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- PDB-6uzr: Crystal structure of GLUN1/GLUN2A ligand-binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6uzr
TitleCrystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and homoquinolinic acid
Components(Glutamate receptor ionotropic, NMDA ...) x 2
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 / 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 / regulation of NMDA receptor activity / dendritic spine organization / 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 / calcium ion transmembrane import into cytosol / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / glycine binding / spinal cord development / response to amine / parallel fiber to Purkinje cell synapse / cellular response to zinc ion / startle response / monoatomic cation transmembrane transport / dopamine metabolic process / positive regulation of reactive oxygen species biosynthetic process / response to lithium ion / positive regulation of calcium ion transport into cytosol / regulation of postsynaptic membrane potential / response to light stimulus / 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
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: 1.87 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 23, 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)65,5717
Polymers65,0382
Non-polymers5325
Water7,296405
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 area3080 Å2
ΔGint-9 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.367, 88.717, 125.483
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

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

#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: 31698.221 Da / Num. of mol.: 1
Fragment: ligand-binding domain (UNP residues 402-539,661-802)
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

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Non-polymers , 4 types, 410 molecules

#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.13 %
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: 0.92013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92013 Å / Relative weight: 1
ReflectionResolution: 1.87→46.36 Å / Num. obs: 50584 / % possible obs: 99.99 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.09 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.5
Reflection shellResolution: 1.87→1.91 Å / Rmerge(I) obs: 0.944 / Num. unique obs: 4950

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Processing

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

4nf8


Resolution: 1.87→46.36 Å / SU ML: 0.1931 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3977
RfactorNum. reflection% reflection
Rfree0.2075 2577 5.09 %
Rwork0.1727 --
obs0.1746 50584 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.18 Å2
Refinement stepCycle: LAST / Resolution: 1.87→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 36 405 4923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714691
X-RAY DIFFRACTIONf_angle_d0.83376359
X-RAY DIFFRACTIONf_chiral_restr0.0576704
X-RAY DIFFRACTIONf_plane_restr0.0051823
X-RAY DIFFRACTIONf_dihedral_angle_d11.5522861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.910.31321290.24492568X-RAY DIFFRACTION99.85
1.91-1.950.25241340.21112644X-RAY DIFFRACTION99.53
1.95-1.990.23071450.20022620X-RAY DIFFRACTION99.89
1.99-2.040.20921680.17922624X-RAY DIFFRACTION99.79
2.04-2.090.20321290.17472630X-RAY DIFFRACTION100
2.09-2.140.23161410.18122611X-RAY DIFFRACTION99.85
2.14-2.210.23171430.1782671X-RAY DIFFRACTION99.96
2.21-2.280.22661350.17822666X-RAY DIFFRACTION99.86
2.28-2.360.21981230.17822678X-RAY DIFFRACTION100
2.36-2.460.26711590.18342632X-RAY DIFFRACTION99.96
2.46-2.570.25021280.19412652X-RAY DIFFRACTION99.93
2.57-2.70.26241240.18862687X-RAY DIFFRACTION99.96
2.7-2.870.19571440.19092680X-RAY DIFFRACTION99.96
2.87-3.090.21151460.18992668X-RAY DIFFRACTION99.89
3.09-3.40.20211620.17192684X-RAY DIFFRACTION100
3.4-3.90.19231540.1562698X-RAY DIFFRACTION99.93
3.9-4.910.18281560.13492728X-RAY DIFFRACTION99.76
4.91-46.360.1671570.17012866X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 40.9689417807 Å / Origin y: 74.2316637169 Å / Origin z: 26.1231482833 Å
111213212223313233
T0.181791939534 Å2-0.00899004938655 Å20.0230935056157 Å2-0.174039034102 Å20.00174136564798 Å2--0.228909917986 Å2
L0.331555068293 °2-0.0978916561417 °20.206242544814 °2-0.486663245188 °20.0328415217717 °2--0.86538656944 °2
S-0.0196548907876 Å °-0.0240026662317 Å °0.0039136893308 Å °0.0304445144588 Å °0.0384296984207 Å °-0.034572952403 Å °-0.00440608595713 Å °-0.0382321534172 Å °-0.0115776096706 Å °
Refinement TLS groupSelection details: all

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