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- PDB-5tq0: Crystal structure of amino terminal domains of the NMDA receptor ... -

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Basic information

Entry
Database: PDB / ID: 5tq0
TitleCrystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in the presence of EDTA
Components
  • FAB, HEAVY CHAINFragment antigen-binding
  • FAB, LIGHT CHAINFragment antigen-binding
  • Glutamate receptor ionotropic, NMDA 2A
  • NMDA glutamate receptor subunitNMDA receptor
KeywordsTRANSPORT PROTEIN / ION CHANNEL / NMDA RECEPTOR / ALLOSTERIC MODULATION / ZINC INHIBITION / IMMUNE SYSTEM
Function / homologyCalmodulin-binding domain C0, NMDA receptor, NR1 subunit / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / N-methyl D-aspartate receptor 2B3 C-terminus / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Receptor family ligand binding region / Ligand-gated ion channel / Receptor, ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor ...Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / N-methyl D-aspartate receptor 2B3 C-terminus / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Receptor family ligand binding region / Ligand-gated ion channel / Receptor, ligand binding region / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Periplasmic binding protein-like I / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / response to ammonium ion / response to other organism / cellular response to lipid / ligand-gated ion channel activity involved in regulation of presynaptic membrane potential / cellular response to dsRNA / glutamate-gated calcium ion channel activity / neurotransmitter binding / calcium ion transmembrane import into cytosol / action potential / glutamate receptor binding / voltage-gated cation channel activity / cellular response to zinc ion / parallel fiber to Purkinje cell synapse / response to carbohydrate / cellular response to magnesium ion / NMDA glutamate receptor activity / glutamate binding / NMDA selective glutamate receptor complex / response to methylmercury / response to manganese ion / spinal cord development / postsynaptic density membrane / response to amine / response to light stimulus / excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / response to cocaine / response to fungicide / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / ionotropic glutamate receptor activity / cellular response to growth factor stimulus / long-term synaptic potentiation / ionotropic glutamate receptor signaling pathway / cellular response to amino acid stimulus / cell adhesion molecule binding / cellular response to manganese ion / positive regulation of cell death / cerebral cortex development / hippocampus development / integral component of presynaptic membrane / regulation of long-term neuronal synaptic plasticity / memory / presynaptic membrane / terminal bouton / rhythmic process / response to organic cyclic compound / response to calcium ion / protein heterotetramerization / response to zinc ion / postsynaptic membrane / protein tetramerization / chemical synaptic transmission / scaffold protein binding / ATPase binding / response to ethanol / dendritic spine / postsynaptic density / protein dimerization activity / protein-containing complex binding / cell junction / response to drug / synapse / neuron projection / glutamatergic synapse / signaling receptor binding / protein heterodimerization activity / protein kinase binding / integral component of plasma membrane / zinc ion binding / plasma membrane / metal ion binding / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A / Glutamate receptor ionotropic, NMDA 1
Function and homology information
Specimen sourceXenopus laevis (African clawed frog)
Rattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.7 Å resolution
AuthorsRomero-Hernandez, A. / Simorowski, N. / Karakas, E. / Furukawa, H.
Funding supportUnited States , 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental HealthMH085926United States
National Institutes of Health/National Institute of General Medical SciencesGM105730United States
CitationJournal: Neuron / Year: 2016
Title: Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain.
Authors: Romero-Hernandez, A. / Simorowski, N. / Karakas, E. / Furukawa, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 21, 2016 / Release: Dec 14, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 14, 2016Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelAuthor supporting evidence / Refinement descriptionpdbx_audit_support / software_pdbx_audit_support.funding_organization / _software.classification / _software.name
1.2May 16, 2018Structure modelData collection / Database referencescitation_citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NMDA glutamate receptor subunit
B: Glutamate receptor ionotropic, NMDA 2A
H: FAB, HEAVY CHAIN
L: FAB, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,77421
Polyers131,9354
Non-polymers1,83917
Water90150
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)9920
ΔGint (kcal/M)-169
Surface area (Å2)46080
Unit cell
γ
α
β
Length a, b, c (Å)79.980, 118.346, 156.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 4 types, 4 molecules ABHL

