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- PDB-6uzx: Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain... -

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Basic information

Entry
Database: PDB / ID: 6uzx
TitleCrystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and UBP791
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsMEMBRANE PROTEIN / NMDAR / ligand-binding domain / 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 / pons maturation / response to environmental enrichment / 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 / pons maturation / response to environmental enrichment / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / auditory behavior / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / olfactory learning / conditioned taste aversion / dendritic branch / response to hydrogen sulfide / regulation of respiratory gaseous exchange / response to other organism / positive regulation of inhibitory postsynaptic potential / protein localization to postsynaptic membrane / cellular response to magnesium ion / regulation of ARF protein signal transduction / response to methylmercury / transmitter-gated monoatomic ion channel activity / conditioned place preference / locomotion / response to glycine / propylene metabolic process / dendritic spine organization / response to carbohydrate / regulation of NMDA receptor activity / sleep / cellular response to dsRNA / cellular response to lipid / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / response to manganese ion / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / cellular response to zinc ion / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / glutamate receptor signaling pathway / glutamate binding / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / regulation of synapse assembly / male mating behavior / glycine binding / spinal cord development / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / suckling behavior / regulation of postsynaptic membrane potential / response to amine / startle response / dopamine metabolic process / social behavior / monoatomic cation transmembrane transport / response to lithium ion / associative learning / modulation of excitatory postsynaptic potential / regulation of neuronal synaptic plasticity / action potential / cellular response to glycine / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / response to light stimulus / positive regulation of protein targeting to membrane / 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 / postsynaptic density, intracellular component / glutamate receptor binding / neuron development / synaptic cleft / prepulse inhibition / multicellular organismal response to stress / phosphatase binding / monoatomic cation channel activity / glutamate-gated receptor activity / calcium ion homeostasis / response to fungicide / cell adhesion molecule binding / regulation of neuron apoptotic process / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / neurogenesis / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential
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
GLYCINE / Chem-QM4 / 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: 2.41 Å
AuthorsWang, J.X. / Furukawa, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis of subtype-selective competitive antagonism for GluN2C/2D-containing NMDA receptors.
Authors: Wang, J.X. / Irvine, M.W. / Burnell, E.S. / Sapkota, K. / Thatcher, R.J. / Li, M. / Simorowski, N. / Volianskis, A. / Collingridge, G.L. / Monaghan, D.T. / Jane, D.E. / Furukawa, H.
History
DepositionNov 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 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

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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)65,9086
Polymers65,1992
Non-polymers7104
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Full-length NMDAR available, showed the same assembly of LBD dimers (dimer of dimer structure)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-7 kcal/mol
Surface area25420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.987, 85.081, 120.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: ligand-binding domain (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 BL21(DE3) (bacteria) / Strain (production host): OrigamiB (DE3) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NR2A


Mass: 31858.482 Da / Num. of mol.: 1
Fragment: ligand-binding domain (UNP residues 402-539,661-802)
Mutation: A414R, K738M, G740R, R741K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): OrigamiB (DE3) / References: UniProt: Q00959

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Non-polymers , 4 types, 119 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-QM4 / (2S,3R)-1-[7-(2-carboxyethyl)phenanthrene-2-carbonyl]piperazine-2,3-dicarboxylic acid


Mass: 450.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H22N2O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 23, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.41→49.15 Å / Num. obs: 23716 / % possible obs: 98.03 % / Redundancy: 5.8 % / Biso Wilson estimate: 37.84 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 11.6
Reflection shellResolution: 2.41→2.49 Å / Rmerge(I) obs: 0.668 / Num. unique obs: 1995

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Processing

Software
NameVersionClassification
HKL-2000data processing
REFMACphasing
PHENIX1.13_2998refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NF6

4nf6


Resolution: 2.41→49.15 Å / SU ML: 0.303 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5749
RfactorNum. reflection% reflection
Rfree0.2453 1178 4.97 %
Rwork0.1914 --
obs0.1941 23716 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.85 Å2
Refinement stepCycle: LAST / Resolution: 2.41→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 50 115 4565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194600
X-RAY DIFFRACTIONf_angle_d0.47776228
X-RAY DIFFRACTIONf_chiral_restr0.0415687
X-RAY DIFFRACTIONf_plane_restr0.003796
X-RAY DIFFRACTIONf_dihedral_angle_d12.11592800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.520.33111170.24782438X-RAY DIFFRACTION86.11
2.52-2.650.30491360.23672781X-RAY DIFFRACTION98.08
2.65-2.810.30031410.22892842X-RAY DIFFRACTION99.97
2.81-3.030.30611380.23782842X-RAY DIFFRACTION100
3.03-3.340.27421590.21182839X-RAY DIFFRACTION100
3.34-3.820.24521430.18182881X-RAY DIFFRACTION100
3.82-4.810.2031750.15032887X-RAY DIFFRACTION100
4.81-49.150.20931690.17663028X-RAY DIFFRACTION99.88
Refinement TLS params.Method: refined / Origin x: 15.1461432142 Å / Origin y: 14.85909994 Å / Origin z: -35.7443282716 Å
111213212223313233
T0.18781574583 Å2-0.023010909571 Å2-0.0228043911168 Å2-0.200135371565 Å20.0216663406992 Å2--0.300870823179 Å2
L0.657436070797 °2-0.234364092475 °2-0.53682776822 °2-0.891135750242 °20.0556518755235 °2--1.65327233727 °2
S0.0092532231883 Å °-0.0893668765851 Å °0.0418465385273 Å °0.0105865816703 Å °0.0117473568602 Å °0.0586133182298 Å °-0.0137640210662 Å °0.246723484859 Å °0.000133034971008 Å °
Refinement TLS groupSelection details: all

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