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Acetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits)

by single particle (icosahedral) reconstruction, at 6 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4aod, Surface level: 1, Image by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-4aoe, Surface level: 1, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 2055
TitleAcetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits)
MapA negative temperature factor of 278.9 A^2 was applied to the map.
SampleAcetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
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
AuthorsSaur M, Moeller V, Kapetanopoulos K, Braukmann S, Gebauer W, Tenzer S, Markl J
DateDeposition: 2012-03-19, Header release: 2012-04-05, Map release: 2012-08-29, Last update: 2012-09-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4aod, Surface level: 1, Image by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-4aoe, Surface level: 1, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-4aod

CiteFit

PDB-4aoe

CiteFit

Cite: data citing same article

Fit: output model of fitting

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Article
Citation - Primary
ArticlePLoS ONE, Vol. 7, Issue 8, Page e43685, Year 2012
TitleAcetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits).
AuthorsMichael Saur, Vanessa Moeller, Katharina Kapetanopoulos, Sandra Braukmann, Wolfgang Gebauer, Stefan Tenzer, Jürgen Markl
Institute of Zoology, Johannes Gutenberg University, Mainz, Germany.
KeywordsAcetylcholine (metabolism), Animals, Biomphalaria (metabolism), Carrier Proteins (chemistry), Hemolymph (metabolism), Protein Structure, Secondary, Protein Structure, Tertiary
LinksDOI: 10.1371/journal.pone.0043685, PubMed: 22916297, PMC: PMC3423370
Map
Fileemd_2055.map.gz ( map file in CCP4 format, 91383 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
286 pix
1 A/pix
= 286. A
286 pix
1 A/pix
= 286. A
286 pix
1 A/pix
= 286. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum: -0.59094787 - 3.62690711
Average (Standard dev.): 0.14051077 (0.43470621)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions286286286
Origin000
Limit285285285
Spacing286286286
Unit CellA= B= C: 286 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z111
M x/y/z286286286
origin x/y/z0.0000.0000.000
length x/y/z286.000286.000286.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS286286286
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.5913.6270.141
Annotation DetailsA negative temperature factor of 278.9 A^2 was applied to the map.
Supplement
Images
Images
Sample
NameAcetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
Number of Components1
Theoretical Mass1.86MDa
Mass-estimation MethodSDS-PAGE
Experimental Mass1.86MDa
Component #1: protein - BgAChBP
Scientific nameBiomphalaria glabrata Acetylcholine Binding Protein
Common NameBgAChBP
Theoretical Mass1.86 MDa
Experimental Mass1.86 MDa
DetailsAs 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.
Oligomeric DetailsDodecapentamer
Number of Copies60
Scientific Name of SpeciesBiomphalaria glabrata
NCBI taxonomy6526
Recombinant expressionNo
Natural SourceOrgan Or Tissue: Hemolymph
Experiment
Sample Preparation
Specimen Conc1.2 mg/ml
Specimen Support DetailsC-flat holey carbon grids CF-2/2-3C-T, 30s glow discharge at 25 mA
Specimen Stateparticle
BufferDetails: 50 mM Tris-HCl, 5 mM MgCl2, 5mM CaCl2, 300mM NaCl
pH: 7.4
Vitrification
Method2 x3.5 microlitres with 2 x 3s blotting
Cryogen NameETHANE
Humidity97
InstrumentGATAN CRYOPLUNGE 3
Temperature97 Kelvin
Imaging #0
MicroscopeFEI TECNAI F20
Date04-JUN-2008
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose30 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
AstigmatismObjective lens astigmatism was corrected at 120,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 5000 nm
Specimen Holder
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature101 K
Camera
DetectorKODAK SO-163 FILM
Imaging #1
MicroscopeFEI TECNAI F20
Date25-MAY-2011
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose30 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000
AstigmatismObjective lens astigmatism was corrected at 120,000 times magnification
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 5000 nm
Specimen Holder
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature101 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
ScannerPRIMESCAN
Number of Digital Images151
Sampling Size5
Quant Bit Number8
Processing
Methodsingle particle (icosahedral) reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareEMAN1.9
CTF Correctionper micrograph
Resolution By Author6 A
Resolution MethodFSC 0.5
Single Particle
Detailsmanual selection with boxer, ctf-correction with FindCTF2d, refinement: EMAN1.9 (15 iterative cycles), final reconstruction using 1-degree references
Number of Projections8374
Number of Class Averages608
Applied SymmetryI (icosahedral)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-2055.xml (9.3 KB)
Map dataemd_2055.map.gz (83.7 MB)
ImagesEMD-2055_gallery.png (978.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-2055
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 27.2 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 27.3 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 1.6 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 1.6 MB