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- PDB-5i56: Agonist-bound GluN1/GluN2A agonist binding domains with TCN201 -

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Basic information

Entry
Database: PDB / ID: 5i56
TitleAgonist-bound GluN1/GluN2A agonist binding domains with TCN201
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / RECEPTOR / NMDA receptor / Antagonist
Function / homology
Function and homology information


regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide ...regulation of response to alcohol / response to ammonium ion / neurotransmitter receptor transport, plasma membrane to endosome / receptor recycling / response to environmental enrichment / directional locomotion / pons maturation / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / regulation of cell communication / auditory behavior / positive regulation of Schwann cell migration / olfactory learning / response to other organism / cellular response to magnesium ion / dendritic branch / conditioned taste aversion / regulation of respiratory gaseous exchange / response to methylmercury / protein localization to postsynaptic membrane / serotonin metabolic process / regulation of ARF protein signal transduction / response to manganese ion / transmitter-gated monoatomic ion channel activity / suckling behavior / positive regulation of inhibitory postsynaptic potential / response to carbohydrate / sleep / cellular response to dsRNA / propylene metabolic process / response to glycine / cellular response to lipid / regulation of NMDA receptor activity / dendritic spine organization / locomotion / RAF/MAP kinase cascade / response to amine / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / response to glycoside / NMDA selective glutamate receptor complex / voltage-gated monoatomic cation channel activity / glutamate binding / neurotransmitter receptor complex / ligand-gated sodium channel activity / glutamate receptor signaling pathway / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / response to morphine / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / regulation of synapse assembly / spinal cord development / glycine binding / startle response / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / dopamine metabolic process / parallel fiber to Purkinje cell synapse / response to lithium ion / monoatomic cation transmembrane transport / monoatomic ion channel complex / regulation of postsynaptic membrane potential / positive regulation of calcium ion transport into cytosol / cellular response to glycine / response to light stimulus / action potential / modulation of excitatory postsynaptic potential / associative learning / positive regulation of dendritic spine maintenance / ligand-gated monoatomic ion channel activity / conditioned place preference / regulation of neuronal synaptic plasticity / social behavior / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of protein targeting to membrane / monoatomic cation transport / glutamate receptor binding / prepulse inhibition / long-term memory / neuron development / multicellular organismal response to stress / positive regulation of synaptic transmission, glutamatergic / phosphatase binding / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / synaptic cleft / calcium ion homeostasis / glutamate-gated receptor activity / cellular response to manganese ion / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / neurogenesis / cell adhesion molecule binding
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. / Periplasmic binding protein-like II / Receptor, ligand binding region / Receptor family ligand binding region / D-Maltodextrin-Binding Protein; domain 2 / Periplasmic binding protein-like I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-67P / 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: 2.28 Å
AuthorsMou, T.-C. / Sprang, S.R. / Hansen, K.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103546 United States
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Structural basis for negative allosteric modulation of GluN2A-containing NMDA receptors
Authors: Yi, F. / Mou, T.-C. / Dorsett, K.N. / Sprang, S.R. / Hansen, K.B.
History
DepositionFeb 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 1.6Nov 6, 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)65,5575
Polymers64,8732
Non-polymers6843
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-6 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.259, 88.402, 126.146
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
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
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, 179 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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-67P / N-({4-[2-(benzenecarbonyl)hydrazinecarbonyl]phenyl}methyl)-3-chloro-4-fluorobenzene-1-sulfonamide


Mass: 461.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17ClFN3O4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.33 Å3/Da / Density % sol: 47.63 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.278→20.032 Å / Num. obs: 27522 / % possible obs: 96.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 34.61 Å2 / Rsym value: 0.1 / Net I/σ(I): 10.42
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.49 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NF8

4nf8


Resolution: 2.28→20.03 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.239 2000 7.27 %
Rwork0.184 --
obs0.188 27513 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.28→20.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4503 0 45 176 4724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044676
X-RAY DIFFRACTIONf_angle_d0.8446316
X-RAY DIFFRACTIONf_dihedral_angle_d14.921744
X-RAY DIFFRACTIONf_chiral_restr0.032693
X-RAY DIFFRACTIONf_plane_restr0.003814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2775-2.33440.32121310.2291679X-RAY DIFFRACTION89
2.3344-2.39740.31731410.22721793X-RAY DIFFRACTION98
2.3974-2.46780.27621430.21111830X-RAY DIFFRACTION98
2.4678-2.54730.27911410.20721793X-RAY DIFFRACTION97
2.5473-2.63820.27111400.21131786X-RAY DIFFRACTION96
2.6382-2.74360.29711440.20631835X-RAY DIFFRACTION98
2.7436-2.86810.24851460.20861861X-RAY DIFFRACTION99
2.8681-3.01880.30491460.20961861X-RAY DIFFRACTION100
3.0188-3.20720.25651460.20081874X-RAY DIFFRACTION100
3.2072-3.45370.25281470.19651868X-RAY DIFFRACTION100
3.4537-3.79910.24151200.19661522X-RAY DIFFRACTION80
3.7991-4.3440.20311480.15951889X-RAY DIFFRACTION99
4.344-5.45460.19541510.14851937X-RAY DIFFRACTION99
5.4546-20.03240.19461560.15971985X-RAY DIFFRACTION99

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