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

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Basic information

Entry
Database: PDB / ID: 5tpz
TitleCrystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in apo closed state
Components
  • Glutamate receptor ionotropic, NMDA 2B
  • NMDA glutamate receptor subunit
KeywordsTRANSPORT PROTEIN / ION CHANNEL / NMDA RECEPTOR / ALLOSTERIC MODULATION
Function / homology
Function and homology information


cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / auditory behavior / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to carbohydrate / fear response ...cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / auditory behavior / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to carbohydrate / fear response / sensitization / suckling behavior / response to other organism / response to methylmercury / response to hydrogen sulfide / dendritic branch / regulation of ARF protein signal transduction / apical dendrite / response to manganese ion / response to glycoside / interleukin-1 receptor binding / cellular response to dsRNA / cellular response to lipid / response to growth hormone / RAF/MAP kinase cascade / positive regulation of inhibitory postsynaptic potential / heterocyclic compound binding / negative regulation of dendritic spine maintenance / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / response to zinc ion / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / positive regulation of glutamate secretion / calcium ion transmembrane import into cytosol / startle response / protein heterotetramerization / small molecule binding / glycine binding / receptor clustering / behavioral response to pain / parallel fiber to Purkinje cell synapse / behavioral fear response / regulation of neuronal synaptic plasticity / associative learning / regulation of postsynaptic membrane potential / regulation of MAPK cascade / action potential / response to electrical stimulus / extracellularly glutamate-gated ion channel activity / neuron development / multicellular organismal response to stress / monoatomic cation transmembrane transport / detection of mechanical stimulus involved in sensory perception of pain / response to magnesium ion / response to mechanical stimulus / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transport / glutamate receptor binding / ligand-gated monoatomic ion channel activity / long-term memory / postsynaptic density, intracellular component / synaptic cleft / response to fungicide / monoatomic cation channel activity / cellular response to manganese ion / glutamate-gated receptor activity / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / response to cytokine / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule binding / D2 dopamine receptor binding / response to amphetamine / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / learning / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / protein tyrosine kinase binding / excitatory postsynaptic potential / hippocampus development / cellular response to forskolin / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / cellular response to amino acid stimulus / protein serine/threonine kinase binding / sodium ion transmembrane transport / response to nicotine / synaptic membrane / response to cocaine / regulation of long-term neuronal synaptic plasticity / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / cerebral cortex development / 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 / 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 / : / : / Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.095 Å
AuthorsRomero-Hernandez, A. / Simorwski, 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)GM1055730 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 / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
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 1.6Nov 20, 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
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9676
Polymers84,0822
Non-polymers8854
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-8 kcal/mol
Surface area30000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.782, 75.782, 548.556
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

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Components

#1: Protein NMDA glutamate receptor subunit


Mass: 42932.055 Da / Num. of mol.: 1 / Fragment: residues 23-405
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 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NR2B


Mass: 41149.625 Da / Num. of mol.: 1 / Fragment: residues 32-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00960
#3: 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.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 3350, 1.4M Sodium formate, 0.3M Sodium thyocyanate, 0.1M sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→37.891 Å / Num. obs: 18198 / % possible obs: 98.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13

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Processing

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

3qel


Resolution: 3.095→37.891 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.42
RfactorNum. reflection% reflection
Rfree0.3001 930 5.11 %
Rwork0.2404 --
obs0.2436 18198 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.19 Å2 / Biso mean: 86.3075 Å2 / Biso min: 48.34 Å2
Refinement stepCycle: final / Resolution: 3.095→37.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 56 4 5022
Biso mean--123.25 71.46 -
Num. residues----706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085134
X-RAY DIFFRACTIONf_angle_d1.0747051
X-RAY DIFFRACTIONf_chiral_restr0.053842
X-RAY DIFFRACTIONf_plane_restr0.007920
X-RAY DIFFRACTIONf_dihedral_angle_d13.7462999
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0953-3.25850.39531340.31132221235593
3.2585-3.46250.35611210.290724642585100
3.4625-3.72960.33281170.259123892506100
3.7296-4.10450.29621490.233524382587100
4.1045-4.69750.26841280.208524892617100
4.6975-5.91470.3081280.244425332661100
5.9147-37.89380.28211530.23392734288799

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