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- PDB-5jty: Glutamate- and DCKA-bound GluN1/GluN2A agonist binding domains wi... -

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Basic information

Entry
Database: PDB / ID: 5jty
TitleGlutamate- and DCKA-bound GluN1/GluN2A agonist binding domains with MPX-007
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / RECEPTOR / NMDA receptor / Antagonist
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
4-hydroxy-5,7-dimethylquinoline-2-carboxylic acid / Chem-6ND / GLUTAMIC 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: 2.72 Å
AuthorsMou, T.-C. / Sprang, S.R. / Hansen, K.B.
CitationJournal: Neuron / Year: 2016
Title: Structural Basis for Negative Allosteric Modulation of GluN2A-Containing NMDA Receptors.
Authors: Yi, F. / Mou, T.C. / Dorsett, K.N. / Volkmann, R.A. / Menniti, F.S. / Sprang, S.R. / Hansen, K.B.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
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

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1,Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6915
Polymers64,8732
Non-polymers8183
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-6 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.569, 89.684, 130.415
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,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 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 (E. coli) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A,Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31533.053 Da / Num. of mol.: 1 / Fragment: unp residues 402-539; 661-800
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, 84 molecules

#3: Chemical ChemComp-2JK / 4-hydroxy-5,7-dimethylquinoline-2-carboxylic acid


Mass: 217.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H11NO3
#4: Chemical ChemComp-6ND / 5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide


Mass: 453.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17F2N5O3S2
#5: Chemical ChemComp-GLU / GLUTAMIC ACID / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / ...GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / hNR2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H9NO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsThe sequence corresponds to the NCBI Reference Sequence NP_036705.3 for GluN2A. residue Thr242 in ...The sequence corresponds to the NCBI Reference Sequence NP_036705.3 for GluN2A. residue Thr242 in this sequence is a Ser758 in Swiss-Prot Q00959.

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 22, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→14.973 Å / Num. obs: 15868 / % possible obs: 89.7 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.7
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.2 / % possible all: 76.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I57

5i57


Resolution: 2.72→14.973 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 28.25
RfactorNum. reflection% reflection
Rfree0.2782 1587 10 %
Rwork0.2241 --
obs0.2296 15867 89.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.72→14.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4312 0 30 81 4423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024447
X-RAY DIFFRACTIONf_angle_d0.4886011
X-RAY DIFFRACTIONf_dihedral_angle_d16.5012660
X-RAY DIFFRACTIONf_chiral_restr0.042662
X-RAY DIFFRACTIONf_plane_restr0.004762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7201-2.80730.3741180.32441073X-RAY DIFFRACTION77
2.8073-2.9070.38731340.31781206X-RAY DIFFRACTION84
2.907-3.02240.36011400.32041258X-RAY DIFFRACTION88
3.0224-3.15880.35761350.29771215X-RAY DIFFRACTION85
3.1588-3.32360.31971440.26871293X-RAY DIFFRACTION91
3.3236-3.52930.30541500.24541354X-RAY DIFFRACTION94
3.5293-3.79760.29371500.21231343X-RAY DIFFRACTION93
3.7976-4.17230.24051520.19331364X-RAY DIFFRACTION94
4.1723-4.7590.23971480.17141340X-RAY DIFFRACTION92
4.759-5.93310.24121560.18191397X-RAY DIFFRACTION95
5.9331-14.97330.21351600.18511437X-RAY DIFFRACTION93

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