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- PDB-5tpw: Crystal structure of amino terminal domains of the NMDA receptor ... -

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Basic information

Entry
Database: PDB / ID: 5tpw
TitleCrystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at the GluN2A
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
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 / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / response to other organism ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / auditory behavior / response to other organism / protein localization to postsynaptic membrane / serotonin metabolic process / regulation of ARF protein signal transduction / cellular response to magnesium ion / positive regulation of inhibitory postsynaptic potential / response to methylmercury / response to manganese ion / sleep / response to carbohydrate / locomotion / regulation of NMDA receptor activity / dendritic spine organization / cellular response to dsRNA / cellular response to lipid / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / voltage-gated monoatomic cation channel activity / response to glycoside / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / glutamate receptor signaling pathway / response to zinc ion / calcium ion transmembrane import into cytosol / spinal cord development / response to amine / parallel fiber to Purkinje cell synapse / cellular response to zinc ion / startle response / monoatomic cation transmembrane transport / dopamine metabolic process / response to lithium ion / regulation of postsynaptic membrane potential / response to light stimulus / cellular response to glycine / modulation of excitatory postsynaptic potential / action potential / conditioned place preference / regulation of neuronal synaptic plasticity / positive regulation of protein targeting to membrane / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / neuron development / positive regulation of synaptic transmission, glutamatergic / multicellular organismal response to stress / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / glutamate-gated receptor activity / cell adhesion molecule binding / cellular response to manganese ion / glutamate-gated calcium ion channel activity / neurogenesis / dendrite membrane / sensory perception of pain / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / sodium ion transmembrane transport / protein tyrosine kinase binding / cytoplasmic vesicle membrane / synaptic membrane / response to amphetamine / learning / response to nicotine / regulation of membrane potential / response to cocaine / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / hippocampus development / cellular response to amino acid stimulus / protein catabolic process / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / response to calcium ion / cerebral cortex development / modulation of chemical synaptic transmission / negative regulation of protein catabolic process / regulation of synaptic plasticity / visual learning / calcium ion transmembrane transport / cellular response to growth factor stimulus / response to lead ion / response to wounding / calcium channel activity / memory / long-term synaptic potentiation / terminal bouton
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
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 / molecular replacement / Resolution: 2.909 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 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)132,94915
Polymers131,6814
Non-polymers1,26811
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9110 Å2
ΔGint-160 kcal/mol
Surface area45430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.560, 118.401, 155.812
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: 43546.734 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, 48 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.8M Ammonium sulfate 2.5% Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.2825 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 55256 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 26.14

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data collection
HKL-2000data reduction
PHENIXmodel building
PDB_EXTRACT3.2data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QEL

3qel


Resolution: 2.909→47.563 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 5481 9.92 %
Rwork0.1997 49775 -
obs0.2042 55256 88.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.42 Å2 / Biso mean: 48.9365 Å2 / Biso min: 6.89 Å2
Refinement stepCycle: final / Resolution: 2.909→47.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8248 0 71 39 8358
Biso mean--73.4 31.12 -
Num. residues----1110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038516
X-RAY DIFFRACTIONf_angle_d0.62211624
X-RAY DIFFRACTIONf_chiral_restr0.0461343
X-RAY DIFFRACTIONf_plane_restr0.0041479
X-RAY DIFFRACTIONf_dihedral_angle_d10.6344980
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 (%)
2.9088-2.94180.346690.330961468333
2.9418-2.97640.4125800.3345923100348
2.9764-3.01270.37371330.29551044117757
3.0127-3.05080.36741460.27071109125560
3.0508-3.0910.34471220.28071216133865
3.091-3.13330.30451580.26081306146470
3.1333-3.17810.34181550.2491439159475
3.1781-3.22550.27271540.26751481163580
3.2255-3.27590.28551650.2531598176385
3.2759-3.32960.34831880.24831706189490
3.3296-3.3870.31432160.24161745196194
3.387-3.44850.27851990.23141828202798
3.4485-3.51490.31491970.235218762073100
3.5149-3.58660.28552050.227819102115100
3.5866-3.66450.27892060.208418372043100
3.6645-3.74970.27052140.20718692083100
3.7497-3.84350.25912050.189318962101100
3.8435-3.94730.22392090.182718622071100
3.9473-4.06340.22012010.18719122113100
4.0634-4.19450.23182020.172318642066100
4.1945-4.34430.22542120.160818622074100
4.3443-4.51820.19442030.164218682071100
4.5182-4.72360.18292070.151419022109100
4.7236-4.97240.20052060.142718472053100
4.9724-5.28360.19641980.157619042102100
5.2836-5.69090.23372100.187518762086100
5.6909-6.26240.20732000.201418662066100
6.2624-7.1660.22562060.204318702076100
7.166-9.01830.20422090.180518722081100
9.0183-47.56890.21592060.201818732079100

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