[English] 日本語
Yorodumi
- EMDB-61755: Structure of ATD truncated glutamate receptor mGluD1 complexed wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61755
TitleStructure of ATD truncated glutamate receptor mGluD1 complexed with D-serine
Map data
Sample
  • Complex: ATD truncated mGluD1 complexed with D-serine
    • Protein or peptide: Glutamate receptor ionotropic, delta-1
  • Ligand: D-SERINE
Keywordsionotropic glutamate receptor / cation channel / complex / neurology / MEMBRANE PROTEIN
Function / homology
Function and homology information


GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels ...GABA receptor activity / trans-synaptic protein complex / negative regulation of synaptic plasticity / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / regulation of postsynapse organization / AMPA glutamate receptor activity / AMPA glutamate receptor complex / social behavior / regulation of postsynaptic membrane neurotransmitter receptor levels / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / GABA-ergic synapse / phospholipase C-activating G protein-coupled receptor signaling pathway / dendritic spine / postsynaptic membrane / glutamatergic synapse / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / 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, delta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsDai Z / Yin YX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030081, 81874235 China
CitationJournal: To Be Published
Title: Structure of ATD truncated glutamate receptor mGluD1 complexed with D-serine
Authors: Dai Z / Yin YX
History
DepositionSep 29, 2024-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61755.png

Downloads & links

-
Map

FileDownload / File: emd_61755.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 340 pix.
= 326.4 Å		0.96 Å/pix.
x 340 pix.
= 326.4 Å		0.96 Å/pix.
x 340 pix.
= 326.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-4.277125 - 6.6354694
Average (Standard dev.)0.0007975987 (±0.08014685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 326.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_61755_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61755_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ATD truncated mGluD1 complexed with D-serine

EntireName: ATD truncated mGluD1 complexed with D-serine
Components
  • Complex: ATD truncated mGluD1 complexed with D-serine
    • Protein or peptide: Glutamate receptor ionotropic, delta-1
  • Ligand: D-SERINE

-
Supramolecule #1: ATD truncated mGluD1 complexed with D-serine

SupramoleculeName: ATD truncated mGluD1 complexed with D-serine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Glutamate receptor ionotropic, delta-1

MacromoleculeName: Glutamate receptor ionotropic, delta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 53.201691 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEALTLWLLP WICQCVTVRA MGSRLQGLTL KVVTVLEEPF VMVAENILGQ PKRYKGFSID VLDALAKALG FKYEIYQAPD GRYGHQLHN TSWNGMIGEL ISKRADLAIS AITITPERES VVDFSKRYMD YSVGILIKKP EEKISIFSLF APFDFAVWAC I AAAIPVVG ...String:
MEALTLWLLP WICQCVTVRA MGSRLQGLTL KVVTVLEEPF VMVAENILGQ PKRYKGFSID VLDALAKALG FKYEIYQAPD GRYGHQLHN TSWNGMIGEL ISKRADLAIS AITITPERES VVDFSKRYMD YSVGILIKKP EEKISIFSLF APFDFAVWAC I AAAIPVVG VLIFVLNRIQ AVRSQSATQP RPSASATLHS AIWIVYGAFV QQGGESSVNS VAMRIVMGSW WLFTLIVCSS YT ANLAAFL TVSRMDNPIR TFQDLSKQLE MSYGTVRDSA VYEYFRAKGT NPLEQDSTFA ELWRTISKNG GADNCVSNPS EGI RKAKKG NYAFLWDVAV VEYAALTDDD CSVTVIGNSI SSKGYGIALQ HGSPYRDLFS QRILELQDTG DLDVLKQKWW PHTG RCDLT SHSSTQTEGK SLKLHSFAGV FCILAIGLLL ACLVAALELW WNSNRCHQET PKEDKEVNLE GGVEGGVEEN LYFQ

UniProtKB: Glutamate receptor ionotropic, delta-1

-
Macromolecule #2: D-SERINE

MacromoleculeName: D-SERINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: DSN
Molecular weightTheoretical: 105.093 Da
Chemical component information

ChemComp-DSN:
D-SERINE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2352980
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71335
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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