#1: Protein/peptide NMDA glutamate receptor subunit / NMDA receptor


Mass: 43801.043 Da / Num. of mol.: 1 / Fragment: residues 24-408 / Mutation: N38Q, N348Q / Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: grin1, NR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91977, UniProt: A0A1L8F5J9*PLUS
#2: Protein/peptide Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 40572.078 Da / Num. of mol.: 1 / Fragment: residues 34-393 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00959
#3: Protein/peptide FAB, HEAVY CHAIN / Fragment antigen-binding


Mass: 23993.883 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse)
#4: Protein/peptide FAB, LIGHT CHAIN / Fragment antigen-binding


Mass: 23568.025 Da / Num. of mol.: 1 / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 5 types, 67 molecules

#5: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Formula: C3H8O3 / Glycerol
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Formula: SO4 / Sulfate
#8: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Formula: C3H8O / Isopropyl alcohol
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Formula: H2O / Water

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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: 2.81 / Density percent sol: 56.19 %
Crystal growTemp: 291 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Ammonium sulfate, 2.5% Isopropanol

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Collection date: Apr 8, 2015
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionD resolution high: 2.7 Å / D resolution low: 50 Å / Number obs: 77929 / Rmerge I obs: 0.129 / NetI over sigmaI: 7.72 / Redundancy: 3.1 % / Percent possible obs: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data collection
PDB_EXTRACT3.20data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TPW
Overall SU ML: 0.39 / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 25.61 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 147.64 Å2 / B iso mean: 66.2492 Å2 / B iso min: 28.67 Å2
Least-squares processR factor R free: 0.2461 / R factor R work: 0.2084 / R factor obs: 0.2122 / Highest resolution: 2.7 Å / Lowest resolution: 47.569 Å / Number reflection R free: 7809 / Number reflection R work: 70120 / Number reflection obs: 77929 / Percent reflection R free: 10.02 / Percent reflection obs: 99.08
Refine hist #finalHighest resolution: 2.7 Å / Lowest resolution: 47.569 Å / B iso mean ligand: 92.05 / B iso mean solvent: 56.5 / Number residues total: 1118
Number of atoms included #finalProtein: 8197 / Nucleic acid: 0 / Ligand: 104 / Solvent: 50 / Total: 8351
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048484
X-RAY DIFFRACTIONf_angle_d0.64911602
X-RAY DIFFRACTIONf_chiral_restr0.0461351
X-RAY DIFFRACTIONf_plane_restr0.0041469
X-RAY DIFFRACTIONf_dihedral_angle_d11.8404942
Refine LS shell

Refine ID: X-RAY DIFFRACTION / Total number of bins used: 30

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.70000.39260.35702.73072532237249095.0000
2.73070.37130.34822.76282612337259898.0000
2.76280.33480.30502.79652822302258499.0000
2.79650.35210.30452.83192492353260299.0000
2.83190.33240.28112.86922542349260399.0000
2.86920.31200.28722.90852862299258599.0000
2.90850.31450.28372.95002812314259599.0000
2.95000.33430.28652.99402512267251898.0000
2.99400.29380.28473.04082842366265098.0000
3.04080.32870.27633.09062612297255899.0000
3.09060.30190.26573.14392582354261299.0000
3.14390.31520.24873.20112592411267099.0000
3.20110.28860.24033.262625723102567100.0000
3.26260.28750.24913.32922452397264299.0000
3.32920.27610.23883.401625523252580100.0000
3.40160.26730.23743.480726023682628100.0000
3.48070.28650.22433.567725423292583100.0000
3.56770.30330.22563.66412502373262399.0000
3.66410.25060.21143.77192642313257799.0000
3.77190.24630.19453.893626323262589100.0000
3.89360.23200.19254.03272662365263199.0000
4.03270.22080.17484.194125623562612100.0000
4.19410.18580.16354.384826123542615100.0000
4.38480.19240.16074.615826423662630100.0000
4.61580.19590.15744.90472532332258599.0000
4.90470.20500.17015.283024723832630100.0000
5.28300.21870.19225.813825823412599100.0000
5.81380.23280.20756.653125423762630100.0000
6.65310.22640.19408.37482582322258099.0000
8.37480.21710.186047.57662652298256398.0000

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