Database: EMDB / ID: EMD-13781
|Title||cryo iDPC-STEM structure recorded with CSA 4.0|
|Map data||cryo iDPC-STEM mao recorded with CSA 4.0|
|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|
Function and homology information
|Biological species||Tobacco mosaic virus (vulgare) / Tobacco mosaic virus|
|Method||helical reconstruction / cryo EM / Resolution: 3.5 Å|
|Authors||Sachse C / Leidl ML|
|Funding support|| Germany, 1 items |
|Citation||Journal: Nat Methods / Year: 2022|
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.
-Downloads & links
|Map data||emd_13781.map.gz||22.1 MB||EMDB map data format|
|Header (meta data)||emd-13781-v30.xml|
|FSC (resolution estimation)||emd_13781_fsc.xml||17.7 KB||Display||FSC data file|
|Masks||emd_13781_msk_1.map||476.8 MB||Mask map|
|Summary document||emd_13781_validation.pdf.gz||729.5 KB||Display||EMDB validaton report|
|Full document||emd_13781_full_validation.pdf.gz||729 KB||Display|
|Data in XML||emd_13781_validation.xml.gz||22.5 KB||Display|
|Data in CIF||emd_13781_validation.cif.gz||29.1 KB||Display|
-Related structure data
|Related structure data|
M: atomic model generated by this map
C: citing same article (ref.)
|Similar structure data|
Similarity search - Function & homologyF&H Search
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|EMDB pages||EMDB (EBI/PDBe) / EMDataResource|
|Related items in Molecule of the Month|
|File||Download / File: emd_13781.map.gz / Format: CCP4 / Size: 143.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Annotation||cryo iDPC-STEM mao recorded with CSA 4.0|
|Projections & slices|
Images are generated by Spider.
generated in cubic-lattice coordinate
|Voxel size||X=Y=Z: 0.98 Å|
|Symmetry||Space group: 1|
|Projections & Slices|
-Half map: half-map1
|Projections & Slices|
-Half map: half-map2
|Projections & Slices|
-Entire : Tobacco mosaic virus
|Entire||Name: Tobacco mosaic virus|
-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|
|Host (natural)||Organism: Tobacco mosaic virus|
|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|
|Source (natural)||Organism: Tobacco mosaic virus (vulgare) / Strain: vulgare|
|Molecular weight||Theoretical: 17.091998 KDa|
SYSITTPSQF VFLSSAWADP IELINLCTNA LGNQFQTQQA RTVVQRQFSE VWKPSPQVTV RFPDSDFKVY RYNAVLDPLV TALLGAFDT RNRIIEVENQ ANPTTAETLD ATRRVDDATV AIRSAINNLI VELIRGTGSY NRSSFESSSG LVWT
-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|
|Source (natural)||Organism: Tobacco mosaic virus (vulgare)|
|Molecular weight||Theoretical: 958.66 Da|
|Aggregation state||helical array|
|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.
|Microscope||FEI TITAN KRIOS|
|Electron beam||Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN|
|Electron optics||Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm|
|Image recording||Film or detector model: OTHER / Average electron dose: 35.0 e/Å2|
Model: Titan Krios / Image courtesy: FEI Company
-Atomic model buiding 1
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