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- PDB-6uzg: Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain... -

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Basic information

Entry
Database: PDB / ID: 6uzg
TitleCrystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and homoquinolinic acid
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsMEMBRANE PROTEIN / NMDAR / ligand-binding domain / agonist
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 hydrogen sulfide / positive regulation of inhibitory postsynaptic potential / directional locomotion / response to environmental enrichment / response to other organism / regulation of ARF protein signal transduction ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / response to hydrogen sulfide / positive regulation of inhibitory postsynaptic potential / directional locomotion / response to environmental enrichment / response to other organism / regulation of ARF protein signal transduction / pons maturation / response to methylmercury / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / olfactory learning / response to carbohydrate / dendritic branch / cellular response to dsRNA / conditioned taste aversion / cellular response to lipid / regulation of respiratory gaseous exchange / cellular response to magnesium ion / protein localization to postsynaptic membrane / conditioned place preference / propylene metabolic process / response to glycine / sleep / locomotion / dendritic spine organization / response to manganese ion / regulation of monoatomic cation transmembrane transport / voltage-gated monoatomic cation channel activity / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of NMDA receptor activity / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / NMDA selective glutamate receptor complex / response to morphine / cellular response to zinc ion / calcium ion transmembrane import into cytosol / glutamate binding / glutamate receptor signaling pathway / neuromuscular process / protein heterotetramerization / regulation of synapse assembly / positive regulation of calcium ion transport into cytosol / positive regulation of reactive oxygen species biosynthetic process / glycine binding / regulation of axonogenesis / male mating behavior / regulation of dendrite morphogenesis / spinal cord development / action potential / suckling behavior / startle response / response to amine / dopamine metabolic process / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / response to lithium ion / modulation of excitatory postsynaptic potential / associative learning / monoatomic cation transport / social behavior / excitatory synapse / ligand-gated monoatomic ion channel activity / regulation of postsynaptic membrane potential / positive regulation of excitatory postsynaptic potential / cellular response to glycine / positive regulation of dendritic spine maintenance / postsynaptic density, intracellular component / response to light stimulus / positive regulation of protein targeting to membrane / neuron development / multicellular organismal response to stress / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to manganese ion / phosphatase binding / glutamate receptor binding / long-term memory / regulation of neuron apoptotic process / prepulse inhibition / monoatomic cation channel activity / calcium ion homeostasis / glutamate-gated receptor activity / synaptic cleft / cell adhesion molecule binding / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sensory perception of pain / response to amphetamine / ionotropic glutamate receptor signaling pathway / protein tyrosine kinase binding
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 / 3-(carboxymethyl)pyridine-2-carboxylic acid / 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: 1.94 Å
AuthorsWang, J.X. / Furukawa, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of subtype-selective competitive antagonism for GluN2C/2D-containing NMDA receptors.
Authors: Wang, J.X. / Irvine, M.W. / Burnell, E.S. / Sapkota, K. / Thatcher, R.J. / Li, M. / Simorowski, N. / Volianskis, A. / Collingridge, G.L. / Monaghan, D.T. / Jane, D.E. / Furukawa, H.
History
DepositionNov 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.3Oct 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)65,4554
Polymers65,1992
Non-polymers2562
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Full-length NMDAR available, showed the same assembly of LBD dimers (dimer of dimer structure)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-8 kcal/mol
Surface area26250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.016, 89.856, 124.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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
Fragment: ligand-binding domain (UNP residues 415-565,684-821)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): OrigamiB (DE3) / 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: 31858.482 Da / Num. of mol.: 1
Fragment: ligand-binding domain (UNP residues 402-539,661-802)
Mutation: A414R, K738M, G740R, R741K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): OrigamiB (DE3) / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-QM1 / 3-(carboxymethyl)pyridine-2-carboxylic acid


Mass: 181.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO4 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist, toxin*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 25, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.94→72.88 Å / Num. obs: 46159 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 34.02 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 9.2
Reflection shellResolution: 1.94→1.97 Å / Rmerge(I) obs: 0.885 / Num. unique obs: 4559

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Processing

Software
NameVersionClassification
autoPROCdata collection
Aimlessdata scaling
pointlessdata scaling
REFMACphasing
PHENIX1.13_2998refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NF8

4nf8


Resolution: 1.94→50.33 Å / SU ML: 0.2567 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.0127
RfactorNum. reflection% reflection
Rfree0.2501 2256 4.89 %
Rwork0.2107 --
obs0.2127 46159 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.97 Å2
Refinement stepCycle: LAST / Resolution: 1.94→50.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4485 0 18 288 4791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01034639
X-RAY DIFFRACTIONf_angle_d0.96016277
X-RAY DIFFRACTIONf_chiral_restr0.0631691
X-RAY DIFFRACTIONf_plane_restr0.0061815
X-RAY DIFFRACTIONf_dihedral_angle_d13.17122817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.33751210.28582720X-RAY DIFFRACTION99.23
1.98-2.030.30291430.26212736X-RAY DIFFRACTION99.83
2.03-2.080.29121340.24692678X-RAY DIFFRACTION99.75
2.08-2.140.28511480.2342724X-RAY DIFFRACTION99.69
2.14-2.20.29621590.23772740X-RAY DIFFRACTION99.76
2.2-2.270.27641570.2262655X-RAY DIFFRACTION99.89
2.27-2.350.26611490.2312731X-RAY DIFFRACTION99.62
2.35-2.450.25971370.23122736X-RAY DIFFRACTION99.45
2.45-2.560.28321310.23822730X-RAY DIFFRACTION99.55
2.56-2.690.28791170.25272765X-RAY DIFFRACTION99.59
2.69-2.860.28791230.24722754X-RAY DIFFRACTION99.48
2.86-3.080.33511590.25832752X-RAY DIFFRACTION99.32
3.08-3.390.26391350.22842722X-RAY DIFFRACTION98.55
3.39-3.880.23141280.20362720X-RAY DIFFRACTION96.8
3.88-4.890.18741570.15472778X-RAY DIFFRACTION98.92
4.89-50.330.21631580.17842962X-RAY DIFFRACTION99.81
Refinement TLS params.Method: refined / Origin x: 40.9161081404 Å / Origin y: 75.4213828129 Å / Origin z: 25.8988711306 Å
111213212223313233
T0.252986980524 Å20.0210053035885 Å2-0.0102025664992 Å2-0.35193230641 Å2-0.0090946294442 Å2--0.265665642226 Å2
L0.855448554841 °20.0694269382777 °20.54458151309 °2-0.6255998741 °20.149112541261 °2--1.29169700942 °2
S-0.0679574508329 Å °-0.119512014553 Å °0.0522599975598 Å °0.109665783972 Å °0.0464310788229 Å °-0.0976068426465 Å °-0.106138479958 Å °-0.0906263942514 Å °0.0327653638369 Å °
Refinement TLS groupSelection details: all

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