[English] 日本語
Yorodumi
- EMDB-61000: Structure of the human GluN1-N2B NMDA receptors in the Mg2+ bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61000
TitleStructure of the human GluN1-N2B NMDA receptors in the Mg2+ bound state
Map data
Sample
  • Complex: Human GluN1-N2B receptors in the Mg2+-bond state
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid
  • Ligand: MAGNESIUM ION
KeywordsGluN1-N2B NMDA receptors / MEMBRANE PROTEIN
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / glutamate receptor signaling pathway / glutamate binding / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / positive regulation of calcium ion transport into cytosol / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / Long-term potentiation / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / monoatomic ion channel complex / synaptic cleft / calcium ion homeostasis / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / EPHB-mediated forward signaling / sodium ion transmembrane transport / Ras activation upon Ca2+ influx through NMDA receptor / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / synaptic membrane / postsynaptic density membrane / terminal bouton / brain development / visual learning / calcium ion transmembrane transport / regulation of synaptic plasticity / long-term synaptic potentiation / late endosome / synaptic vesicle / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / dendritic spine / response to ethanol / postsynaptic membrane / cytoskeleton / learning or memory / lysosome / calmodulin binding / neuron projection / postsynaptic density / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsHuang X / Sun X / Zhu S
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022ZD0212700 China
National Natural Science Foundation of China (NSFC)32221003 China
Chinese Academy of Sciencesto S.Z. China
CitationJournal: Neuron / Year: 2025
Title: Structural insights into the diverse actions of magnesium on NMDA receptors.
Authors: Xuejing Huang / Xiaole Sun / Qinrui Wang / Jilin Zhang / Han Wen / Wan-Jin Chen / Shujia Zhu /
Abstract: Magnesium (Mg) is a key regulatory ion of N-methyl-ᴅ-aspartate (NMDA) receptors, including conferring them to function as coincidence detectors for excitatory synaptic transmission. However, the ...Magnesium (Mg) is a key regulatory ion of N-methyl-ᴅ-aspartate (NMDA) receptors, including conferring them to function as coincidence detectors for excitatory synaptic transmission. However, the structural basis underlying the Mg action on NMDA receptors remains unclear. Here, we report the cryo-EM structures of GluN1-N2B receptors and identify three distinct Mg-binding pockets. Specifically, site Ⅰ is located at the selectivity filter where an asparagine ring forms coordination bonds with Mg and is responsible for the voltage-dependent block. Sites Ⅱ and Ⅲ are located at the N-terminal domain (NTD) of the GluN2B subunit and involved in the allosteric potentiation and inhibition, respectively. Site Ⅱ consists of three acidic residues, and the combination of three mutations abolishes the GluN2B-specific Mg potentiation, while site Ⅲ overlaps with the Zn pocket, and mutations here significantly reduce the inhibition. Our study enhances the understanding of multifaceted roles of Mg in NMDA receptors and synaptic plasticity.
History
DepositionJul 31, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61000.png

Downloads & links

-
Map

FileDownload / File: emd_61000.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 350 pix.
= 259. Å		0.74 Å/pix.
x 350 pix.
= 259. Å		0.74 Å/pix.
x 350 pix.
= 259. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.019695124 - 0.041425083
Average (Standard dev.)0.00016603002 (±0.00193881)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 259.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_61000_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61000_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61000_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human GluN1-N2B receptors in the Mg2+-bond state

EntireName: Human GluN1-N2B receptors in the Mg2+-bond state
Components
  • Complex: Human GluN1-N2B receptors in the Mg2+-bond state
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Human GluN1-N2B receptors in the Mg2+-bond state

