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- PDB-6uzw: Crystal structure of GLUN1/GLUN2A ligand-binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 6uzw
TitleCrystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and UBP791
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsMEMBRANE PROTEIN / NMDAR / ligand-binding domain / antagonist
Function / homology
Function and homology information


response to ammonium ion / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion ...response to ammonium ion / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / protein localization to postsynaptic membrane / dendritic branch / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / response to other organism / sleep / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity / locomotion / response to morphine / glutamate-gated calcium ion channel activity / cellular response to dsRNA / response to carbohydrate / regulation of monoatomic cation transmembrane transport / dendritic spine organization / cellular response to lipid / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / response to manganese ion / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / cellular response to zinc ion / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / male mating behavior / regulation of dendrite morphogenesis / regulation of axonogenesis / dopamine metabolic process / spinal cord development / suckling behavior / startle response / regulation of neuronal synaptic plasticity / response to amine / monoatomic cation transmembrane transport / regulation of NMDA receptor activity / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / response to light stimulus / excitatory synapse / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / positive regulation of dendritic spine maintenance / glutamate receptor binding / regulation of postsynaptic membrane potential / phosphatase binding / calcium ion homeostasis / cellular response to manganese ion / prepulse inhibition / long-term memory / regulation of neuron apoptotic process / glutamate-gated receptor activity / synaptic cleft / presynaptic active zone membrane / response to fungicide / monoatomic cation channel activity / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / cell adhesion molecule binding / neurogenesis / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / response to cocaine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / learning / long-term synaptic potentiation / hippocampus development / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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: 2.13 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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
B: Glutamate receptor ionotropic, NMDA 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5644
Polymers65,0382
Non-polymers5262
Water1,18966
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 area2280 Å2
ΔGint-6 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.374, 85.745, 119.873
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

#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: 31698.221 Da / Num. of mol.: 1
Fragment: ligand-binding domain (UNP residues 402-539,661-802)
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
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.57 %
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: 0.92013 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 9, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92013 Å / Relative weight: 1
ReflectionResolution: 2.13→69.74 Å / Num. obs: 26485 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 46.43 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.7
Reflection shellResolution: 2.52→2.56 Å / Rmerge(I) obs: 0.903 / Num. unique obs: 178

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
autoPROCdata processing
XDSdata processing
Aimlessdata scaling
pointlessdata processing
STARANISOdata processing
REFMACphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NF6

4nf6


Resolution: 2.13→69.74 Å / SU ML: 0.2719 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.7206
Details: Note: we used STARANISO; overall statistics as shown on collection statistics refer to data to 2.52 A resolution, but some anisotropic data went to 2.13 A which were included in the refinement
RfactorNum. reflection% reflection
Rfree0.2466 1335 5.04 %
Rwork0.1998 --
obs0.2023 26485 75.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.37 Å2
Refinement stepCycle: LAST / Resolution: 2.13→69.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 33 66 4512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544571
X-RAY DIFFRACTIONf_angle_d0.74366184
X-RAY DIFFRACTIONf_chiral_restr0.0472680
X-RAY DIFFRACTIONf_plane_restr0.0043790
X-RAY DIFFRACTIONf_dihedral_angle_d12.34492773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.20.3143120.2491166X-RAY DIFFRACTION5.18
2.2-2.290.2886290.2671728X-RAY DIFFRACTION21.97
2.29-2.40.3051960.26951656X-RAY DIFFRACTION50.81
2.4-2.520.32251320.26372509X-RAY DIFFRACTION75.83
2.52-2.680.2971600.26343240X-RAY DIFFRACTION97.67
2.68-2.890.32031600.2613299X-RAY DIFFRACTION99.88
2.89-3.180.29061720.23583338X-RAY DIFFRACTION99.94
3.18-3.640.24321870.20273330X-RAY DIFFRACTION99.91
3.64-4.580.211920.15843366X-RAY DIFFRACTION99.8
4.58-69.740.22691950.17823518X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: 15.3556806266 Å / Origin y: 14.7895537039 Å / Origin z: -35.5446108033 Å
111213212223313233
T0.223965716782 Å2-0.0203733007471 Å2-0.0215435869614 Å2-0.254108458282 Å20.0123671590826 Å2--0.390933434667 Å2
L0.558949413559 °2-0.196933325563 °2-0.434771188443 °2-1.10991319567 °2-0.0320657442954 °2--1.47512588023 °2
S-0.0101696278598 Å °-0.0788339814781 Å °-0.0182926507216 Å °0.0710871124718 Å °0.0010444725832 Å °0.0883780058323 Å °-0.0464717244209 Å °0.213262889596 Å °0.00675395948462 Å °
Refinement TLS groupSelection details: all

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