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Open data
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Basic information
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Title | cryo iDPC-STEM structure recorded with CSA 4.5 | |||||||||
![]() | cryo iDPC-STEM map recorded with CSA 4.5 | |||||||||
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![]() | tobacco mosaic virus / RNA virus / VIRUS | |||||||||
Function / homology | Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
![]() | Sachse C / Leidl ML | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Single-particle cryo-EM structures from iDPC-STEM at near-atomic resolution. Authors: Ivan Lazić / Maarten Wirix / Max Leo Leidl / Felix de Haas / Daniel Mann / Maximilian Beckers / Evgeniya V Pechnikova / Knut Müller-Caspary / Ricardo Egoavil / Eric G T Bosch / Carsten Sachse / ![]() ![]() Abstract: In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently ...In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently computationally combined into a high-resolution three-dimensional structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC-STEM to two cryo-EM test specimens, keyhole limpet hemocyanin (KLH) and tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination for KLH at 6.5 Å resolution, as well as for TMV at 3.5 Å resolution using single-particle reconstruction methods, which share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. These data show that STEM imaging in general, and in particular the iDPC-STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 36.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.7 KB 15.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.5 KB | Display | ![]() |
Images | ![]() | 131.7 KB | ||
Masks | ![]() | 476.8 MB | ![]() | |
Filedesc metadata | ![]() | 5.4 KB | ||
Others | ![]() ![]() | 382 MB 381.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7q2sMC ![]() 7q22C ![]() 7q23C ![]() 7q2qC ![]() 7q2rC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | cryo iDPC-STEM map recorded with CSA 4.5 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.75 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: half-map1
File | emd_13782_additional_1.map | ||||||||||||
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Annotation | half-map1 | ||||||||||||
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-Additional map: half-map2
File | emd_13782_additional_2.map | ||||||||||||
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Annotation | half-map2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Tobacco mosaic virus
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Tobacco mosaic virus
Supramolecule | Name: Tobacco mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12242 / Sci species name: Tobacco mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 131 kDa/nm |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 17.091998 KDa |
Sequence | String: SYSITTPSQF VFLSSAWADP IELINLCTNA LGNQFQTQQA RTVVQRQFSE VWKPSPQVTV RFPDSDFKVY RYNAVLDPLV TALLGAFDT RNRIIEVENQ ANPTTAETLD ATRRVDDATV AIRSAINNLI VELIRGTGSY NRSSFESSSG LVWT UniProtKB: Capsid protein |
-Macromolecule #2: RNA (5'-R(P*GP*AP*A)-3')
Macromolecule | Name: RNA (5'-R(P*GP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 958.66 Da |
Sequence | String: GAA |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 90 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: blot force of +10 and a duration for blotting of 10 seconds. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | iDPC-STEM |
Image recording | Film or detector model: OTHER / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |