Glutamate receptor ionotropic, NMDA 1
Rattus norvegicus
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 1–959 Chain C； UniProt 1–959 | Not recorded | Glutamate receptor ionotropic, NMDA 2B × 2 （Q00960） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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 |
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 6WHU | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1PB7 CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH GLYCINE AT 1.35 ANGSTROMS RESOLUTION Deposited 2003-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Fragment：Ligand Binding Core
Chain A
663–800（138 aa）
Fragment：Ligand Binding Core
|
Not recorded | GLY GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 1000, sodium cacodylate, lithium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.35 Å R-free 0.216 |
| 1PB8 CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-SERINE AT 1.45 ANGSTROMS RESOLUTION Deposited 2003-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Fragment：Ligand Binding Core
Chain A
663–800（138 aa）
Fragment：Ligand Binding Core
|
Not recorded | DSN D-SERINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 1000, sodium cacodylate, lithium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.45 Å R-free 0.226 |
| 1PB9 CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-CYCLOSERINE AT 1.60 ANGSTROMS RESOLUTION Deposited 2003-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Fragment：Ligand Binding Core
Chain A
663–800（138 aa）
Fragment：Ligand Binding Core
|
Not recorded | 4AX (R)-4-AMINO-ISOXAZOLIDIN-3-ONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG 1000, sodium cacodylate, lithium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.227 |
| 1PBQ CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH 5,7-DICHLOROKYNURENIC ACID (DCKA) AT 1.90 ANGSTROMS RESOLUTION Deposited 2003-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Fragment：Ligand Binding Core
Chain A
663–800（138 aa）
Fragment：Ligand Binding Core
|
Not recorded | DK1 5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG2000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.270 |
| 1PBQ CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH 5,7-DICHLOROKYNURENIC ACID (DCKA) AT 1.90 ANGSTROMS RESOLUTION Deposited 2003-05-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain not uniquely mapped
Reference range not declared
Fragment：Ligand Binding Core
|
Not recorded | DK1 5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG2000, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.270 |
| 1Y1M Crystal structure of the NR1 ligand binding core in complex with cycloleucine Deposited 2004-11-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Fragment：ligand-binding core
Chain A
663–800（138 aa）
Fragment：ligand-binding core
|
Not recorded | AC5 1-AMINOCYCLOPENTANECARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.224 |
| 1Y1M Crystal structure of the NR1 ligand binding core in complex with cycloleucine Deposited 2004-11-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
394–544（151 aa）
Fragment：ligand-binding core
Chain B
663–800（138 aa）
Fragment：ligand-binding core
|
Not recorded | AC5 1-AMINOCYCLOPENTANECARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.224 |
| 1Y1M Crystal structure of the NR1 ligand binding core in complex with cycloleucine Deposited 2004-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Fragment：ligand-binding core
Chain A
663–800（138 aa）
Fragment：ligand-binding core
Chain B
394–544（151 aa）
Fragment：ligand-binding core
Chain B
663–800（138 aa）
Fragment：ligand-binding core
|
Not recorded | AC5 1-AMINOCYCLOPENTANECARBOXYLIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；PEG, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.224 |
| 1Y1Z Crystal structure of the NR1 ligand binding core in complex with ACBC Deposited 2004-11-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Fragment：ligand-binding core
Chain A
663–800（138 aa）
Fragment：ligand-binding core
|
Not recorded | 192 1-AMINOCYCLOBUTANECARBOXLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG, pH 6., VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.50 Å R-free 0.237 |
| 1Y20 Crystal structure of the NR1 ligand-binding core in complex with ACPC Deposited 2004-11-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Fragment：ligand-binding core
Chain A
663–800（138 aa）
