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3jpy

Crystal structure of the zinc-bound amino terminal domain of the NMDA receptor subunit NR2B

Method: X-RAY DIFFRACTION Dmax: 69.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate [NMDA] receptor subunit epsilon-2

Rattus norvegicus

UniProt Q00960

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 32–394 Fragment：Amino terminal domain Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 5 NA SODIUM ION × 1 ZN ZINC ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；303 K；3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, 0.1mM ZnCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 3.21 Å R-free 0.233
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 32–394 Fragment：Amino terminal domain Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CL CHLORIDE ION × 10 NA SODIUM ION × 2 ZN ZINC ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；303 K；3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, 0.1mM ZnCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K Resolution 3.21 Å R-free 0.233

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3JPY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3JPW Crystal structure of amino terminal domain of the NMDA receptor subunit NR2B Deposited 2009-09-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–394（363 aa） Fragment：Amino terminal domain
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 17 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；303 K；3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Resolution 2.80 Å R-free 0.231
3JPW Crystal structure of amino terminal domain of the NMDA receptor subunit NR2B Deposited 2009-09-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–394（363 aa） Fragment：Amino terminal domain
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CL CHLORIDE ION × 34 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；303 K；3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Resolution 2.80 Å R-free 0.231
3QEL Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with ifenprodil Deposited 2011-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394
Chain D 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394
Mutation：N348D Mutation：N348D NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.60 Å R-free 0.238
3QEL Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with ifenprodil Deposited 2011-01-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394
Chain D 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394
Mutation：N348D Mutation：N348D NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.60 Å R-free 0.238
3QEM Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with Ro 25-6981 Deposited 2011-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 QEM 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 3.00 Å R-free 0.250
3QEM Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with Ro 25-6981 Deposited 2011-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 31–394（364 aa） Fragment：Amino Terminal Domain, residues 31-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 1 QEM 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 3.00 Å R-free 0.250
4PE5 Crystal Structure of GluN1a/GluN2B NMDA Receptor Ion Channel Deposited 2014-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa） Fragment：UNP residues 27-852
Chain D 27–852（826 aa） Fragment：UNP residues 27-852
Mutation：S214C, N348D, D557C, C588S, I815C, C838S, C849S, del(C395), del(P396), del(E397), del(E399), del(E400), del(E402) Mutation：S214C, N348D, D557C, C588S, I815C, C838S, C849S, del(C395), del(P396), del(E397), del(E399), del(E400), del(E402) W TUNGSTEN ION × 84 GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 QEL 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol × 2 GLU GLUTAMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；291 K；PEG 4000, Tris-HCl, NaCl, Magnesium acetate, metatungstate
Resolution 3.96 Å R-free 0.295
5B3J Activation of NMDA receptors and the mechanism of inhibition by ifenprodil Deposited 2016-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 31–394（364 aa） Fragment：UNP residues 31-394
Mutation：N348D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；0.1M sodium acetate, 27% PEG3350, 2.2M sodium formate, 0.05 M calcium chloride
Resolution 2.90 Å R-free 0.302
5B3J Activation of NMDA receptors and the mechanism of inhibition by ifenprodil Deposited 2016-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 31–394（364 aa） Fragment：UNP residues 31-394
Mutation：N348D NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；0.1M sodium acetate, 27% PEG3350, 2.2M sodium formate, 0.05 M calcium chloride
Resolution 2.90 Å R-free 0.302
5FXG GLUN1B-GLUN2B NMDA RECEPTOR IN ACTIVE CONFORMATION Deposited 2016-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa） Fragment：UNP RESIDUES 27-852
Chain D 27–852（826 aa） Fragment：UNP RESIDUES 27-852
Mutation：YES Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3
cryo-EM vitrification conditions Cryogen ETHANE；ETHANE
Resolution 6.80 Å
5FXH GluN1b-GluN2B NMDA receptor in non-active-1 conformation Deposited 2016-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa） Fragment：UNP RESIDUES 27-852
Chain D 27–852（826 aa） Fragment：UNP RESIDUES 27-852
Mutation：YES Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3
cryo-EM vitrification conditions Cryogen ETHANE；ETHANE
Resolution 5.00 Å
5FXI GluN1b-GluN2B NMDA receptor structure in non-active-2 conformation Deposited 2016-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa） Fragment：UNP RESIDUES 27-852
Chain D 27–852（826 aa） Fragment：UNP RESIDUES 27-852
Mutation：YES Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3
cryo-EM vitrification conditions Cryogen ETHANE；ETHANE
Resolution 6.40 Å
5FXJ GluN1b-GluN2B NMDA receptor structure-Class X Deposited 2016-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa） Fragment：ATD, LBD, TMD, UNP RESIDUES 27-852
Chain D 27–852（826 aa） Fragment：ATD, LBD, TMD, UNP RESIDUES 27-852
Mutation：YES Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002% MNG-3
cryo-EM vitrification conditions Cryogen ETHANE；ETHANE
Resolution 6.25 Å
5FXK GluN1b-GluN2B NMDA receptor structure-Class Y Deposited 2016-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa） Fragment：UNP RESIDUES 27-852
Chain D 27–852（826 aa） Fragment：UNP RESIDUES 27-852
Mutation：YES Mutation：YES No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3；pH 7；200 MM NACL, 20 MM HEPES PH 7.0, 10 MM GLYCINE, 10 MM L-GLUTAMATE, 0.002 % MNG-3
cryo-EM vitrification conditions Cryogen ETHANE；ETHANE
Resolution 6.40 Å
5TPZ Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in apo closed state Deposited 2016-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–393（362 aa） Fragment：residues 32-393
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；20% PEG 3350, 1.4M Sodium formate, 0.3M Sodium thyocyanate, 0.1M sodium acetate pH 5.0
Resolution 3.10 Å R-free 0.300
6CNA GluN1-GluN2B NMDA receptors with exon 5 Deposited 2018-03-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 34–843（810 aa） Fragment：residues 34-843
Chain D 34–843（810 aa） Fragment：residues 34-843
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6E7R Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYS N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.10 Å R-free 0.218
6E7R Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYS N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.10 Å R-free 0.218
6E7S Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HZ4 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](ethyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.72 Å R-free 0.234
6E7S Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-5 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 3 HZ4 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](ethyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.72 Å R-free 0.234
6E7T Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–393（362 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HYY N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.31 Å R-free 0.225
6E7T Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–393（362 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HYY N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.31 Å R-free 0.225
6E7U Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HX7 N-{4-[(2S)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.27 Å R-free 0.237
6E7U Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-31 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HX7 N-{4-[(2S)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.27 Å R-free 0.237
6E7V Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-88 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 6 T88 N-{4-[(2R)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.60 Å R-free 0.233
6E7V Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-88 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 5 T88 N-{4-[(2R)-3-{butyl[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.60 Å R-free 0.233
6E7W Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 6 HXM N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propan-2-yl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.67 Å R-free 0.232
6E7W Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 CL CHLORIDE ION × 5 HXM N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propan-2-yl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.67 Å R-free 0.232
6E7X Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-97 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 5 T97 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](2-methylpropyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.58 Å R-free 0.216
6E7X Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-97 Deposited 2018-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–394（363 aa） Fragment：Extracellular residues 32-394
Mutation：N348D NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 CL CHLORIDE ION × 4 T97 N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](2-methylpropyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；3.0-3.5 M sodium formate, 0.1 M HEPES, 35 mM sodium chloride, 7 mM Tris-HCl, 50 uM Ifenprodil
Resolution 2.58 Å R-free 0.216
6WHR GluN1b-GluN2B NMDA receptor in non-active 2 conformation at 4 angstrom resolution Deposited 2020-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.99 Å
6WHS GluN1b-GluN2B NMDA receptor in non-active 1 conformation at 3.95 angstrom resolution Deposited 2020-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6WHT GluN1b-GluN2B NMDA receptor in active conformation at 4.4 angstrom resolution Deposited 2020-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.39 Å
6WHU GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 1 Deposited 2020-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded QGM (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 QGP (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
6WHV GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 2 Deposited 2020-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 QGP (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid × 2 QGM (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
6WI0 GluN1b-GluN2B NMDA receptor in complex with GluN1 antagonist L689,560, class 2 Deposited 2020-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded QGM (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.27 Å
7SAA Glycine and glutamate bound GluN1a-GluN2B NMDA receptors in non-active 1 conformation at 2.97 Angstrom resolution Deposited 2021-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
7SAB Phencyclidine-bound GluN1a-GluN2B NMDA receptors Deposited 2021-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 1PC 1-(PHENYL-1-CYCLOHEXYL)PIPERIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7SAC S-(+)-ketamine bound GluN1a-GluN2B NMDA receptors at 3.69 Angstrom resolution Deposited 2021-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 JC9 (2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
7SAD Memantine-bound GluN1a-GluN2B NMDA receptors Deposited 2021-09-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 377 Memantine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
7TE6 Crystal structure of GluN1b-2B ATD complexed to Fab5 anti-GluN2B antibody Deposited 2022-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 31–394（364 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；2.1 M sodium/potassium phosphate, 100 mM lithium sulfate, 100 mM CAPS, pH 10.5, 4% formamide
Resolution 4.55 Å R-free 0.324
7TE6 Crystal structure of GluN1b-2B ATD complexed to Fab5 anti-GluN2B antibody Deposited 2022-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 31–394（364 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；2.1 M sodium/potassium phosphate, 100 mM lithium sulfate, 100 mM CAPS, pH 10.5, 4% formamide
Resolution 4.55 Å R-free 0.324
7TE9 Cryo-EM structure of GluN1b-2B NMDAR complexed to Fab2 class1 Deposited 2022-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 31–852（822 aa）
Chain D 31–852（822 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
7TEB Cryo-EM structure of GluN1b-2B NMDAR complexed to Fab2 non-active1-like Deposited 2022-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.23 Å
7TEE Cryo-EM structure of GluN1b-2B NMDAR complexed to Fab2 Non-active2-like Deposited 2022-01-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.59 Å
7TEQ Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 active conformation Deposited 2022-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
7TER Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 non-active2 conformation Deposited 2022-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.23 Å
7TES Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 in Non-active1 conformation Deposited 2022-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
7TET Cryo-EM structure of GluN1b-2B NMDAR in complex with Fab5 in non-active2-like conformation Deposited 2022-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.45 Å
8G18 Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108 Deposited 2023-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 32–394（363 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 YGW N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；sodium formate, HEPES, sodium chloride, Tris
Resolution 2.85 Å R-free 0.246
8G18 Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-108 Deposited 2023-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 32–394（363 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1 YGW N-(4-{3-[4-(3,4-difluorophenyl)piperazin-1-yl]-2-oxopropoxy}phenyl)methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；sodium formate, HEPES, sodium chloride, Tris
Resolution 2.85 Å R-free 0.246
8VUY Rat GluN1-2B with Fab 003-102 Deposited 2024-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 34–845（812 aa）
Chain D 34–845（812 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.81 Å
8VVH rat GluN1a-2B Fab 003-102 local refinement Deposited 2024-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 34–387（354 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
8XLK Structure of native tri-heteromeric GluN1-GluN2A-GluN2B NMDA receptor in rat cortex and hippocampus Deposited 2023-12-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–1482（1482 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9ARE Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in open-channel conformation Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.72 Å
9ARF Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in nonactive1 conformation Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GLU GLUTAMIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9ARG Rat GluN1-GluN2B NMDA receptor channel in apo conformation Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9ARH Rat GluN1-GluN2B NMDA receptor channel in complex with glycine Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
9ARI Rat GluN1-GluN2B NMDA receptor channel in complex with glutamate Deposited 2024-02-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded GLU GLUTAMIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9JNN Structure of native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus Deposited 2024-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 35–845（811 aa）
Chain D 35–845（811 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 7RC (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
9OBS glutamate/glycine-bound GluN1a/2B NMDAR Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 CLR CHOLESTEROL × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
9OBT TMD of glutamate/glycine-bound GluN1a/2B NMDAR Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.01 Å
9OBU glycine/glutamate and Mg2+-bound GluN1a/2B NMDAR Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9OBV Mg2+-bound GluN1a/2B NMDAR (upper) Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
9OBW Mg2+ bound GluN1a/2B NMDAR (lower) Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9OBX glutamate/glycine and Ca2+-bound GluN1a/2B NMDAR Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
9OBY Ca2+-bound GluN1a/2B NMDAR (S1) Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9OBZ Ca2+-bound GluN1a/2B NMDAR (S2) Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
9OC0 Ca2+-bound GluN1a/2B NMDAR (S3) Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9OC1 Ca2+-bound GluN1a/2B NMDAR (S4) Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded CA CALCIUM ION × 1 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.76 Å
9OC2 Ca2+-bound GluN1a/2B NMDAR (S5) Deposited 2025-04-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 CLR CHOLESTEROL × 2 CA CALCIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9OOU Glycine/Glutamate/EU 1622-240 rGluN1a-2B NMDAR Deposited 2025-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–852（826 aa）
Chain D 27–852（826 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2 A1AFT (5M)-5-(3-bromo-4-fluorophenyl)-6-ethynyl-3-[2-(3-fluoro-3-methylazetidin-1-yl)-2-oxoethyl]thieno[2,3-d]pyrimidin-4(3H)-one × 4 CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å

59 other PDB entries and 72 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NMDE2_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–363； UniProt 32–394

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3jpy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3jpy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3jpy
Deposition date deposition_date2009-09-04
Structure title titleCrystal structure of the zinc-bound amino terminal domain of the NMDA receptor subunit NR2B
Keywords keywords;NMDA receptor, amino terminal domain, phenylethanolamine, Cell junction, Cell membrane, Glycoprotein, Ion transport, Ionic channel, Magnesium, Membrane, Phosphoprotein, Postsynaptic cell membrane, Receptor, Synapse, Transmembrane, Transport, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.36 Å
Radius of gyration Rg (electron density) rg_electron21.34 Å
Forward intensity I(0) i024798600.00
Molecular weight molecular_weight37836.0 kDa
Excluded volume excluded_volume47040 ų
Envelope volume envelope_volume56544 ų
Hydration-shell volume shell_volume22282 ų
Envelope diameter envelope_diameter71.2 Å
Shell Rg shell_rg27.75 Å
Envelope Rg envelope_rg21.62 Å
Shape Rg shape_rg21.36 Å
Total Rg total_rg22.09 Å
Total atoms total_atoms2645
Residues n_residues358
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.8 Å
Rg (real space) rg_real22.34 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real2.4800e+07
I(0) uncertainty (real space) i0_real_error3.2450e+05
Rg (reciprocal space) rg_reciprocal22.34 Å
I(0) (reciprocal space) i0_reciprocal24800000.0000
Solution quality estimate total_estimate0.8879
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.4 Å
Skewness Skewness skewness0.344
Kurtosis Kurtosis kurtosis-0.390
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10090000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.855
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3jpyA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id3jpyA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
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8. Citations (1)

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9. Files and Curves (10)