFRACTION100
4.019-5.06080.20151480.1492390X-RAY DIFFRACTION100
5.0608-32.850.2111550.18692507X-RAY DIFFRACTION99

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