Fragment：ligand-binding core
|
Not recorded | 1AC 1-AMINOCYCLOPROPANECARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；PEG, pH 6., VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.40 Å R-free 0.220 |
| 2A5T Crystal Structure Of The NR1/NR2A ligand-binding cores complex Deposited 2005-06-30 | 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 × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Fragment：S1S2 ligand-binding core
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；277 K；PEG 8000, HEPES, Calcium acetate, pH 7., EVAPORATION, temperature 277K
|
Resolution 2.00 Å R-free 0.253 |
| 3Q41 Crystal structure of the GluN1 N-terminal domain (NTD) Deposited 2010-12-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
21–393（373 aa）
Fragment：N-TERMINAL DOMAIN, UNP residues 21-393
Chain B
21–393（373 aa）
Fragment：N-TERMINAL DOMAIN, UNP residues 21-393
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CL CHLORIDE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；protein in (20mM Tris-HCl pH 7.5, 150mM NaCl) was mixed 1:1 with 4M Formate and 20mM TCEP, temperature 277K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 3.40 Å R-free 0.279 |
| 3Q41 Crystal structure of the GluN1 N-terminal domain (NTD) Deposited 2010-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
21–393（373 aa）
Fragment：N-TERMINAL DOMAIN, UNP residues 21-393
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；protein in (20mM Tris-HCl pH 7.5, 150mM NaCl) was mixed 1:1 with 4M Formate and 20mM TCEP, temperature 277K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 3.40 Å R-free 0.279 |
| 4KCC Crystal Structure of the NMDA Receptor GluN1 Ligand Binding Domain Apo State Deposited 2013-04-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Fragment：Ligand Binding Domain (UNP residues 394-544, 663-800)
Chain A
663–800（138 aa）
Fragment：Ligand Binding Domain (UNP residues 394-544, 663-800)
|
Not recorded | PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.2 M NaKphosphate, 20% PEG 3350, 2% glycerol, 0.2 M NaCl, 0.01 M Tris, 0.001 M EDTA, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.89 Å R-free 0.206 |
| 4KFQ Crystal structure of the NMDA receptor GluN1 ligand binding domain in complex with 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one Deposited 2013-04-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
394–544（151 aa）
Fragment：UNP residues 394-554, 663-800
Chain A
663–800（138 aa）
Fragment：UNP residues 394-554, 663-800
|
Not recorded | KFQ 1-sulfanyl[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one × 1 GOL GLYCEROL × 9 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight.
0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
|
Resolution 2.20 Å R-free 0.232 |
| 4KFQ Crystal structure of the NMDA receptor GluN1 ligand binding domain in complex with 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one Deposited 2013-04-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
394–544（151 aa）
Fragment：UNP residues 394-554, 663-800
Chain B
663–800（138 aa）
Fragment：UNP residues 394-554, 663-800
|
Not recorded | KFQ 1-sulfanyl[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one × 1 GOL GLYCEROL × 9 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight.
0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
|
Resolution 2.20 Å R-free 0.232 |
| 4NF4 Crystal structure of GluN1/GluN2A ligand-binding domain in complex with DCKA and glutamate Deposited 2013-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
393–543（151 aa）
Fragment：Ligand-binding domain, unp residues 393-543; unp residues 663-800
Chain A
663–800（138 aa）
Fragment：Ligand-binding domain, unp residues 393-543; unp residues 663-800
|
Not recorded | 2JK 4-hydroxy-5,7-dimethylquinoline-2-carboxylic acid × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；300 K；PEG2000MME, HEPES, pH 7, VAPOR DIFFUSION, temperature 300K
|
Resolution 2.00 Å R-free 0.217 |
| 4NF5 Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and D-AP5 Deposited 2013-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
393–543（151 aa）
Fragment：unp residues 393-543; unp residues 663-800
Chain A
663–800（138 aa）
Fragment：unp residues 393-543; unp residues 663-800
|
Not recorded | GLY GLYCINE × 1 GOL GLYCEROL × 3 2JJ 5-phosphono-D-norvaline × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；300 K；PEG2000MME, HEPES, pH 7, VAPOR DIFFUSION, temperature 300K
