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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3645 | |||||||||
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Title | CryoEM density of TcdA1 in prepore state (SPHIRE tutorial) | |||||||||
![]() | CryoEM density of TcdA1 in prepore state | |||||||||
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Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Raunser S / Gatsogiannis S / Roderer S | |||||||||
![]() | ![]() Title: High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE. Authors: Toshio Moriya / Michael Saur / Markus Stabrin / Felipe Merino / Horatiu Voicu / Zhong Huang / Pawel A Penczek / Stefan Raunser / Christos Gatsogiannis / ![]() ![]() Abstract: SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) ...SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.5 KB 11.5 KB | Display Display | ![]() |
Images | ![]() | 90 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 237.5 KB | Display | ![]() |
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Full document | ![]() | 236.7 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
EM raw data | ![]() Data size: 72.8 Data #1: Unaligned multi-frame micrographs of TcdA1 in prepore state (SPHIRE tutorial dataset) [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | CryoEM density of TcdA1 in prepore state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : TcdA1
Entire | Name: TcdA1 |
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Components |
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-Supramolecule #1: TcdA1
Supramolecule | Name: TcdA1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Prepore state |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1.4 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 5 Component:
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Grid | Model: Quantifoil 2/1 2nm C / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Cs corrected microscope |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 112 / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |