6IRF

Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 6.3, Class I

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): 

  • Deposited: 2018-11-12 Released: 2019-01-16 
  • Deposition Author(s): Zhang, J., Chang, S., Zhang, X., Zhu, S.
  • Funding Organization(s): National Basic Research Program of China(973 Program); National Natural Science Foundation of China; Chinese Academy of Sciences 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of the Proton Sensitivity of Human GluN1-GluN2A NMDA Receptors

Zhang, J.B.Chang, S.Xu, P.Miao, M.Wu, H.Zhang, Y.Zhang, T.Wang, H.Zhang, J.Xie, C.Song, N.Luo, C.Zhang, X.Zhu, S.

(2018) Cell Rep 25: 3582-3590.e4

  • DOI: 10.1016/j.celrep.2018.11.071
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N-methyl-D-aspartate (NMDA) receptors are critical for synaptic development and plasticity. While glutamate is the primary agonist, protons can modulate NMDA receptor activity at synapses during vesicle exocytosis by mechanisms that are unknown. We u ...

    N-methyl-D-aspartate (NMDA) receptors are critical for synaptic development and plasticity. While glutamate is the primary agonist, protons can modulate NMDA receptor activity at synapses during vesicle exocytosis by mechanisms that are unknown. We used cryo-electron microscopy to solve the structures of the human GluN1-GluN2A NMDA receptor at pH 7.8 and pH 6.3. Our structures demonstrate that the proton sensor predominantly resides in the N-terminal domain (NTD) of the GluN2A subunit and reveal the allosteric coupling mechanism between the proton sensor and the channel gate. Under high-pH conditions, the GluN2A-NTD adopts an "open-and-twisted" conformation. However, upon protonation at the lower pH, the GluN2A-NTD transitsĀ from an open- to closed-cleft conformation, causingĀ rearrangements between the tetrameric NTDs andĀ agonist-binding domains. The conformational mobility observed in our structures (presumably from protonation) is supported by molecular dynamics simulation. Our findings reveal the structural mechanisms by which protons allosterically inhibit human GluN1-GluN2A receptor activity.


    Organizational Affiliation

    Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing, China. Electronic address: cluo@simm.ac.cn.,Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing, China. Electronic address: shujiazhu@ion.ac.cn.,Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China. Electronic address: xzhang1999@zju.edu.cn.,Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing, China.,Department of Biophysics, and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Center of Cryo Electron Microscopy, Zhejiang University School of Medicine, Hangzhou, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 1
A, C
847Homo sapiensMutation(s): 1 
Gene Names: GRIN1 (NMDAR1)
Find proteins for Q05586 (Homo sapiens)
Go to Gene View: GRIN1
Go to UniProtKB:  Q05586
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 2A
B, D
841Homo sapiensMutation(s): 2 
Gene Names: GRIN2A (NMDAR2A)
Find proteins for Q12879 (Homo sapiens)
Go to Gene View: GRIN2A
Go to UniProtKB:  Q12879
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China(973 Program)China2017YFA0504803
National Basic Research Program of China(973 Program)China2018YFA0507700
National Basic Research Program of China(973 Program)China2017YFA0505700
National Natural Science Foundation of ChinaChina31771115
Chinese Academy of SciencesChinaXDBS32020000

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Advisory, Data collection, Derived calculations, Refinement description