|
Resolution 1.90 Å R-free 0.213 |
| 4NF6 Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and PPDA Deposited 2013-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
393–543（151 aa）
Fragment：Ligand-binding domain, unp residues 393-543; unp residues 663-800
Chain A
663–800（138 aa）
Fragment：Ligand-binding domain, unp residues 393-543; unp residues 663-800
|
Not recorded | GLY GLYCINE × 1 2JL (2S,3R)-1-(phenanthren-2-ylcarbonyl)piperazine-2,3-dicarboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；300 K；PEG2000MMG and HEPES, pH 7, VAPOR DIFFUSION, temperature 300K
|
Resolution 2.10 Å R-free 0.215 |
| 4NF8 Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and glutamate in PEG2000MME Deposited 2013-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
393–543（151 aa）
Fragment：Ligand-binding domain, unp residues 393-543; unp residues 663-800
Chain A
663–800（138 aa）
Fragment：Ligand-binding domain, unp residues 393-543; unp residues 663-800
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；300 K；PEG2000MME and HEPES, pH 7, VAPOR DIFFUSION, temperature 300K
|
Resolution 1.86 Å R-free 0.218 |
| 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 method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
23–847（825 aa）
Fragment：UNP residues 23-847
Chain C
23–847（825 aa）
Fragment：UNP residues 23-847
|
Mutation：N61Q, N239D, N350Q, N471Q, N491Q, T561C, E594Q, E595S, E597S, E598T, N771Q, F810C, R844N, R845G, K846A Mutation：N61Q, N239D, N350Q, N471Q, N491Q, T561C, E594Q, E595S, E597S, E598T, N771Q, F810C, R844N, R845G, K846A | 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 |
| 5DEX Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, phenyl-ACEPC Deposited 2015-08-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Fragment：UNP residues 394-544, 663-800
Chain A
663–800（138 aa）
Fragment：UNP residues 394-544, 663-800
|
Not recorded | GLY GLYCINE × 1 5E0 5-[(2R)-2-amino-2-carboxyethyl]-1-phenyl-1H-pyrazole-3-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；AMMONIUM ACETATE, PEG 4000
|
Resolution 2.40 Å R-free 0.285 |
| 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 conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
23–847（825 aa）
Fragment：UNP RESIDUES 23-868
Chain C
23–847（825 aa）
Fragment：UNP RESIDUES 23-868
|
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 conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
23–847（825 aa）
Fragment：UNP RESIDUES 23-868
Chain C
23–847（825 aa）
Fragment：UNP RESIDUES 23-868
|
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 conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
23–847（825 aa）
Fragment：UNP RESIDUES 23-868
Chain C
23–847（825 aa）
Fragment：UNP RESIDUES 23-868
|
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 conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
23–847（825 aa）
Fragment：ATD.LBD, TMD, UNP RESIDUES 23-868
Chain C
23–847（825 aa）
Fragment：ATD.LBD, TMD, UNP RESIDUES 23-868
|
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 conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
23–847（825 aa）
Fragment：UNP RESIDUES 23-868
Chain C
23–847（825 aa）
Fragment：UNP RESIDUES 23-868
|
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 |
| 5I56 Agonist-bound GluN1/GluN2A agonist binding domains with TCN201 Deposited 2016-02-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Chain A
684–821（138 aa）
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 67P N-({4-[2-(benzenecarbonyl)hydrazinecarbonyl]phenyl}methyl)-3-chloro-4-fluorobenzene-1-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate and 16-22% PEG 4000
|
Resolution 2.28 Å R-free 0.239 |
| 5I57 Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains Deposited 2016-02-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：unp residues 415-565; 684-821
Chain A
684–821（138 aa）
Fragment：unp residues 415-565; 684-821
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate and 16-22% PEG 4000
|
Resolution 1.70 Å R-free 0.222 |
| 5I58 GLUTAMATE- AND GLYCINE-BOUND GLUN1/GLUN2A AGONIST BINDING DOMAINS WITH MPX-004 Deposited 2016-02-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Chain A
684–821（138 aa）
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 67R 5-({[(3-chloro-4-fluorophenyl)sulfonyl]amino}methyl)-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；273 K；0.2 M ammonium sulfate and 16-22% PEG 4000
|
Resolution 2.52 Å R-free 0.292 |
