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Open data
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Basic information
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Title | Cryo-EM reconstruction of TMV coat protein | |||||||||
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![]() | cryo-EM / single particle reconstruction / Tobacco mosaic virus / helical reconstruction / ESRF / Titan Krios / K2 Summit / VIRAL PROTEIN | |||||||||
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 / Capsid protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
![]() | Kandiah E / Effantin G | |||||||||
Funding support | 1 items
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![]() | ![]() Title: CM01: a facility for cryo-electron microscopy at the European Synchrotron. Authors: Eaazhisai Kandiah / Thierry Giraud / Alejandro de Maria Antolinos / Fabien Dobias / Gregory Effantin / David Flot / Michael Hons / Guy Schoehn / Jean Susini / Olof Svensson / Gordon A ...Authors: Eaazhisai Kandiah / Thierry Giraud / Alejandro de Maria Antolinos / Fabien Dobias / Gregory Effantin / David Flot / Michael Hons / Guy Schoehn / Jean Susini / Olof Svensson / Gordon A Leonard / Christoph Mueller-Dieckmann / ![]() Abstract: Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, ...Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, and many national and international centres have since been created in order to exploit this. Here, a new facility for cryo-electron microscopy focused on single-particle reconstruction of biological macromolecules that has been commissioned at the European Synchrotron Radiation Facility (ESRF) is presented. The facility is operated by a consortium of institutes co-located on the European Photon and Neutron Campus and is managed in a similar fashion to a synchrotron X-ray beamline. It has been open to the ESRF structural biology user community since November 2017 and will remain open during the 2019 ESRF-EBS shutdown. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 24.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
Images | ![]() | 120.3 KB | ||
Filedesc metadata | ![]() | 4.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 478.3 KB | Display | ![]() |
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Full document | ![]() | 477.9 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rlpMC 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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Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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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: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / 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: 24 |
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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
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 1.41 Å Applied symmetry - Helical parameters - Δ&Phi: 22.04 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109763 |
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Startup model | Type of model: INSILICO MODEL |
Final angle assignment | Type: NOT APPLICABLE |