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Open data
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Basic information
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Title | The Structure of Spiroplasma Virus 4 | |||||||||
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![]() | Microviridae / bacteriophage / capsid / Spiroplasma virus 4 / SpV4 / VIRUS | |||||||||
Function / homology | ![]() T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / structural molecule activity / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.52 Å | |||||||||
![]() | Mietzsch M / McKenna R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The Structure of Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae Authors: Mietzsch M / Kailasan S / Bennett A / Chipman P / Bentley F / Huiskonen JT / Clarke IN / McKenna R | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 589.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.6 KB 14.6 KB | Display Display | ![]() |
Images | ![]() | 58.6 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 151.5 MB 151.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 956 KB | Display | ![]() |
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Full document | ![]() | 955.6 KB | Display | |
Data in XML | ![]() | 21.1 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9cgmMC 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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.061 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_45583_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_45583_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Spiromicrovirus SpV4
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Spiromicrovirus SpV4
Supramolecule | Name: Spiromicrovirus SpV4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: SpV4 was propagated in the S. melliferum strain G1 / NCBI-ID: 10855 / Sci species name: Spiromicrovirus SpV4 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No |
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Virus shell | Shell ID: 1 / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 62.294344 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MKKKMSKLNA RVHDFSMFKG NHIPRSKIHI PHKTIRAFNV GEIIPIYQTP VYPGEHIKMD LTSLYRPSTF IVPPMDDLIV DTYAFAVPW RIVWKDLEKF FGENSDSWDV KNAPPVPDIV APSGGWDYGT LADHFGITPK VPGIRVKSLR FRAYAKIIND W FRDQNLSS ...String: MKKKMSKLNA RVHDFSMFKG NHIPRSKIHI PHKTIRAFNV GEIIPIYQTP VYPGEHIKMD LTSLYRPSTF IVPPMDDLIV DTYAFAVPW RIVWKDLEKF FGENSDSWDV KNAPPVPDIV APSGGWDYGT LADHFGITPK VPGIRVKSLR FRAYAKIIND W FRDQNLSS ECALTLDSSN SQGSNGSNQV TDIQLGGKPY IANKYHDYFT SCLPAPQKGA PTTLNVGGMA PVTTKFRDVP NL SGTPLIF RDNKGRTIKT GQLGIGPVDA GFLVAQNTAQ AANGERAIPS NLWADLSNAT GISISDLRLA ITYQHYKEMD ARG GTRYVE FTLNHFGVHT ADARLQRSEF LGGHSQSLLV QSVPQTSSTV EKMTPQGNLA AFSETMIQNN YLVNKTFTEH SYII VLAVV RYKHTYQQGI EADWFRGQDK FDMYDPLLAN ISEQPVKNRE IMVQGNSQDN EIFGFQEAWA DLRFKPNSVA GVMRS SHPQ SLDYWHFADH YAQLPKLSSE WLKEDYKNVD RTLALKASDN TPQLRVDFMF NTIAEKPMPL YSTPGLRRI UniProtKB: Capsid protein VP1 |
-Macromolecule #2: DNA binding protein ORF8
Macromolecule | Name: DNA binding protein ORF8 / type: protein_or_peptide / ID: 2 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.644519 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRRKVKNTKR HQWRLTHSAR SIKRANIMPS NPRGGRRF UniProtKB: DNA binding protein ORF8 |
-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: 7.4 |
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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 (6k x 4k) / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77204 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: PROJECTION MATCHING |