| 5I59 Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains with MPX 007 Deposited 2016-02-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：unp residues 415-565, unp residues 684-821 unp residues 6402-539, unp residues 661-800
Chain A
684–821（138 aa）
Fragment：unp residues 415-565, unp residues 684-821 unp residues 6402-539, unp residues 661-800
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 67Q 5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-4H-1lambda~4~,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate and 16-22% PEG 4000
|
Resolution 2.25 Å R-free 0.264 |
| 5JTY Glutamate- and DCKA-bound GluN1/GluN2A agonist binding domains with MPX-007 Deposited 2016-05-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：unp residues 415-565; 684-821
Chain A
684–821（138 aa）
Fragment：unp residues 415-565; 684-821
|
Not recorded | 2JK 4-hydroxy-5,7-dimethylquinoline-2-carboxylic acid × 1 6ND 5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000
|
Resolution 2.72 Å R-free 0.278 |
| 5U8C CRYSTAL STRUCTURE OF GLUN1/GLUN2A LIGAND-BINDING DOMAIN IN COMPLEX WITH GLYCINE AND NVP-AAM077 Deposited 2016-12-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Fragment：UNP residues 394-554, 663-800
Chain A
663–800（138 aa）
Fragment：UNP residues 394-554, 663-800
|
Not recorded | GLY GLYCINE × 1 GOL GLYCEROL × 1 84J [(R)-{[(1S)-1-(4-bromophenyl)ethyl]amino}(2,3-dihydroxyquinoxalin-5-yl)methyl]phosphonic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；18% Polyethylene glycol monoethylether 2000 (PEG2000 MME), 100mM HEPES-NaOH pH 7.0, and 75mM NaCl
|
Resolution 1.60 Å R-free 0.204 |
| 5VIH Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-fluorophenyl-ACEPC Deposited 2017-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Chain A
684–821（138 aa）
|
Not recorded | GLY GLYCINE × 1 5DZ 5-[(2R)-2-amino-2-carboxyethyl]-1-(4-fluorophenyl)-1H-pyrazole-3-carboxylic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Ammonia Acetate, PEG 4000
|
Resolution 2.40 Å R-free 0.272 |
| 5VII Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-(3-fluoropropyl)phenyl-ACEPC Deposited 2017-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Chain A
684–821（138 aa）
|
Not recorded | GLY GLYCINE × 1 5DY 5-[(2R)-2-amino-2-carboxyethyl]-1-[4-(3-fluoropropyl)phenyl]-1H-pyrazole-3-carboxylic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Ammonia Acetate, PEG 4000
|
Resolution 1.95 Å R-free 0.259 |
| 5VIJ Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-bromophenyl-ACEPC Deposited 2017-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Chain A
684–821（138 aa）
|
Not recorded | GLY GLYCINE × 1 5DX 5-[(2R)-2-amino-2-carboxyethyl]-1-(4-bromophenyl)-1H-pyrazole-3-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Ammonia Acetate, PEG 4000
|
Resolution 2.10 Å R-free 0.255 |
| 6CNA GluN1-GluN2B NMDA receptors with exon 5 Deposited 2018-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
25–859（835 aa）
Fragment：residues 25-859
Chain C
25–859（835 aa）
Fragment：residues 25-859
|
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 |
| 6MM9 Diheteromeric NMDA receptor GluN1/GluN2A in the '1-Knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1 Deposited 2018-09-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.1
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 5.97 Å |
| 6MMA Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1 Deposited 2018-09-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.1
cryo-EM vitrification conditions
Cryogen ETHANE；sample was blotted for 3 seconds at blot force 1.
|
Resolution 6.31 Å |
| 6MMB Diheteromeric NMDA receptor GluN1/GluN2A in the 'Super-Splayed' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 6.1 Deposited 2018-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.1
cryo-EM vitrification conditions
Cryogen ETHANE；sample was blotted for 3 seconds at blot force 1.
|
Resolution 12.70 Å |
| 6MMG Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar EDTA, and at pH 7.4 Deposited 2018-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；sample was blotted for 3 seconds at blot force 1.
|
Resolution 6.23 Å |
| 6MMH Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-2' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar zinc chloride, and at pH 7.4 Deposited 2018-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；sample was blotted for 3 seconds at blot force 1.
