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- PDB-4kfq: Crystal structure of the NMDA receptor GluN1 ligand binding domai... -

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Basic information

Entry
Database: PDB / ID: 4kfq
TitleCrystal structure of the NMDA receptor GluN1 ligand binding domain in complex with 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one
ComponentsGlutamate receptor ionotropic, NMDA 1
KeywordsMEMBRANE PROTEIN / ligand binding domain / Ionotropic Glutamate Receptor
Function / homology
Function and homology information


pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane ...pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / response to glycine / propylene metabolic process / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / glutamate binding / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / regulation of synapse assembly / male mating behavior / glycine binding / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / suckling behavior / response to amine / startle response / social behavior / monoatomic cation transmembrane transport / associative learning / regulation of neuronal synaptic plasticity / cellular response to glycine / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / 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 / glutamate receptor binding / synaptic cleft / prepulse inhibition / phosphatase binding / monoatomic cation channel activity / glutamate-gated receptor activity / calcium ion homeostasis / response to fungicide / regulation of neuron apoptotic process / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / sensory perception of pain / sodium ion transmembrane transport / response to amphetamine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / learning / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / terminal bouton / : / visual learning / cerebral cortex development / calcium ion transmembrane transport / regulation of synaptic plasticity / calcium channel activity / memory / neuron cellular homeostasis / intracellular calcium ion homeostasis / synaptic vesicle membrane / response to calcium ion / calcium ion transport / rhythmic process / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / protein-containing complex assembly / chemical synaptic transmission / dendritic spine / negative regulation of neuron apoptotic process
Similarity search - Function
: / : / 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. ...: / : / 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-KFQ / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSteffensen, T.B. / Tabrizi, F.M. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Crystal structure and pharmacological characterization of a novel N-methyl-D-aspartate (NMDA) receptor antagonist at the GluN1 glycine binding site.
Authors: Kvist, T. / Steffensen, T.B. / Greenwood, J.R. / Mehrzad Tabrizi, F. / Hansen, K.B. / Gajhede, M. / Pickering, D.S. / Traynelis, S.F. / Kastrup, J.S. / Brauner-Osborne, H.
#1: Journal: Embo J. / Year: 2003
Title: Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA RECEPTOR NR1 ligand-binding core
Authors: Furukawa, H. / Gouaux, E.
History
DepositionApr 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references / Structure summary
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,54330
Polymers66,6802
Non-polymers2,86328
Water7,458414
1
A: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77115
Polymers33,3401
Non-polymers1,43114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,77115
Polymers33,3401
Non-polymers1,43114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.950, 78.590, 109.630
Angle α, β, γ (deg.)90.00, 94.21, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / Fragment: UNP residues 394-554, 663-800
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (394-554, 663-800)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, GRIN1 OR NMDAR1, Nmdar1 / Plasmid: pET22c / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P35439
#2: Chemical ChemComp-KFQ / 1-sulfanyl[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one


Mass: 218.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6N4OS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight. 0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG ...Details: 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight. 0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.2→39.69 Å / Num. all: 37896 / Num. obs: 37846 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5498 / Rsym value: 0.392 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PBQ

1pbq


Resolution: 2.2→39.69 Å / SU ML: 0.62 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 1890 4.99 %RANDOM
Rwork0.1739 ---
obs0.1768 37839 99.9 %-
all-37896 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.896 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--3.3764 Å2-0 Å20.2882 Å2
2---1.2115 Å20 Å2
3---4.5879 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 178 414 5171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074858
X-RAY DIFFRACTIONf_angle_d1.026531
X-RAY DIFFRACTIONf_dihedral_angle_d15.3891843
X-RAY DIFFRACTIONf_chiral_restr0.069689
X-RAY DIFFRACTIONf_plane_restr0.004820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2-2.25950.29381250.215827382738100
2.2595-2.3260.26291460.201127782778100
2.326-2.40110.26181310.195327532753100
2.4011-2.48690.28781500.195227292729100
2.4869-2.58640.25351440.187827882788100
2.5864-2.70410.2371630.178827302730100
2.7041-2.84660.25391370.178727622762100
2.8466-3.02490.25741640.177527572757100
3.0249-3.25840.24221290.169927722772100
3.2584-3.58610.21531430.156928002800100
3.5861-4.10450.20531500.150527592759100
4.1045-5.16950.19111490.146227722772100
5.1695-39.690.21831590.22811281199

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