[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleDistinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits.
Journal, issue, pagesNat Struct Mol Biol, Vol. 30, Issue 5, Page 629-639, Year 2023
Publish dateMar 23, 2023
AuthorsJilin Zhang / Ming Zhang / Qinrui Wang / Han Wen / Zheyi Liu / Fangjun Wang / Yuhang Wang / Fenyong Yao / Nan Song / Zengwei Kou / Yang Li / Fei Guo / Shujia Zhu /
PubMed AbstractN-methyl-D-aspartate (NMDA) receptors are heterotetramers comprising two GluN1 and two alternate GluN2 (N2A-N2D) subunits. Here we report full-length cryo-EM structures of the human N1-N2D di- ...N-methyl-D-aspartate (NMDA) receptors are heterotetramers comprising two GluN1 and two alternate GluN2 (N2A-N2D) subunits. Here we report full-length cryo-EM structures of the human N1-N2D di-heterotetramer (di-receptor), rat N1-N2C di-receptor and N1-N2A-N2C tri-heterotetramer (tri-receptor) at a best resolution of 3.0 Å. The bilobate N-terminal domain (NTD) in N2D intrinsically adopts a closed conformation, leading to a compact NTD tetramer in the N1-N2D receptor. Additionally, crosslinking the ligand-binding domain (LBD) of two N1 protomers significantly elevated the channel open probability (Po) in N1-N2D di-receptors. Surprisingly, the N1-N2C di-receptor adopted both symmetric (minor) and asymmetric (major) conformations, the latter further locked by an allosteric potentiator, PYD-106, binding to a pocket between the NTD and LBD in only one N2C protomer. Finally, the N2A and N2C subunits in the N1-N2A-N2C tri-receptor display a conformation close to one protomer in the N1-N2A and N1-N2C di-receptors, respectively. These findings provide a comprehensive structural understanding of diverse function in major NMDA receptor subtypes.
External linksNat Struct Mol Biol / PubMed:36959261
MethodsEM (single particle)
Resolution3.0 - 6.4 Å
Structure data

33788

7yff

EMDB-33788, PDB-7yff:
Structure of GluN1a-GluN2D NMDA receptor in complex with agonist glycine and competitive antagonist CPP.
Method: EM (single particle) / Resolution: 3.6 Å

33789

7yfg

EMDB-33789, PDB-7yfg:
Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (major class in asymmetry)
Method: EM (single particle) / Resolution: 3.6 Å

33790

7yfh

EMDB-33790, PDB-7yfh:
Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106
Method: EM (single particle) / Resolution: 3.0 Å

33791

7yfi

EMDB-33791, PDB-7yfi:
Structure of the Rat tri-heteromeric GluN1-GluN2A-GluN2C NMDA receptor in complex with glycine and glutamate
Method: EM (single particle) / Resolution: 3.3 Å

33792

7yfl

EMDB-33792, PDB-7yfl:
Structure of GluN1a-GluN2D NMDA receptor in complex with agonists glycine and glutamate.
Method: EM (single particle) / Resolution: 3.9 Å

33793

7yfm

EMDB-33793, PDB-7yfm:
Structure of GluN1b-GluN2D NMDA receptor in complex with agonists glycine and glutamate.
Method: EM (single particle) / Resolution: 5.1 Å

33795

7yfo

EMDB-33795, PDB-7yfo:
Structure of GluN1a E698C-GluN2D NMDA receptor in cystines crosslinked state.
Method: EM (single particle) / Resolution: 6.4 Å

33798

7yfr

EMDB-33798, PDB-7yfr:
Structure of GluN1a E698C-GluN2D NMDA receptor in cystines non-crosslinked state.
Method: EM (single particle) / Resolution: 5.1 Å

34674

8hdk

EMDB-34674, PDB-8hdk:
Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (minor class in symmetry)
Method: EM (single particle) / Resolution: 4.3 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-GLY:
GLYCINE

ChemComp-7RC:
(2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid

ChemComp-GLU:
GLUTAMIC ACID

ChemComp-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

Source
  • homo sapiens (human)
  • rattus norvegicus (Norway rat)
KeywordsELECTRON TRANSPORT / ion channel / cryo-EM structure / glutamate receptor / synaptic protein / MEMBRANE PROTEIN / NMDA receptor / GluN2C / GluN2A

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more