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- PDB-5un1: Crystal structure of GluN1/GluN2B delta-ATD NMDA receptor -

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Basic information

Entry
Database: PDB / ID: 5un1
TitleCrystal structure of GluN1/GluN2B delta-ATD NMDA receptor
Components
  • Ionotropic glutamate receptor subunit NR2B
  • N-methyl-D-aspartate receptor subunit NR1-3a
KeywordsMEMBRANE PROTEINS/INHIBITOR / Complex / Arrangement / channel blocker / MEMBRANE PROTEINS-INHIBITOR complex
Function / homology
Function and homology information


NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / response to zinc ion / response to magnesium ion / late endosome / postsynaptic membrane / lysosome / metal ion binding / plasma membrane
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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BMK / GLUTAMIC ACID / GLYCINE / CHOLESTEROL HEMISUCCINATE / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsSong, X. / Gouaux, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01-NS038631 United States
CitationJournal: Nature / Year: 2018
Title: Mechanism of NMDA receptor channel block by MK-801 and memantine.
Authors: Song, X. / Jensen, M.O. / Jogini, V. / Stein, R.A. / Lee, C.H. / Mchaourab, H.S. / Shaw, D.E. / Gouaux, E.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 13, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.5Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: N-methyl-D-aspartate receptor subunit NR1-3a
A: N-methyl-D-aspartate receptor subunit NR1-3a
B: Ionotropic glutamate receptor subunit NR2B
H: Ionotropic glutamate receptor subunit NR2B
E: N-methyl-D-aspartate receptor subunit NR1-3a
F: Ionotropic glutamate receptor subunit NR2B
C: N-methyl-D-aspartate receptor subunit NR1-3a
D: Ionotropic glutamate receptor subunit NR2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,39626
Polymers405,1078
Non-polymers3,28918
Water00
1
G: N-methyl-D-aspartate receptor subunit NR1-3a
H: Ionotropic glutamate receptor subunit NR2B
E: N-methyl-D-aspartate receptor subunit NR1-3a
F: Ionotropic glutamate receptor subunit NR2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,56414
Polymers202,5534
Non-polymers2,01010
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11090 Å2
ΔGint-95 kcal/mol
Surface area83740 Å2
MethodPISA
2
A: N-methyl-D-aspartate receptor subunit NR1-3a
B: Ionotropic glutamate receptor subunit NR2B
C: N-methyl-D-aspartate receptor subunit NR1-3a
D: Ionotropic glutamate receptor subunit NR2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,83212
Polymers202,5534
Non-polymers1,2798
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12510 Å2
ΔGint-115 kcal/mol
Surface area79850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.570, 108.470, 182.460
Angle α, β, γ (deg.)90.00, 111.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules GAECBHFD

#1: Protein
N-methyl-D-aspartate receptor subunit NR1-3a


Mass: 51107.777 Da / Num. of mol.: 4 / Fragment: UNP residues 394-836
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C0KD15, UniProt: A0A1L8F5J9*PLUS
#2: Protein
Ionotropic glutamate receptor subunit NR2B


Mass: 50168.961 Da / Num. of mol.: 4 / Fragment: UNP residues 400-839
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: NR2B, XELAEV_18025529mg / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A7XY94

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Sugars , 1 types, 6 molecules

#4: 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.: 6 / Source method: obtained synthetically / 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 , 6 types, 12 molecules

#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Chemical ChemComp-BMK / (5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene


Mass: 221.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N / Comment: neurotransmitter*YM
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4

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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: 4.13 Å3/Da / Density % sol: 70.21 %
Crystal growTemperature: 293.15 K / Method: evaporation / Details: 2-ethanesulfonic acid, sodium fluoride, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Feb 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.58→50 Å / Num. obs: 76987 / % possible obs: 86 % / Redundancy: 5.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.33
Reflection shellResolution: 3.58→3.68 Å / Redundancy: 4.08 % / Rmerge(I) obs: 0.57 / Num. unique obs: 2414 / CC1/2: 0.12 / % possible all: 38.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2597: ???)refinement
XDSNov 1, 2016data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TLL

4tll


Resolution: 3.6→49.994 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 33.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3162 3562 5.09 %
Rwork0.2877 --
obs0.2892 69975 91.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→49.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19915 0 228 0 20143
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00620504
X-RAY DIFFRACTIONf_angle_d0.81828271
X-RAY DIFFRACTIONf_dihedral_angle_d16.3645673
X-RAY DIFFRACTIONf_chiral_restr0.0483401
X-RAY DIFFRACTIONf_plane_restr0.0043844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.64940.393500.36881030X-RAY DIFFRACTION36
3.6494-3.70150.355740.351418X-RAY DIFFRACTION49
3.7015-3.75680.3621100.34541874X-RAY DIFFRACTION65
3.7568-3.81540.34881360.32922204X-RAY DIFFRACTION77
3.8154-3.8780.37121200.31222555X-RAY DIFFRACTION87
3.878-3.94480.38371530.30272748X-RAY DIFFRACTION96
3.9448-4.01650.32731660.29572838X-RAY DIFFRACTION98
4.0165-4.09370.33741510.28722822X-RAY DIFFRACTION97
4.0937-4.17730.31481530.28852764X-RAY DIFFRACTION95
4.1773-4.2680.31351600.27082713X-RAY DIFFRACTION95
4.268-4.36730.33781510.26292925X-RAY DIFFRACTION99
4.3673-4.47640.27921480.25192870X-RAY DIFFRACTION100
4.4764-4.59740.30241370.24952922X-RAY DIFFRACTION99
4.5974-4.73250.29681270.24822924X-RAY DIFFRACTION99
4.7325-4.88520.29981600.23922888X-RAY DIFFRACTION99
4.8852-5.05960.29041510.2522896X-RAY DIFFRACTION99
5.0596-5.2620.31331420.25942888X-RAY DIFFRACTION99
5.262-5.50120.33181600.25922878X-RAY DIFFRACTION99
5.5012-5.79080.29581740.28532874X-RAY DIFFRACTION99
5.7908-6.1530.34471530.29992821X-RAY DIFFRACTION97
6.153-6.62710.34521510.29542848X-RAY DIFFRACTION96
6.6271-7.29220.31241440.28862949X-RAY DIFFRACTION99
7.2922-8.34320.30581660.29142914X-RAY DIFFRACTION100
8.3432-10.49550.26661520.26662941X-RAY DIFFRACTION99
10.4955-49.99860.32111730.32892909X-RAY DIFFRACTION96

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