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- PDB-5vij: Crystal structure of GluN1/GluN2A NMDA receptor agonist binding d... -

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Basic information

Entry
Database: PDB / ID: 5vij
TitleCrystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-bromophenyl-ACEPC
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
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 / pons maturation / response to environmental enrichment / 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 / pons maturation / response to environmental enrichment / 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 / serotonin metabolic process / response to other organism / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / transmitter-gated monoatomic ion channel activity / cellular response to magnesium ion / positive regulation of inhibitory postsynaptic potential / suckling behavior / response to methylmercury / response to glycine / propylene metabolic process / response to manganese ion / response to carbohydrate / sleep / regulation of NMDA receptor activity / locomotion / dendritic spine organization / cellular response to dsRNA / cellular response to lipid / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / 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 / glutamate receptor signaling pathway / response to morphine / calcium ion transmembrane import into cytosol / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / glycine binding / regulation of synapse assembly / spinal cord development / response to amine / parallel fiber to Purkinje cell synapse / cellular response to zinc ion / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / dopamine metabolic process / response to lithium ion / response to light stimulus / positive regulation of calcium ion transport into cytosol / regulation of postsynaptic membrane potential / cellular response to glycine / associative learning / modulation of excitatory postsynaptic potential / action potential / excitatory synapse / conditioned place preference / monoatomic cation transport / positive regulation of dendritic spine maintenance / social behavior / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of protein targeting to membrane / glutamate receptor binding / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / synaptic cleft / neuron development / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / phosphatase binding / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / 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
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-5DX / 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: 2.105 Å
AuthorsMou, T.-C. / Conti, P. / Pinto, A. / Tamborini, L. / 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: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.
Authors: Lind, G.E. / Mou, T.C. / Tamborini, L. / Pomper, M.G. / De Micheli, C. / Conti, P. / Pinto, A. / Hansen, K.B.
History
DepositionApr 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
SupersessionMay 17, 2017ID: 5DDN
Revision 1.1May 17, 2017Group: Other
Revision 1.2Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Oct 4, 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 1.8Oct 16, 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

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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)65,5554
Polymers65,1252
Non-polymers4292
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-6 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.886, 87.158, 122.254
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 / GluN1


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-5DX / 5-[(2R)-2-amino-2-carboxyethyl]-1-(4-bromophenyl)-1H-pyrazole-3-carboxylic acid


Mass: 354.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12BrN3O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SAMPLE SEQUENCE MATCHES WITH NCBI REFERENCE SEQUENCE NP_036705.3 FOR GLUN2A

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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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonia Acetate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.105→19.98 Å / Num. obs: 34022 / % possible obs: 98.1 % / Redundancy: 3 % / Rsym value: 0.119 / Net I/σ(I): 8.78
Reflection shellResolution: 2.11→2.18 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.95 / Num. unique obs: 2941 / Rsym value: 0.649 / % possible all: 86.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NF8

4nf8


Resolution: 2.105→19.98 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 1994 5.88 %
Rwork0.1932 --
obs0.1969 33940 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.105→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 26 272 4682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094505
X-RAY DIFFRACTIONf_angle_d1.1096085
X-RAY DIFFRACTIONf_dihedral_angle_d16.4212703
X-RAY DIFFRACTIONf_chiral_restr0.059671
X-RAY DIFFRACTIONf_plane_restr0.006777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.105-2.15760.33851140.29811869X-RAY DIFFRACTION82
2.1576-2.21580.34451360.28892145X-RAY DIFFRACTION94
2.2158-2.2810.3451390.27052219X-RAY DIFFRACTION96
2.281-2.35450.31711400.24862263X-RAY DIFFRACTION99
2.3545-2.43850.28841420.2322275X-RAY DIFFRACTION99
2.4385-2.53590.30381450.22732313X-RAY DIFFRACTION100
2.5359-2.65110.32111440.22082315X-RAY DIFFRACTION100
2.6511-2.79050.30941450.22242314X-RAY DIFFRACTION100
2.7905-2.96480.26741450.20372318X-RAY DIFFRACTION100
2.9648-3.19290.27731450.2052338X-RAY DIFFRACTION100
3.1929-3.51270.25861470.18732337X-RAY DIFFRACTION100
3.5127-4.01740.23511470.1662355X-RAY DIFFRACTION100
4.0174-5.04790.18951490.14582386X-RAY DIFFRACTION100
5.0479-19.98060.20951560.16232499X-RAY DIFFRACTION100

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