|
Resolution 8.21 Å |
| 6MMI Diheteromeric NMDA receptor GluN1/GluN2A in the 'Splayed-Open' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar zinc chloride, and at pH 7.4 Deposited 2018-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；sample was blotted for 3 seconds at blot force 1.
|
Resolution 8.93 Å |
| 6MMJ Diheteromeric NMDA receptor GluN1/GluN2A in the 'Super-Splayed' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar zinc chloride, and at pH 7.4 Deposited 2018-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；sample was blotted for 3 seconds at blot force 1.
|
Resolution 16.50 Å |
| 6MMK Diheteromeric NMDA receptor GluN1/GluN2A in the '1-Knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 Deposited 2018-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 6.08 Å |
| 6MML Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 Deposited 2018-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 7.14 Å |
| 6MMM Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 Deposited 2018-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 6.84 Å |
| 6MMN Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 8.0 Deposited 2018-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；sample was blotted for 3 seconds at blot force 1.
|
Resolution 7.51 Å |
| 6MMP Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 0.1 millimolar EDTA, and at pH 8.0 Deposited 2018-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；sample was blotted for 3 seconds at blot force 1.
|
Resolution 6.88 Å |
| 6MMR Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar zinc chloride, 3 millimolar EDTA, and at pH 7.4 Deposited 2018-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 5.13 Å |
| 6MMS Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar EDTA, and at pH 7.4 Deposited 2018-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 5.38 Å |
| 6MMT Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* in the '1-Knuckle' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 Deposited 2018-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 7.46 Å |
| 6MMU Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* in the '2-Knuckle-Asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 Deposited 2018-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 5.30 Å |
| 6MMV Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* Extracellular Domain in the '2-Knuckle-Asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 Deposited 2018-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–797（797 aa）
Fragment：UNP residues 1-838
Chain C
1–797（797 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 4.71 Å |
| 6MMW Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 Deposited 2018-10-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 6.20 Å |
| 6MMX Triheteromeric NMDA receptor GluN1/GluN2A/GluN2A* in the 'Extended' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4 Deposited 2018-10-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–838（838 aa）
Fragment：UNP residues 1-838
Chain C
1–838（838 aa）
Fragment：UNP residues 1-838
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Sample was blotted for 3 seconds at blot force 1.
|
Resolution 6.99 Å |
| 6OVD Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 3-ethylphenyl-ACEPC Deposited 2019-05-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Chain A
684–821（138 aa）
|
Not recorded | GLY GLYCINE × 1 N9A (3S,5S)-5-[(2R)-2-amino-2-carboxyethyl]-1-(3-ethylphenyl)pyrazolidine-3-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000
|
Resolution 2.10 Å R-free 0.240 |
| 6OVE Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-propylphenyl-ACEPC Deposited 2019-05-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Chain A
684–821（138 aa）
|
Not recorded | GLY GLYCINE × 1 N9D (3R,5S)-5-[(2R)-2-amino-2-carboxyethyl]-1-(4-propylphenyl)pyrazolidine-3-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000
|
Resolution 2.00 Å R-free 0.216 |
| 6OVE Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-propylphenyl-ACEPC Deposited 2019-05-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
415–565（151 aa）
Chain A
684–821（138 aa）
|
Not recorded | GLY GLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2 M AMMONIUM SULFATE AND 16-22% PEG 4000
|
Resolution 2.00 Å R-free 0.216 |
| 6USU Crystal structure of GluN1/GluN2A ligand-binding domain in complex with L689,560 and glutamate Deposited 2019-10-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：UNP residues 415-565, 684-821
Chain A
684–821（138 aa）
Fragment：UNP residues 415-565, 684-821
|
Not recorded | QGM (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；291 K；0.2 M HEPES, pH 7.0, 60-90 mM sodium chloride, 15-20% PEG2000 MME
|
Resolution 2.09 Å R-free 0.222 |
| 6USV Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and SDZ 220-040 Deposited 2019-10-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：UNP residues 415-565, 684-821
Chain A
684–821（138 aa）
Fragment：UNP residues 415-565, 684-821
|
