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- PDB-9da9: Crystal structure of GluN1/GluN2A agonist-binding domains in comp... -

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Basic information

Entry
Database: PDB / ID: 9da9
TitleCrystal structure of GluN1/GluN2A agonist-binding domains in complex with 7CKA and glutamate
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsSIGNALING PROTEIN / Glutamate receptor Ligand-gated ion channel Neurotransmitter receptor Synaptic transmission Neuropharmacology
Function / homology
Function and homology information


Assembly and cell surface presentation of NMDA receptors / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / RAF/MAP kinase cascade / neurotransmitter receptor complex ...Assembly and cell surface presentation of NMDA receptors / Synaptic adhesion-like molecules / EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / RAF/MAP kinase cascade / neurotransmitter receptor complex / directional locomotion / pons maturation / response to environmental enrichment / regulation of cell communication / auditory behavior / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / olfactory learning / conditioned taste aversion / response to hydrogen sulfide / regulation of respiratory gaseous exchange / positive regulation of inhibitory postsynaptic potential / response to other organism / protein localization to postsynaptic membrane / cellular response to magnesium ion / regulation of ARF protein signal transduction / response to methylmercury / conditioned place preference / locomotion / dendritic spine organization / propylene metabolic process / response to carbohydrate / sleep / regulation of NMDA receptor activity / cellular response to dsRNA / cellular response to lipid / voltage-gated monoatomic cation channel activity / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / response to manganese ion / NMDA selective glutamate receptor complex / cellular response to zinc ion / ligand-gated sodium channel activity / response to morphine / glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / glutamate binding / regulation of axonogenesis / neuromuscular process / protein heterotetramerization / male mating behavior / regulation of dendrite morphogenesis / regulation of synapse assembly / transport vesicle membrane / spinal cord development / glycine binding / parallel fiber to Purkinje cell synapse / suckling behavior / response to amine / startle response / dopamine metabolic process / social behavior / modulation of excitatory postsynaptic potential / response to lithium ion / associative learning / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / monoatomic cation transport / response to light stimulus / cellular response to glycine / positive regulation of excitatory postsynaptic potential / action potential / positive regulation of protein targeting to membrane / regulation of postsynaptic membrane potential / 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 / multicellular organismal response to stress / prepulse inhibition / monoatomic cation channel activity / calcium ion homeostasis / glutamate-gated receptor activity / response to fungicide / cell adhesion molecule binding / regulation of neuron apoptotic process / dendrite membrane / glutamate-gated calcium ion channel activity / sensory perception of pain / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoplasmic vesicle membrane / response to amphetamine / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / adult locomotory behavior
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 I
Similarity search - Domain/homology
7-Chlorokynurenic acid / GLUTAMIC ACID / 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: 2.05 Å
AuthorsBosco, J. / Yates-Hansen, C.K. / McClelland, L.J. / Voronina, E. / Hansen, K.B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS097536 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS116055 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM140963 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109053 United States
CitationJournal: Sci Rep / Year: 2025
Title: A galactose-based auto-expression system improves T7-inducible protein production in Escherichia coli.
Authors: Bosco, J. / Gagliano, E. / Boshae, K.L. / Statz, J.P. / Wheeler, T.B. / Cuello, D. / Sliter, A. / Newby, C. / Lin, B. / Demeler, A. / Pierpont, C.L. / Yates-Hansen, C. / Sydor, M.J. / ...Authors: Bosco, J. / Gagliano, E. / Boshae, K.L. / Statz, J.P. / Wheeler, T.B. / Cuello, D. / Sliter, A. / Newby, C. / Lin, B. / Demeler, A. / Pierpont, C.L. / Yates-Hansen, C. / Sydor, M.J. / Ferrini, M.E. / Kuch, K.C. / Cooper, B.S. / Piggott, B.J. / Certel, S.J. / Hansen, K.B. / Sprang, S.R. / Bowler, B. / McClelland, L. / Berkmen, M. / Voronina, E.
History
DepositionAug 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 16, 2025Group: Database references / Category: struct_ref / Item: _struct_ref.db_code

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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)65,4964
Polymers65,1252
Non-polymers3712
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.244, 87.338, 135.896
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Glurz1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35438
#2: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / ...GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NMDAR2A / NR2A


Mass: 31785.299 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
#3: Chemical ChemComp-CKA / 7-Chlorokynurenic acid / 7-CKA


Mass: 223.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6ClNO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant, antagonist*YM
#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.: 202 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium acetate and 14-18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.05→33.97 Å / Num. obs: 41091 / % possible obs: 99.37 % / Redundancy: 8.1 % / Biso Wilson estimate: 37.34 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1023 / Rpim(I) all: 0.03707 / Rrim(I) all: 0.1091 / Net I/σ(I): 7.87
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.086 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 3954 / CC1/2: 0.519 / CC star: 0.826 / Rpim(I) all: 0.5283 / Rrim(I) all: 1.217 / % possible all: 97.49

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→33.97 Å / SU ML: 0.2435 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2281 2055 5 %
Rwork0.1679 39011 -
obs0.1709 41066 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.8 Å2
Refinement stepCycle: LAST / Resolution: 2.05→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4459 0 25 202 4686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01244686
X-RAY DIFFRACTIONf_angle_d1.13216344
X-RAY DIFFRACTIONf_chiral_restr0.063694
X-RAY DIFFRACTIONf_plane_restr0.0096820
X-RAY DIFFRACTIONf_dihedral_angle_d6.249636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.35071290.27872485X-RAY DIFFRACTION96.46
2.1-2.150.33541170.24822579X-RAY DIFFRACTION99.7
2.15-2.210.29071380.22432542X-RAY DIFFRACTION99.7
2.21-2.270.26151580.2032583X-RAY DIFFRACTION100
2.27-2.350.2621300.19082595X-RAY DIFFRACTION99.96
2.35-2.430.26671360.18762576X-RAY DIFFRACTION99.96
2.43-2.530.27051490.18992533X-RAY DIFFRACTION98.49
2.53-2.640.27041490.18952585X-RAY DIFFRACTION99.96
2.64-2.780.24111510.17542584X-RAY DIFFRACTION99.89
2.78-2.960.23791320.17752600X-RAY DIFFRACTION99.85
2.96-3.180.28021210.19282652X-RAY DIFFRACTION99.96
3.18-3.50.26451210.17482624X-RAY DIFFRACTION99.89
3.5-4.010.22711300.15522611X-RAY DIFFRACTION98.31
4.01-5.050.17991270.12492703X-RAY DIFFRACTION100
5.05-33.970.171670.15022759X-RAY DIFFRACTION98.99

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