SupramoleculeName: Human GluN1-N2B receptors in the Mg2+-bond state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.55157 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VNIGAVLSTR KHEQMFREAV NQANKRHGSW KIQLNATSVT HKPNAIQMAL SVCEDLISSQ VYAILVSHPP TPNDHFTPTP VSYTAGFYR IPVLGLTTRM SIYSDKSIHL SFLRTVPPYS HQSSVWFEMM RVYSWNHIIL LVSDDHEGRA AQKRLETLLE E RESKAEKV ...String:
VNIGAVLSTR KHEQMFREAV NQANKRHGSW KIQLNATSVT HKPNAIQMAL SVCEDLISSQ VYAILVSHPP TPNDHFTPTP VSYTAGFYR IPVLGLTTRM SIYSDKSIHL SFLRTVPPYS HQSSVWFEMM RVYSWNHIIL LVSDDHEGRA AQKRLETLLE E RESKAEKV LQFDPGTKNV TALLMEAKEL EARVIILSAS EDDAATVYRA AAMLNMTGSG YVWLVGEREI SGNALRYAPD GI LGLQLIN GKNESAHISD AVGVVAQAVH ELLEKENITD PPRGCVGNTN IWKTGPLFKR VLMSSKYADG VTGRVEFNED GDR KFANYS IMNLQNRKLV QVGIYNGTHV IPNDRKIIWP GGETEKPRGY QMSTRLKIVT IHQEPFVYVK PTLSDGTCKE EFTV NGDPV KKVICTGPND TSPGSPRHTV PQCCYGFCID LLIKLARTMN FTYEVHLVAD GKFGTQERVN NSNKKEWNGM MGELL SGQA DMIVAPLTIN NERAQYIEFS KPFKYQGLTI LVKKEIPRST LDSFMQPFQS TLWLLVGLSV HVVAVMLYLL DRFSPF GRF KVNSEEEEED ALTLSSAMWF SWGVLLNSGI GEGAPRSFSA RILGMVWAGF AMIIVASYTA NLAAFLVLDR PEERITG IN DPRLRNPSDK FIYATVKQSS VDIYFRRQVE LSTMYRHMEK HNYESAAEAI QAVRDNKLHA FIWDSAVLEF EASQKCDL V TTGELFFRSG FGIGMRKDSP WKQNVSLSIL KSHENGFMED LDKTWVRYQE CDSRSNAPAT LTFENMAGVF MLVAGGIVA GIFLIFIEIA YKRH

UniProtKB: Glutamate receptor ionotropic, NMDA 1

-
Macromolecule #2: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.688602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IGIAVILVGT SDEVAIKDAH EKDDFHHLSV VPRVELVAMN ETDPKSIITR ICDLMSDRKI QGVVFADDTD QEAIAQILDF ISAQTLTPI LGIHGGSSMI MADKDESSMF FQFGPSIEQQ ASVMLNIMEE YDWYIFSIVT TYFPGYQDFV NKIRSTIENS F VGWELEEV ...String:
IGIAVILVGT SDEVAIKDAH EKDDFHHLSV VPRVELVAMN ETDPKSIITR ICDLMSDRKI QGVVFADDTD QEAIAQILDF ISAQTLTPI LGIHGGSSMI MADKDESSMF FQFGPSIEQQ ASVMLNIMEE YDWYIFSIVT TYFPGYQDFV NKIRSTIENS F VGWELEEV LLLDMSLDDG DSKIQNQLKK LQSPIILLYC TKEEATYIFE VANSVGLTGY GYTWIVPSLV AGDTDTVPAE FP TGLISVS YDEWDYGLPA RVRDGIAIIT TAASDMLSEH SFIPEPKSSC YNTHEKRIYQ SNMLNRYLIN VTFEGRNLSF SED GYQMHP KLVIILLNKE RKWERVGKWK DKSLQMKYYV WPRMCPETEE QEDDHLSIVT LEEAPFVIVE SVDPLSGTCM RNTV PCQKR IVTENKTDEE PGYIKKCCKG FCIDILKKIS KSVKFTYDLY LVTNGKHGKK INGTWNGMIG EVVMKRAYMA VGSLT INEE RSEVVDFSVP FIETGISVMV SRSNGTVSPS AFLEPFSADV WVMMFVMLLI VSAVAVFVFE YFSPVGYNRC LADGRE PGG PSFTIGKAIW LLWGLVFNNS VPVQNPKGTT SKIMVSVWAF FAVIFLASYT ANLAAFMIQE EYVDQVSGLS DKKFQRP ND FSPPFRFGTV PNGSTERNIR NNYAEMHAYM GKFNQRGVDD ALLSLKTGKL DAFIYDAAVL NYMAGRDEGC KLVTIGSG K VFASTGYGIA IQKDSGWKRQ VDLAILQLFG DGEMEELEAL WLTGICHNEK NEVMSSQLDI DNMAGVFYML GAAMALSLI TFICEHLF

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

-
Macromolecule #3: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #5: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid

MacromoleculeName: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid
type: ligand / ID: 5 / Number of copies: 2 / Formula: 7RC
Molecular weightTheoretical: 252.205 Da
Chemical component information

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

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7eu8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 157704
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

+
About Yorodumi

-
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

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more