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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 CHAIN
  • FAB, LIGHT CHAIN
  • Glutamate receptor ionotropic, NMDA 2A
  • NMDA glutamate receptor subunit
KeywordsTRANSPORT PROTEIN / ION CHANNEL / NMDA RECEPTOR / ALLOSTERIC MODULATION / ZINC INHIBITION / IMMUNE SYSTEM
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 / response to environmental enrichment / auditory behavior / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / response to hydrogen sulfide ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / auditory behavior / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / response to hydrogen sulfide / 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 / conditioned place preference / locomotion / 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 / voltage-gated monoatomic cation channel activity / response to manganese ion / NMDA selective glutamate receptor complex / cellular response to zinc ion / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / glutamate receptor signaling pathway / glutamate binding / response to zinc ion / spinal cord development / parallel fiber to Purkinje cell synapse / regulation of postsynaptic membrane potential / response to amine / startle response / dopamine metabolic process / monoatomic cation transmembrane transport / response to lithium ion / modulation of excitatory postsynaptic potential / regulation of neuronal synaptic plasticity / action potential / cellular response to glycine / positive regulation of excitatory postsynaptic potential / response to light stimulus / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to manganese ion / postsynaptic density, intracellular component / glutamate receptor binding / neuron development / multicellular organismal response to stress / monoatomic cation channel activity / glutamate-gated receptor activity / response to fungicide / cell adhesion molecule binding / glutamate-gated calcium ion channel activity / neurogenesis / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / sensory perception of pain / sodium ion transmembrane transport / response to amphetamine / ionotropic glutamate receptor signaling pathway / cytoplasmic vesicle membrane / positive regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / hippocampus development / learning / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / cellular response to amino acid stimulus / response to nicotine / response to cocaine / regulation of long-term neuronal synaptic plasticity / synaptic membrane / modulation of chemical synaptic transmission / response to lead ion / protein catabolic process / postsynaptic density membrane / terminal bouton / : / visual learning / cellular response to growth factor stimulus / negative regulation of protein catabolic process / cerebral cortex development / calcium ion transmembrane transport / regulation of synaptic plasticity / calcium channel activity / memory / response to wounding / long-term synaptic potentiation / response to calcium ion
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Response regulator / 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 / : / : / Response regulator / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Rattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRomero-Hernandez, A. / Simorowski, N. / Karakas, E. / Furukawa, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105730 United 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.
History
DepositionOct 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification / _software.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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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
Polymers131,9354
Non-polymers1,83917
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-169 kcal/mol
Surface area46080 Å2
Unit cell
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-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein NMDA glutamate receptor subunit


Mass: 43801.043 Da / Num. of mol.: 1 / Fragment: residues 24-408 / Mutation: N38Q, N348Q
Source method: isolated from a genetically manipulated source
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 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 method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00959

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Antibody , 2 types, 2 molecules HL

#3: Antibody FAB, HEAVY CHAIN


Mass: 23993.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Antibody FAB, LIGHT CHAIN


Mass: 23568.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 1 types, 2 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 65 molecules

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


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


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


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 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 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 77929 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 7.72

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data collection
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TPW

5tpw


Resolution: 2.7→47.569 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2461 7809 10.02 %
Rwork0.2084 70120 -
obs0.2122 77929 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.64 Å2 / Biso mean: 66.2492 Å2 / Biso min: 28.67 Å2
Refinement stepCycle: final / Resolution: 2.7→47.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8197 0 104 50 8351
Biso mean--92.05 56.5 -
Num. residues----1118
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_d11.844942
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.73070.39262530.3572237249095
2.7307-2.76280.37132610.34822337259898
2.7628-2.79650.33482820.3052302258499
2.7965-2.83190.35212490.30452353260299
2.8319-2.86920.33242540.28112349260399
2.8692-2.90850.3122860.28722299258599
2.9085-2.950.31452810.28372314259599
2.95-2.9940.33432510.28652267251898
2.994-3.04080.29382840.28472366265098
3.0408-3.09060.32872610.27632297255899
3.0906-3.14390.30192580.26572354261299
3.1439-3.20110.31522590.24872411267099
3.2011-3.26260.28862570.240323102567100
3.2626-3.32920.28752450.24912397264299
3.3292-3.40160.27612550.238823252580100
3.4016-3.48070.26732600.237423682628100
3.4807-3.56770.28652540.224323292583100
3.5677-3.66410.30332500.22562373262399
3.6641-3.77190.25062640.21142313257799
3.7719-3.89360.24632630.194523262589100
3.8936-4.03270.2322660.19252365263199
4.0327-4.19410.22082560.174823562612100
4.1941-4.38480.18582610.163523542615100
4.3848-4.61580.19242640.160723662630100
4.6158-4.90470.19592530.15742332258599
4.9047-5.2830.2052470.170123832630100
5.283-5.81380.21872580.192223412599100
5.8138-6.65310.23282540.207523762630100
6.6531-8.37480.22642580.1942322258099
8.3748-47.57660.21712650.1862298256398

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