Not recorded | GLY GLYCINE × 1 QGP (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 7；291 K；0.2 M HEPES, pH 7.0, 60-90 mM sodium chloride, 15-20% PEG2000 MME
|
Resolution 2.30 Å R-free 0.259 |
| 6UZ6 Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and glutamate Deposited 2019-11-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
Chain A
684–821（138 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
|
Not recorded | GLY GLYCINE × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME
|
Resolution 1.66 Å R-free 0.212 |
| 6UZG Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and homoquinolinic acid Deposited 2019-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
Chain A
684–821（138 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
|
Not recorded | GLY GLYCINE × 1 QM1 3-(carboxymethyl)pyridine-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME
|
Resolution 1.94 Å R-free 0.250 |
| 6UZR Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and homoquinolinic acid Deposited 2019-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
Chain A
684–821（138 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
|
Not recorded | GLY GLYCINE × 1 GOL GLYCEROL × 3 QM1 3-(carboxymethyl)pyridine-2-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME
|
Resolution 1.87 Å R-free 0.207 |
| 6UZW Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and UBP791 Deposited 2019-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
Chain A
684–821（138 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
|
Not recorded | GLY GLYCINE × 1 QM4 (2S,3R)-1-[7-(2-carboxyethyl)phenanthrene-2-carbonyl]piperazine-2,3-dicarboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME
|
Resolution 2.13 Å R-free 0.247 |
| 6UZX Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with glycine and UBP791 Deposited 2019-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
415–565（151 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
Chain A
684–821（138 aa）
Fragment：ligand-binding domain (UNP residues 415-565,684-821)
|
Not recorded | GOL GLYCEROL × 2 GLY GLYCINE × 1 QM4 (2S,3R)-1-[7-(2-carboxyethyl)phenanthrene-2-carbonyl]piperazine-2,3-dicarboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；100 mM HEPES, pH 7.0, 75 mM sodium chloride, 18% PEG2000 MME
|
Resolution 2.41 Å R-free 0.245 |
| 6WHR GluN1b-GluN2B NMDA receptor in non-active 2 conformation at 4 angstrom resolution Deposited 2020-04-08 | Different ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–959（959 aa）
Chain C
1–959（959 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 ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–959（959 aa）
Chain C
1–959（959 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 ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–959（959 aa）
Chain C
1–959（959 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 |
| 6WHV GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 2 Deposited 2020-04-08 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–959（959 aa）
Chain C
1–959（959 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 ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–959（959 aa）
Chain C
1–959（959 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 |
| 7TE9 Cryo-EM structure of GluN1b-2B NMDAR complexed to Fab2 class1 Deposited 2022-01-04 | Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–859（859 aa）
Chain C
1–859（859 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–859（859 aa）
Chain C
1–859（859 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–859（859 aa）
Chain C
1–859（859 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–859（859 aa）
Chain C
1–859（859 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–859（859 aa）
Chain C
1–859（859 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–859（859 aa）
Chain C
1–859（859 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–859（859 aa）
Chain C
1–859（859 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 |
| 7YFG Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (major class in asymmetry) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7YFH Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106 Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 IWB methyl 4-[(2~{R})-3-ethanoyl-1-[2-(2-methyl-1~{H}-indol-3-yl)ethyl]-4-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-2-yl]benzoate × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7YFI Structure of the Rat tri-heteromeric GluN1-GluN2A-GluN2C NMDA receptor in complex with glycine and glutamate Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–798（798 aa）
Chain C
1–798（798 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 GLY GLYCINE × 2 GLU GLUTAMIC ACID × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8HDK Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (minor class in symmetry) Deposited 2022-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–796（796 aa）
Chain C
1–796（796 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
|
Resolution not provided |
| 8JF7 Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab Deposited 2023-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.73 Å |
