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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
#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA
#2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA
#3: Surface view with fitted model, atomic models: PDB-4aod, Surface level: 1, Made by UCSF CHIMERA
#4: Surface view with fitted model, atomic models: PDB-4aoe, Surface level: 1, Made by UCSF CHIMERA
 Entry | |
| Summary | |
| Database / ID | EM DATA BANK (EMDB) / 2055 |
|---|---|
| Title | Acetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits) |
| Map | A negative temperature factor of 278.9 A^2 was applied to the map. |
| Sample | Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata |
| Keywords |  ligand 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 |
| Authors | Saur M, Moeller V, Kapetanopoulos K, Braukmann S, Gebauer W, Tenzer S, Markl J |
| Date | Deposition: 2012-03-19, Header release: 2012-04-05, Map release: 2012-08-29, Last update: 2012-09-26 |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie Page#1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA #3: Surface view with fitted model, atomic models: PDB-4aod, Surface level: 1, Made by UCSF CHIMERA #4: Surface view with fitted model, atomic models: PDB-4aoe, Surface level: 1, Made by UCSF CHIMERA |
| Supplemental images | |
| Structure viewers |  Yorodumi,  Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe) |
| Related Structure Data | |
| Related Entries |
Cite: data citing same article Fit: output model of fitting |
| Similar strucutres (beta) |
 List of similar structure data  about Omokage system |
 Article | |
| Citation - Primary | |
| Article | PLoS ONE, Vol. 7, Issue 8, Page e43685, 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 Institute of Zoology, Johannes Gutenberg University, Mainz, Germany. |
| Keywords | Acetylcholine (metabolism, 51-84-3), Animals, Biomphalaria (metabolism), Carrier Proteins (chemistry), Hemolymph (metabolism), Protein Structure, Secondary, Protein Structure, Tertiary |
| Links | DOI: 10.1371/journal.pone.0043685, PubMed: 22916297, PMC: PMC3423370 |
 Map | |||||||||||||||||||||||||
| File |  EMD-2055.map ( map file in CCP4 format, 95553 KB ) | ||||||||||||||||||||||||
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| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
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| Data Type | Image stored as Reals | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A = 286.0 A , B = 286.0 A , C = 286.0 A , alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 1 A , Y = 1 A , Z = 1 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | A negative temperature factor of 278.9 A^2 was applied to the map. | ||||||||||||||||||||||||
 Supplement | |
| Images | |
| Images | |
|---|---|
 Sample | |
| Name | Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata |
|---|---|
| Number of Components | 1 |
| Theoretical Mass | 1.86 MDa |
| Mass-estimation Method | SDS-PAGE |
| Experimental Mass | 1.86 MDa |
| Component #1: protein - BgAChBP | |
| Scientific name | Biomphalaria glabrata Acetylcholine Binding Protein |
| Common Name | BgAChBP |
| Theoretical Mass | 1.86 MDa |
| Experimental Mass | 1.86 MDa |
| 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. |
| Oligomeric Details | Dodecapentamer |
| Number of Copies | 60 |
| Scientific Name of Species | Biomphalaria glabrata (NCBI Taxonomy: 6526) |
| Recombinant expression | No |
| Natural Source | Organ Or Tissue: Hemolymph |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 1.2 mg/ml |
|---|---|
| Specimen Support Details | C-flat holey carbon grids CF-2/2-3C-T, 30s glow discharge at 25 mA |
| Specimen State | particle |
| Buffer | Details: 50 mM Tris-HCl, 5 mM MgCl2, 5mM CaCl2, 300mM NaCl pH: 7.4 |
| Vitrification | |
| Method | 2 x3.5 microlitres with 2 x 3s blotting |
| Cryogen Name | ETHANE |
| Humidity | 97 |
| Instrument | GATAN CRYOPLUNGE 3 |
| Temperature | 97 Kelvin |
| Imaging | |
| Microscope | FEI TECNAI F20 |
| Date | 04-JUN-2008 |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 30 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 50000 X, |
| Astigmatism | Objective lens astigmatism was corrected at 120,000 times magnification |
| Nominal Cs | 2.0 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 2000 nm - 5000 nm |
| Specimen Holder | |
| Holder | ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Temperature | 101 Kelvin |
| Camera | |
| Detector | Kodak SO163 |
| Image Acquisition | |
| Scanner | PRIMESCAN |
| Number of Digital Images | 151 |
| Sampling Size | 5 microns |
| Quant Bit Number | 8 |
 Processing | |
| Method | single particle (icosahedral) reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | Projection matching |
| Software | EMAN1.9 |
| CTF Correction | per micrograph |
| Resolution By Author | 6 |
| Resolution Method | FSC at 0.5 cut-off |
| Single Particle | |
| Details | manual selection with boxer, ctf-correction with FindCTF2d, refinement: EMAN1.9 (15 iterative cycles), final reconstruction using 1-degree references |
| Number of Projections | 8374 |
| Number of Class Averages | 608 |
| Applied Symmetry | I (icosahedral) |
| Fitted Coordinate | |
| PDB entry ID | |
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