[English] 日本語
Yorodumi
- EMDB-60794: Cryo-EM structure of MT3-Muscarinic acetylcholine receptor 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60794
TitleCryo-EM structure of MT3-Muscarinic acetylcholine receptor 4
Map data
Sample
  • Complex: MT3-alpha2AAR complex
    • Protein or peptide: Muscarinic toxin 3
    • Protein or peptide: Muscarinic acetylcholine receptor M4,Soluble cytochrome b562
Keywordscomplex / MEMBRANE PROTEIN
Function / homology
Function and homology information


Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / regulation of locomotion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled acetylcholine receptor signaling pathway / toxin activity / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane ...Muscarinic acetylcholine receptors / G protein-coupled acetylcholine receptor activity / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / regulation of locomotion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / G protein-coupled acetylcholine receptor signaling pathway / toxin activity / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / cell surface receptor signaling pathway / synapse / dendrite / signal transduction / extracellular region / plasma membrane
Similarity search - Function
Muscarinic acetylcholine receptor M4 / Snake cytotoxin, cobra-type / Muscarinic acetylcholine receptor family / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx ...Muscarinic acetylcholine receptor M4 / Snake cytotoxin, cobra-type / Muscarinic acetylcholine receptor family / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Muscarinic acetylcholine receptor M4 / Muscarinic toxin 3
Similarity search - Component
Biological speciesHomo sapiens (human) / Dendroaspis angusticeps (eastern green mamba)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZhong YX / Tao HH / Tao YY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of MT3-alpha2AAR
Authors: Zhong YX / Tao HH / Tao YY
History
DepositionJul 13, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60794.png

Downloads & links

-
Map

FileDownload / File: emd_60794.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.546
Minimum - Maximum-1.7069795 - 2.8597615
Average (Standard dev.)0.0005547446 (±0.046579957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_60794_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60794_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MT3-alpha2AAR complex

EntireName: MT3-alpha2AAR complex
Components
  • Complex: MT3-alpha2AAR complex
    • Protein or peptide: Muscarinic toxin 3
    • Protein or peptide: Muscarinic acetylcholine receptor M4,Soluble cytochrome b562

-
Supramolecule #1: MT3-alpha2AAR complex

SupramoleculeName: MT3-alpha2AAR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Muscarinic toxin 3

MacromoleculeName: Muscarinic toxin 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dendroaspis angusticeps (eastern green mamba)
Molecular weightTheoretical: 7.396488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LTCVTKNTIF GITTENCPAG QNLCFKRWHY VIPRYTEITR GCAATCPIPE NYDSIHCCKT DKCNE

UniProtKB: Muscarinic toxin 3

-
Macromolecule #2: Muscarinic acetylcholine receptor M4,Soluble cytochrome b562

MacromoleculeName: Muscarinic acetylcholine receptor M4,Soluble cytochrome b562
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.768914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HNRYETVEMV FIATVTGSLS LVTVVGNILV MLSIKVNRQL QTVNNYFLFS LACADLIIGA FSMNLYTVYI IKGYWPLGAV VCDLWLALD YVVSNASVMN LLIISFDRYF CVTKPLTYPA RRTTKMAGLM IAAAWVLSFV LWAPAILFWQ FVVGKRTVPD N QCFIQFLS ...String:
HNRYETVEMV FIATVTGSLS LVTVVGNILV MLSIKVNRQL QTVNNYFLFS LACADLIIGA FSMNLYTVYI IKGYWPLGAV VCDLWLALD YVVSNASVMN LLIISFDRYF CVTKPLTYPA RRTTKMAGLM IAAAWVLSFV LWAPAILFWQ FVVGKRTVPD N QCFIQFLS NPAVTFGTAI AAFYLPVVIM TVLYIHISLA SRSRVADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AA LDAQKAS GSGSPEMKDF RHGFDILVGQ IDDALKLANE GKVKEAQAAA EQLKTTRNAY IQKYLRMAAR ERKVTRTIFA ILL AFILTW TPYNVMVLVN TFCQSCIPDT VWSIGYWLCY VNSTINPACY ALCNATFKKT FRHLLLKIAA LKEKIAALKE KIAA LKEAE EKRASRLEEE LRRRLTEGSH HHHHHHH

UniProtKB: Muscarinic acetylcholine receptor M4, Muscarinic acetylcholine receptor M4

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5747771
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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