| 8USW CNQX-bound GluN1a-3A NMDA receptor Deposited 2023-10-30 | Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | DQC 7-nitro-2,3-dioxo-1,2,3,4-tetrahydroquinoxaline-6-carbonitrile × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.23 Å |
| 8VUY Rat GluN1-2B with Fab 003-102 Deposited 2024-01-30 | Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
25–838（814 aa）
Chain C
25–838（814 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 structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
25–393（369 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–938（938 aa）
Chain C
1–938（938 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 ligand/ion Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–959（959 aa）
Chain C
1–959（959 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–959（959 aa）
Chain C
1–959（959 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 |
| 9BIB Rat GluN1-GluN2B NMDA receptor channel in complex with glycine, glutamate, and EU-1622-A, in open-channel conformation, C1 symmetry Deposited 2024-04-23 | Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 3.81 Å |
| 9C7C Diheteromeric GluN1/GluN2A (delM653) in nanodisc complexed with glycine, glutamate, and GNE-4123, open conformation Deposited 2024-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | A1AUV 4-cyclohexyl-N-[(8R)-2-cyclopropyl-7-hydroxy-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]benzene-1-sulfonamide × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 HP6 HEPTANE × 1 Y01 CHOLESTEROL HEMISUCCINATE × 8 GLY GLYCINE × 2 D12 DODECANE × 2 GLU GLUTAMIC ACID × 2 D10 DECANE × 2 HEX HEXANE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9C7E Diheteromeric GluN1/GluN2A (delM653) in nanodisc complex with glycine, glutamate, and GNE-4123, open conformation, C2 symmetry Deposited 2024-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | A1AUV 4-cyclohexyl-N-[(8R)-2-cyclopropyl-7-hydroxy-5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-6-yl]benzene-1-sulfonamide × 2 Y01 CHOLESTEROL HEMISUCCINATE × 6 D12 DODECANE × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 9C7P Diheteromeric GluN1/GluN2A (delM653) in digitonin complexed with glycine, glutamate, and GNE-4123 Deposited 2024-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.61 Å |
| 9C7Q Diheteromeric NMDA receptor GluN1/GluN2A, in complex with glycine and glutamate Deposited 2024-06-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.05 Å |
| 9C7R Diheteromeric GluN1/GluN2A (M817V) in digitonin complexed with glycine, glutamate, and GNE-4123 Deposited 2024-06-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.99 Å |
| 9JNN Structure of native di-heteromeric GluN1-GluN2B NMDA receptor in rat cortex and hippocampus Deposited 2024-09-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
25–841（817 aa）
Chain C
25–841（817 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 |
| 9NYZ Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with UCM-101 Deposited 2025-03-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
394–544（151 aa）
Chain A
663–800（138 aa）
|
Not recorded | DK1 5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID × 1 A1B7E N-(cyclohexylmethyl)-2-[(5-{[(1R)-1-phenylpropyl]amino}-1,3,4-thiadiazol-2-yl)sulfanyl]acetamide × 1 GLU GLUTAMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；ammonium acetate, PEG 4000
|
Resolution 1.71 Å R-free 0.202 |
| 9OBS glutamate/glycine-bound GluN1a/2B NMDAR Deposited 2025-04-23 | Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 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 structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Mutation：N61Q, N239D, N350Q, N471Q, N491Q, N771Q, R844Q, R845G, K846A Mutation：N61Q, N239D, N350Q, N471Q, N491Q, N771Q, R844Q, R845G, K846A | 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 |
| 9PZQ GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 1), glycine- and glutamate-bound state Deposited 2025-08-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.07 Å |
| 9PZR GluN1/GluN2A in complex with polyclonal autoantibody Fab fragments (class 2), glycine- and glutamate-bound state Deposited 2025-08-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.92 Å |
| 9PZW GluN1/GluN2A in complex with 3D2 Fab, glycine and glutamate-bound state Deposited 2025-08-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–847（847 aa）
Chain C
1–847（847 aa）
|
Not recorded | GLY GLYCINE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 GLU GLUTAMIC ACID × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.43 Å |
| 9PZX GluN1/GluN2A in complex with 3D2 Fab, local ATD dimer Deposited 2025-08-11 | 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 A
1–847（847 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.76 Å |
114 other PDB entries and 120 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | NMDZ1_RAT |
| Isoform | P35439-2 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–959； UniProt 1–959 Author chain C； PDBConstruct 1–959； UniProt 1–959 |
