[English] 日本語
Yorodumi
- EMDB-2055: Acetylcholine-binding protein in the hemolymph of the planorbid s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2055
TitleAcetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits)
Map dataA negative temperature factor of 278.9 A^2 was applied to the map.
Sample
  • Sample: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
  • Protein or peptide: Biomphalaria glabrata Acetylcholine Binding Protein
Keywordsligand gated ion channel / LGIC / Cys-loop receptor / AChBP / acetylcholine binding protein / acetylcholine / AChR / acetylcholine receptor / Myasthenia gravis / pentagonal dodecahedron / nicotinic / dodecahedron / Schistosoma mansoni / bilharziosis / Biomphalaria glabrata / snail
Function / homologyextracellular ligand-gated monoatomic ion channel activity / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / transmembrane signaling receptor activity / membrane => GO:0016020 / Acetylcholine-binding protein type 2 / Acetylcholine-binding protein type 1
Function and homology information
Biological speciesBiomphalaria glabrata (bloodfluke planorb)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsSaur M / Moeller V / Kapetanopoulos K / Braukmann S / Gebauer W / Tenzer S / Markl J
CitationJournal: PLoS One / Year: 2012
Title: Acetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits).
Authors: Michael Saur / Vanessa Moeller / Katharina Kapetanopoulos / Sandra Braukmann / Wolfgang Gebauer / Stefan Tenzer / Jürgen Markl /
Abstract: Nicotinic acetylcholine receptors (nAChR) play important neurophysiological roles and are of considerable medical relevance. They have been studied extensively, greatly facilitated by the gastropod ...Nicotinic acetylcholine receptors (nAChR) play important neurophysiological roles and are of considerable medical relevance. They have been studied extensively, greatly facilitated by the gastropod acetylcholine-binding proteins (AChBP) which represent soluble structural and functional homologues of the ligand-binding domain of nAChR. All these proteins are ring-like pentamers. Here we report that AChBP exists in the hemolymph of the planorbid snail Biomphalaria glabrata (vector of the schistosomiasis parasite) as a regular pentagonal dodecahedron, 22 nm in diameter (12 pentamers, 60 active sites). We sequenced and recombinantly expressed two ∼25 kDa polypeptides (BgAChBP1 and BgAChBP2) with a specific active site, N-glycan site and disulfide bridge variation. We also provide the exon/intron structures. Recombinant BgAChBP1 formed pentamers and dodecahedra, recombinant BgAChBP2 formed pentamers and probably disulfide-bridged di-pentamers, but not dodecahedra. Three-dimensional electron cryo-microscopy (3D-EM) yielded a 3D reconstruction of the dodecahedron with a resolution of 6 Å. Homology models of the pentamers docked to the 6 Å structure revealed opportunities for chemical bonding at the inter-pentamer interfaces. Definition of the ligand-binding pocket and the gating C-loop in the 6 Å structure suggests that 3D-EM might lead to the identification of functional states in the BgAChBP dodecahedron.
History
DepositionMar 19, 2012-
Header (metadata) releaseApr 5, 2012-
Map releaseAug 29, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4aod
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4aoe
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4aoe
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2055_gal...

Downloads & links

-
Map

FileDownload / File: emd_2055.map.gz / Format: CCP4 / Size: 87.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA negative temperature factor of 278.9 A^2 was applied to the map.
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.59094787 - 3.62690711
Average (Standard dev.)0.14051077 (±0.43470621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions286286286
Spacing286286286
CellA=B=C: 286.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z286286286
origin x/y/z0.0000.0000.000
length x/y/z286.000286.000286.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS286286286
D min/max/mean-0.5913.6270.141

-
Supplemental data

-
Sample components

-
Entire : Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata

EntireName: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
Components
  • Sample: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
  • Protein or peptide: Biomphalaria glabrata Acetylcholine Binding Protein

-
Supramolecule #1000: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata

SupramoleculeName: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 1.86 MDa / Theoretical: 1.86 MDa / Method: SDS-PAGE

-
Macromolecule #1: Biomphalaria glabrata Acetylcholine Binding Protein

MacromoleculeName: Biomphalaria glabrata Acetylcholine Binding Protein / type: protein_or_peptide / ID: 1 / Name.synonym: BgAChBP
Details: As yet, it is not entirely clear whether the dodecahedron is a homomeric assembly of either type one and/or two, or a heteromeric assembly of types one and two.
Number of copies: 60 / Oligomeric state: Dodecapentamer / Recombinant expression: No
Source (natural)Organism: Biomphalaria glabrata (bloodfluke planorb) / Tissue: Hemolymph
Molecular weightExperimental: 1.86 MDa / Theoretical: 1.86 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.4 / Details: 50 mM Tris-HCl, 5 mM MgCl2, 5mM CaCl2, 300mM NaCl
GridDetails: C-flat holey carbon grids CF-2/2-3C-T, 30s glow discharge at 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 97 % / Chamber temperature: 97 K / Instrument: GATAN CRYOPLUNGE 3 / Method: 2 x3.5 microlitres with 2 x 3s blotting

-
Electron microscopy #1

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 101 K
Microscopy ID1
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
DateJun 4, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5 µm / Number real images: 151 / Average electron dose: 30 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Electron microscopy #2

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 101 K
Microscopy ID2
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
DateMay 25, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5 µm / Number real images: 151 / Average electron dose: 30 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: per micrograph
Final two d classificationNumber classes: 608
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1.9 / Number images used: 8374
Detailsmanual selection with boxer, ctf-correction with FindCTF2d, refinement: EMAN1.9 (15 iterative cycles), final reconstruction using 1-degree references

+
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