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- PDB-4nf8: Crystal structure of GluN1/GluN2A ligand-binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 4nf8
TitleCrystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and glutamate in PEG2000MME
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
Keywordstransport protein / receptor / glycine and glutamate
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 / serotonin metabolic process / regulation of respiratory gaseous exchange / response to other organism / protein localization to postsynaptic membrane / 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 / regulation of NMDA receptor activity / locomotion / 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 / neuromuscular process / calcium ion transmembrane import into cytosol / 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 / dopamine metabolic process / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / 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 / conditioned place preference / excitatory synapse / positive regulation of dendritic spine maintenance / monoatomic cation transport / social behavior / regulation of neuronal synaptic plasticity / positive regulation of protein targeting to membrane / monoatomic ion channel complex / 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 / multicellular organismal response to stress / positive regulation of synaptic transmission, glutamatergic / 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 / presynaptic active zone membrane / neurogenesis
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
GLUTAMIC ACID / 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: 1.856 Å
AuthorsJespersen, A. / Tajima, N. / Furukawa, H.
CitationJournal: Neuron / Year: 2014
Title: Structural Insights into Competitive Antagonism in NMDA Receptors.
Authors: Jespersen, A. / Tajima, N. / Fernandez-Cuervo, G. / Garnier-Amblard, E.C. / Furukawa, H.
History
DepositionOct 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Oct 16, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)65,3484
Polymers65,1252
Non-polymers2222
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-7 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.377, 89.653, 125.414
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
Fragment: Ligand-binding domain, unp residues 393-543; unp residues 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
Fragment: Ligand-binding domain; unp residues 402-539; unp residues 661-802
Mutation: S758T
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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7
Details: PEG2000MME and HEPES, pH 7, VAPOR DIFFUSION, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 51950 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.856→19.857 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 2649 5.1 %
Rwork0.1768 --
obs0.1789 51950 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.856→19.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4493 0 15 593 5101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074677
X-RAY DIFFRACTIONf_angle_d1.0846328
X-RAY DIFFRACTIONf_dihedral_angle_d14.8391764
X-RAY DIFFRACTIONf_chiral_restr0.078702
X-RAY DIFFRACTIONf_plane_restr0.004816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8561-1.88990.31491200.2722278X-RAY DIFFRACTION88
1.8899-1.92620.31131290.25252597X-RAY DIFFRACTION100
1.9262-1.96550.24931370.22482565X-RAY DIFFRACTION100
1.9655-2.00820.30051450.22122592X-RAY DIFFRACTION100
2.0082-2.05480.27351620.2162557X-RAY DIFFRACTION100
2.0548-2.10620.28411200.21472600X-RAY DIFFRACTION99
2.1062-2.1630.29551470.20512575X-RAY DIFFRACTION100
2.163-2.22660.26591260.20182582X-RAY DIFFRACTION100
2.2266-2.29840.22631340.19542628X-RAY DIFFRACTION100
2.2984-2.38040.27021250.18452620X-RAY DIFFRACTION100
2.3804-2.47550.23621530.18672610X-RAY DIFFRACTION100
2.4755-2.5880.26581320.18712612X-RAY DIFFRACTION100
2.588-2.72410.22481250.182638X-RAY DIFFRACTION100
2.7241-2.89430.22621310.18562592X-RAY DIFFRACTION99
2.8943-3.1170.22061490.18222625X-RAY DIFFRACTION100
3.117-3.42920.20721600.16582642X-RAY DIFFRACTION100
3.4292-3.92210.17351560.15012653X-RAY DIFFRACTION100
3.9221-4.92890.1731470.13772638X-RAY DIFFRACTION98
4.9289-19.85830.18841510.17182697X-RAY DIFFRACTION96

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