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- PDB-5tq2: Crystal structure of amino terminal domains of the NMDA receptor ... -

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Basic information

Entry
Database: PDB / ID: 5tq2
TitleCrystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at GluN1 and GluN2A
Components
  • FAB, HEAVY CHAINFragment antigen-binding
  • FAB, LIGHT CHAINFragment antigen-binding
  • Glutamate receptor ionotropic, NMDA 2A
  • NMDA glutamate receptor subunitNMDA receptor
KeywordsTRANSPORT PROTEIN / ION CHANNEL / NMDA RECEPTOR / ALLOSTERIC MODULATION / ZINC INHIBITION
Function / homology
Function and homology information


response to ammonium ion / directional locomotion / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / protein localization to postsynaptic membrane / response to other organism / sleep / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity ...response to ammonium ion / directional locomotion / serotonin metabolic process / Assembly and cell surface presentation of NMDA receptors / protein localization to postsynaptic membrane / response to other organism / sleep / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity / locomotion / glutamate-gated calcium ion channel activity / cellular response to dsRNA / response to carbohydrate / dendritic spine organization / regulation of monoatomic cation transmembrane transport / cellular response to lipid / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / response to manganese ion / glutamate binding / cellular response to zinc ion / action potential / regulation of neuronal synaptic plasticity / dopamine metabolic process / spinal cord development / response to zinc ion / startle response / response to amine / monoatomic cation transmembrane transport / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / response to light stimulus / neuron development / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / cellular response to manganese ion / glutamate-gated receptor activity / response to fungicide / monoatomic cation channel activity / sensory perception of pain / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / excitatory postsynaptic potential / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / cell adhesion molecule binding / neurogenesis / positive regulation of synaptic transmission, glutamatergic / response to cocaine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / learning / synaptic transmission, glutamatergic / long-term synaptic potentiation / hippocampus development / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / regulation of synaptic plasticity / protein catabolic process / modulation of chemical synaptic transmission / calcium channel activity / visual learning / cytoplasmic vesicle membrane / negative regulation of protein catabolic process / terminal bouton / response to organic cyclic compound / cerebral cortex development / memory / cellular response to growth factor stimulus / response to wounding / response to calcium ion / rhythmic process / calcium ion transport / synaptic vesicle / presynaptic membrane / ATPase binding / chemical synaptic transmission / postsynaptic membrane / postsynapse / scaffold protein binding / response to ethanol / dendritic spine / postsynaptic density / learning or memory / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / signaling receptor binding / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Response regulator / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Response regulator / 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 / 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 / Resolution: 3.289 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
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

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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)132,82214
Polymers131,6814
Non-polymers1,14210
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-127 kcal/mol
Surface area45210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.163, 117.826, 158.992
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 / NMDA receptor


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 / Fragment antigen-binding


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 / Fragment antigen-binding


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

#6: 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 / N-Acetylglucosamine


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, 19 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.75 %
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-D / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 3.28→48.333 Å / Num. obs: 41205 / % possible obs: 96 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.84

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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: 3.289→48.333 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 4107 9.97 %
Rwork0.2238 37098 -
obs0.2276 41205 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.84 Å2 / Biso mean: 90.3301 Å2 / Biso min: 38.65 Å2
Refinement stepCycle: final / Resolution: 3.289→48.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7926 0 62 11 7999
Biso mean--103.22 65.36 -
Num. residues----1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058186
X-RAY DIFFRACTIONf_angle_d0.75311211
X-RAY DIFFRACTIONf_chiral_restr0.0511318
X-RAY DIFFRACTIONf_plane_restr0.0051438
X-RAY DIFFRACTIONf_dihedral_angle_d10.3084734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2887-3.32740.40631320.38051068120081
3.3274-3.36790.35781420.32311298144095
3.3679-3.41050.34251480.31091272142095
3.4105-3.45540.34271540.30981248140295
3.4554-3.50270.36421210.29881277139895
3.5027-3.55280.33841680.29261320148896
3.5528-3.60580.32391220.29571243136593
3.6058-3.66210.29721400.28621240138094
3.6621-3.72210.31941340.29771292142695
3.7221-3.78630.31151470.26481232137995
3.7863-3.85510.30021400.2531299143996
3.8551-3.92920.29871430.26281329147297
3.9292-4.00940.2871320.24181264139696
4.0094-4.09650.32911540.22921292144697
4.0965-4.19170.24381380.20671273141196
4.1917-4.29650.22351260.19651304143095
4.2965-4.41260.21831490.18621250139995
4.4126-4.54240.22151450.19241303144896
4.5424-4.68890.25591410.19041272141396
4.6889-4.85630.2441450.17881303144897
4.8563-5.05050.22281420.19781301144398
5.0505-5.28010.32021430.19321308145197
5.2801-5.55810.26091370.22081319145698
5.5581-5.90580.26691390.23241299143896
5.9058-6.36090.27241450.21841279142497
6.3609-6.99930.28991480.24091317146598
6.9993-8.00810.23321390.21931306144598
8.0081-10.07430.1851540.17381299145397
10.0743-48.33830.2011390.21151291143096

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