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- PDB-4nf5: Crystal structure of GluN1/GluN2A ligand-binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 4nf5
TitleCrystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and D-AP5
Components(Glutamate receptor ionotropic, NMDA ...) x 2
Keywordstransport protein / receptor / glycine and D-AP5
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 environmental enrichment / directional locomotion / positive regulation of Schwann cell migration / pons maturation / 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 / response to environmental enrichment / directional locomotion / positive regulation of Schwann cell migration / pons maturation / 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 / regulation of ARF protein signal transduction / protein localization to postsynaptic membrane / cellular response to magnesium ion / serotonin metabolic process / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / response to methylmercury / suckling behavior / response to manganese ion / response to glycine / response to carbohydrate / propylene metabolic process / sleep / dendritic spine organization / cellular response to dsRNA / locomotion / regulation of NMDA receptor activity / cellular response to lipid / RAF/MAP kinase cascade / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / response to glycoside / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / glutamate binding / neurotransmitter receptor complex / ligand-gated sodium channel activity / response to morphine / glutamate receptor signaling pathway / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / spinal cord development / response to amine / glycine binding / cellular response to zinc ion / startle response / parallel fiber to Purkinje cell synapse / positive regulation of reactive oxygen species biosynthetic process / dopamine metabolic process / monoatomic cation transmembrane transport / response to lithium ion / positive regulation of calcium ion transport into cytosol / cellular response to glycine / response to light stimulus / modulation of excitatory postsynaptic potential / regulation of postsynaptic membrane potential / action potential / associative learning / conditioned place preference / excitatory synapse / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / social behavior / regulation of neuronal synaptic plasticity / monoatomic cation transport / glutamate receptor binding / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / long-term memory / synaptic cleft / neuron development / phosphatase binding / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / calcium ion homeostasis / 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
5-phosphono-D-norvaline / 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: 1.903 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 30, 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)65,6747
Polymers65,1252
Non-polymers5485
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-4 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.029, 87.344, 121.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 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: 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

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Non-polymers , 4 types, 624 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-2JJ / 5-phosphono-D-norvaline


Type: D-peptide linking / Mass: 197.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO5P / Comment: antagonist*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7
Details: PEG2000MME, HEPES, pH 7, VAPOR DIFFUSION, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 44333 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→19.997 Å / SU ML: 0.19 / σ(F): 1.36 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 2339 5.06 %
Rwork0.1709 --
obs0.173 43949 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.903→19.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 35 619 4970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084501
X-RAY DIFFRACTIONf_angle_d1.0956081
X-RAY DIFFRACTIONf_dihedral_angle_d13.8871684
X-RAY DIFFRACTIONf_chiral_restr0.078676
X-RAY DIFFRACTIONf_plane_restr0.005775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9029-1.94170.27541330.24432382X-RAY DIFFRACTION94
1.9417-1.98390.2281210.21892530X-RAY DIFFRACTION98
1.9839-2.030.27081500.20962543X-RAY DIFFRACTION99
2.03-2.08070.24871250.18982554X-RAY DIFFRACTION100
2.0807-2.13690.25891260.18362573X-RAY DIFFRACTION100
2.1369-2.19970.2461420.18482586X-RAY DIFFRACTION100
2.1997-2.27060.26241220.1812560X-RAY DIFFRACTION100
2.2706-2.35160.2371630.17932552X-RAY DIFFRACTION99
2.3516-2.44560.22191530.18032569X-RAY DIFFRACTION100
2.4456-2.55670.24371530.17362562X-RAY DIFFRACTION100
2.5567-2.69120.22111240.17282601X-RAY DIFFRACTION100
2.6912-2.85940.22151350.17372586X-RAY DIFFRACTION99
2.8594-3.07940.20491460.17362591X-RAY DIFFRACTION100
3.0794-3.3880.20131340.16322616X-RAY DIFFRACTION100
3.388-3.87510.22191450.15132624X-RAY DIFFRACTION100
3.8751-4.87060.16981250.13922688X-RAY DIFFRACTION100
4.8706-19.99860.1721420.17932780X-RAY DIFFRACTION100

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