[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

TitleMolecular mechanism of calcium permeability and magnesium block in NMDA receptors.
Journal, issue, pagesNat Neurosci, Year 2026
Publish dateMay 5, 2026
AuthorsRuben Steigerwald / Max Epstein / Tsung-Han Chou / Noriko Simorowski / Hiro Furukawa /
PubMed AbstractHebbian neuroplasticity, which is thought to be a cellular substrate of learning and memory, can occur by means of coincidental detection of presynaptic neurotransmitter release and Ca influx upon ...Hebbian neuroplasticity, which is thought to be a cellular substrate of learning and memory, can occur by means of coincidental detection of presynaptic neurotransmitter release and Ca influx upon postsynaptic depolarization. This is mediated at a molecular level by N-methyl-D-aspartate-type glutamate receptors, which bind glutamate and glycine and facilitate Ca influx upon relief of Mg channel block during membrane depolarization. However, the structural mechanism underlying Ca permeability and Mg blockade in N-methyl-D-aspartate-type glutamate receptors has yet to be fully elucidated. Here we demonstrate using single-particle cryo-electron microscopy that Ca permeation through the narrow constriction of the cation selectivity filter involves partial dehydration, as evidenced by several Ca binding sites. In contrast, Mg binds outside of the selectivity filter through a water network and remains hydrated, thereby acting as a channel blocker. Furthermore, the lipid network around the selectivity filter influences the stability of Mg binding in a voltage-dependent manner. Our study details the transmembrane chemistry essential for initiating neuroplasticity.
External linksNat Neurosci / PubMed:42086762
MethodsEM (single particle)
Resolution2.59 - 3.6 Å
Structure data

70297

9obs

EMDB-70297, PDB-9obs:
glutamate/glycine-bound GluN1a/2B NMDAR
Method: EM (single particle) / Resolution: 3.18 Å

70298

9obt

EMDB-70298, PDB-9obt:
TMD of glutamate/glycine-bound GluN1a/2B NMDAR
Method: EM (single particle) / Resolution: 3.01 Å

70299

9obu

EMDB-70299, PDB-9obu:
glycine/glutamate and Mg2+-bound GluN1a/2B NMDAR
Method: EM (single particle) / Resolution: 3.16 Å

70300

9obv

EMDB-70300, PDB-9obv:
Mg2+-bound GluN1a/2B NMDAR (upper)
Method: EM (single particle) / Resolution: 3.21 Å

70301

9obw

EMDB-70301, PDB-9obw:
Mg2+ bound GluN1a/2B NMDAR (lower)
Method: EM (single particle) / Resolution: 3.15 Å

70302

9obx

EMDB-70302, PDB-9obx:
glutamate/glycine and Ca2+-bound GluN1a/2B NMDAR
Method: EM (single particle) / Resolution: 2.59 Å

70303

9oby

EMDB-70303, PDB-9oby:
Ca2+-bound GluN1a/2B NMDAR (S1)
Method: EM (single particle) / Resolution: 3.6 Å

70304

9obz

EMDB-70304, PDB-9obz:
Ca2+-bound GluN1a/2B NMDAR (S2)
Method: EM (single particle) / Resolution: 2.81 Å

70305

9oc0

EMDB-70305, PDB-9oc0:
Ca2+-bound GluN1a/2B NMDAR (S3)
Method: EM (single particle) / Resolution: 2.97 Å

70306

9oc1

EMDB-70306, PDB-9oc1:
Ca2+-bound GluN1a/2B NMDAR (S4)
Method: EM (single particle) / Resolution: 2.76 Å

70307

9oc2

EMDB-70307, PDB-9oc2:
Ca2+-bound GluN1a/2B NMDAR (S5)
Method: EM (single particle) / Resolution: 2.69 Å

Chemicals

ChemComp-GLY:
GLYCINE

ChemComp-GLU:
GLUTAMIC ACID

ChemComp-CLR:
CHOLESTEROL

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

ChemComp-HOH:
WATER

ChemComp-MG:
Unknown entry

ChemComp-CA:
Unknown entry

Source
  • rattus norvegicus (Norway rat)
KeywordsMEMBRANE PROTEIN / Ion Channels / NMDAR / membrane proteins / ion channel

+
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