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- PDB-6uz6: Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain... -

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Basic information

Entry
Database: PDB / ID: 6uz6
TitleCrystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and glutamate
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsMEMBRANE PROTEIN / NMDAR / ligand-binding domain / agonist
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 / auditory behavior ...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 / auditory behavior / positive regulation of Schwann cell migration / regulation of cell communication / cellular response to magnesium ion / olfactory learning / response to other organism / response to hydrogen sulfide / serotonin metabolic process / dendritic branch / conditioned taste aversion / response to methylmercury / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / regulation of respiratory gaseous exchange / response to manganese ion / transmitter-gated monoatomic ion channel activity / suckling behavior / sleep / positive regulation of inhibitory postsynaptic potential / regulation of NMDA receptor activity / response to carbohydrate / cellular response to lipid / propylene metabolic process / response to glycine / dendritic spine organization / locomotion / cellular response to dsRNA / RAF/MAP kinase cascade / response to amine / neurotransmitter receptor complex / Synaptic adhesion-like molecules / response to glycoside / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / glutamate binding / glutamate receptor signaling pathway / ligand-gated sodium channel activity / neuromuscular process / regulation of axonogenesis / calcium ion transmembrane import into cytosol / regulation of dendrite morphogenesis / male mating behavior / regulation of synapse assembly / protein heterotetramerization / response to morphine / spinal cord development / glycine binding / startle response / dopamine metabolic process / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / response to lithium ion / parallel fiber to Purkinje cell synapse / monoatomic ion channel complex / regulation of postsynaptic membrane potential / monoatomic cation transmembrane transport / action potential / positive regulation of calcium ion transport into cytosol / modulation of excitatory postsynaptic potential / cellular response to glycine / associative learning / positive regulation of dendritic spine maintenance / response to light stimulus / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / regulation of neuronal synaptic plasticity / monoatomic cation transport / glutamate receptor binding / conditioned place preference / social behavior / ligand-gated monoatomic ion channel activity / multicellular organismal response to stress / neuron development / phosphatase binding / long-term memory / prepulse inhibition / postsynaptic density, intracellular component / monoatomic cation channel activity / synaptic cleft / response to fungicide / calcium ion homeostasis / cellular response to manganese ion / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule binding / neurogenesis / excitatory synapse
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 / 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 / : / : / 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. / 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
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: 1.66 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 14, 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
Revision 1.3Oct 16, 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)65,1684
Polymers64,9462
Non-polymers2222
Water10,935607
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 area2180 Å2
ΔGint-5 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.635, 90.063, 125.151
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: 31606.236 Da / Num. of mol.: 1
Fragment: ligand-binding domain (UNP residues 402-539,661-800)
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
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48.01 % / Description: long rod-shaped crystals
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: Apr 18, 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: 1.66→73.1 Å / Num. obs: 71406 / % possible obs: 96.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.21 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 3.9 % / Num. unique obs: 5481 / CC1/2: 0.515

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Processing

Software
NameVersionClassification
autoPROCdata collection
XDSdata reduction
PHENIX1.13_2998refinement
Aimlessdata scaling
pointlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NF8

4nf8


Resolution: 1.66→50.07 Å / SU ML: 0.1746 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.333
RfactorNum. reflection% reflection
Rfree0.2118 3628 5.08 %
Rwork0.1794 --
obs0.1811 71406 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.05 Å2
Refinement stepCycle: LAST / Resolution: 1.66→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 15 607 5119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924676
X-RAY DIFFRACTIONf_angle_d0.99686335
X-RAY DIFFRACTIONf_chiral_restr0.0664701
X-RAY DIFFRACTIONf_plane_restr0.0068815
X-RAY DIFFRACTIONf_dihedral_angle_d13.89752854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.23871060.20191915X-RAY DIFFRACTION72.08
1.68-1.70.2391980.20972049X-RAY DIFFRACTION75.33
1.7-1.730.25621080.20072131X-RAY DIFFRACTION80.6
1.73-1.750.21781150.20582322X-RAY DIFFRACTION86.3
1.75-1.780.2171320.20292515X-RAY DIFFRACTION94.4
1.78-1.810.25251570.21472613X-RAY DIFFRACTION98.58
1.81-1.840.2521290.1952662X-RAY DIFFRACTION98.83
1.84-1.870.24471530.19832656X-RAY DIFFRACTION100
1.87-1.910.22131460.18742682X-RAY DIFFRACTION99.96
1.91-1.950.19691280.17912707X-RAY DIFFRACTION99.96
1.95-1.990.22551450.18872655X-RAY DIFFRACTION100
1.99-2.040.20881550.18352658X-RAY DIFFRACTION100
2.04-2.090.23981520.1862696X-RAY DIFFRACTION100
2.09-2.140.22861390.18692690X-RAY DIFFRACTION100
2.14-2.210.22341500.18242702X-RAY DIFFRACTION100
2.21-2.280.20591460.18642675X-RAY DIFFRACTION100
2.28-2.360.25291170.18332720X-RAY DIFFRACTION100
2.36-2.460.22961620.18442673X-RAY DIFFRACTION99.96
2.46-2.570.23961330.19412729X-RAY DIFFRACTION99.97
2.57-2.70.23211210.19432716X-RAY DIFFRACTION99.86
2.7-2.870.22731450.18842734X-RAY DIFFRACTION100
2.87-3.090.21811490.19712721X-RAY DIFFRACTION100
3.09-3.40.2191650.1792726X-RAY DIFFRACTION100
3.4-3.90.18881550.16362752X-RAY DIFFRACTION99.97
3.9-4.910.17341560.13972769X-RAY DIFFRACTION99.86
4.91-50.070.19181660.17862910X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: 40.641021733 Å / Origin y: 75.7939187105 Å / Origin z: 25.8618815501 Å
111213212223313233
T0.120877267696 Å20.011177973847 Å2-0.00993028708522 Å2-0.120861570207 Å2-0.0121694689064 Å2--0.1350322277 Å2
L0.488895915089 °20.0276130656443 °20.345632831137 °2-0.334070916736 °20.115681141885 °2--0.766871497565 °2
S-0.0476689282065 Å °-0.0529783100083 Å °0.0543292491198 Å °0.0262555929198 Å °0.0362754184958 Å °-0.0700900186789 Å °-0.0684946246588 Å °-0.0494018452899 Å °-0.00479742315588 Å °
Refinement TLS groupSelection details: all

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