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- PDB-5u8c: CRYSTAL STRUCTURE OF GLUN1/GLUN2A LIGAND-BINDING DOMAIN IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 5u8c
TitleCRYSTAL STRUCTURE OF GLUN1/GLUN2A LIGAND-BINDING DOMAIN IN COMPLEX WITH GLYCINE AND NVP-AAM077
Components
  • GLUTAMATE RECEPTOR IONOTROPIC, NMDA 2A
  • Glutamate receptor ionotropic, NMDA 1
KeywordsTRANSPORT PROTEIN / RECEPTOR / GLYCINE AND NVP-AAM077
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 / auditory behavior / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / olfactory learning / conditioned taste aversion / dendritic branch / response to hydrogen sulfide / regulation of respiratory gaseous exchange / response to other organism / positive regulation of inhibitory postsynaptic potential / protein localization to postsynaptic membrane / cellular response to magnesium ion / regulation of ARF protein signal transduction / response to methylmercury / transmitter-gated monoatomic ion channel activity / conditioned place preference / locomotion / response to glycine / propylene metabolic process / dendritic spine organization / response to carbohydrate / regulation of NMDA receptor activity / sleep / cellular response to dsRNA / cellular response to lipid / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / response to manganese ion / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / cellular response to zinc ion / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / glutamate receptor signaling pathway / glutamate binding / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / regulation of synapse assembly / male mating behavior / glycine binding / spinal cord development / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / suckling behavior / regulation of postsynaptic membrane potential / response to amine / startle response / dopamine metabolic process / social behavior / monoatomic cation transmembrane transport / response to lithium ion / associative learning / modulation of excitatory postsynaptic potential / regulation of neuronal synaptic plasticity / action potential / cellular response to glycine / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / response to light stimulus / positive regulation of protein targeting to membrane / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / cellular response to manganese ion / postsynaptic density, intracellular component / glutamate receptor binding / neuron development / synaptic cleft / prepulse inhibition / multicellular organismal response to stress / phosphatase binding / monoatomic cation channel activity / glutamate-gated receptor activity / calcium ion homeostasis / response to fungicide / cell adhesion molecule binding / regulation of neuron apoptotic process / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / neurogenesis / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential
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-84J / 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 / molecular replacement / Resolution: 1.598 Å
AuthorsRomero-Hernandez, A. / Furukawa, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105730 United States
CitationJournal: Mol. Pharmacol. / Year: 2017
Title: Novel Mode of Antagonist Binding in NMDA Receptors Revealed by the Crystal Structure of the GluN1-GluN2A Ligand-Binding Domain Complexed to NVP-AAM077.
Authors: Romero-Hernandez, A. / Furukawa, H.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references / Other
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)65,7475
Polymers65,1252
Non-polymers6213
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-5 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.550, 84.227, 121.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 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: UNP residues 394-554, 663-800
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


Mass: 31785.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q00959*PLUS

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Non-polymers , 4 types, 435 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-84J / [(R)-{[(1S)-1-(4-bromophenyl)ethyl]amino}(2,3-dihydroxyquinoxalin-5-yl)methyl]phosphonic acid


Mass: 454.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17BrN3O5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 47.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% Polyethylene glycol monoethylether 2000 (PEG2000 MME), 100mM HEPES-NaOH pH 7.0, and 75mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.598→50 Å / Num. obs: 72757 / % possible obs: 89.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 19.69 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.84

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NF8

4nf8


Resolution: 1.598→49.196 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2041 3652 5.02 %
Rwork0.1885 --
obs0.1893 72757 89.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.87 Å2 / Biso mean: 24.8213 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 1.598→49.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4415 0 38 432 4885
Biso mean--20.73 30.7 -
Num. residues----567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084549
X-RAY DIFFRACTIONf_angle_d0.936161
X-RAY DIFFRACTIONf_chiral_restr0.057685
X-RAY DIFFRACTIONf_plane_restr0.006786
X-RAY DIFFRACTIONf_dihedral_angle_d13.3862730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5984-1.61940.347620.33811317137944
1.6194-1.64160.3648890.32441614170356
1.6416-1.6650.31821000.31121899199964
1.665-1.68990.29371190.30712059217871
1.6899-1.71630.32931210.28462297241878
1.7163-1.74440.29661400.25652450259085
1.7444-1.77450.2591470.24292611275889
1.7745-1.80680.25421350.22892715285090
1.8068-1.84150.25191310.21682714284593
1.8415-1.87910.22961320.19782709284192
1.8791-1.920.25181500.20382707285792
1.92-1.96470.22461410.20452765290694
1.9647-2.01380.22751340.20662773290793
2.0138-2.06820.23671360.20322790292695
2.0682-2.12910.25581340.19992855298996
2.1291-2.19780.21951650.18692857302297
2.1978-2.27640.22121630.18732915307898
2.2764-2.36750.22031520.18882913306599
2.3675-2.47530.19571610.19162949311099
2.4753-2.60580.23581500.19342955310599
2.6058-2.7690.21131620.198829723134100
2.769-2.98280.20791600.198229953155100
2.9828-3.28290.22531720.185429863158100
3.2829-3.75780.15431540.167830353189100
3.7578-4.73380.14881640.143430613225100
4.7338-49.21910.15351780.162231923370100

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