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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Capsid of Vibrio cholerae phage mature VP1 | ||||||||||||
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![]() | phage / virus / vibrio cholera phage / VIRAL PROTEIN | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||
![]() | Liu HR / Pang H | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Three-dimensional structures of Vibrio cholerae typing podophage VP1 in two states Authors: Liu HR / Pang H | ||||||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | |||
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Header (meta data) | ![]() | |||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9in6MC ![]() 60197 ![]() 60199 ![]() 8zkkC ![]() 8zkmC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 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 : Vibrio cholerae phage
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Vibrio cholerae phage
Supramolecule | Name: Vibrio cholerae phage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 666 / Sci species name: Vibrio cholerae phage / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: major capsid of VP1
Macromolecule | Name: major capsid of VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.886555 KDa |
Sequence | String: MATIAGLRGT GDWGNQERPT DFRETILWME PNGQAPLQAL MSKMSSQPTT DPEFSWWEEK LTHNRLEVKT EAAAGVTTLA VDTDQAWAC VKGDILMVES VGGLWANEIL KVVEDPTAGN ALKVARGFAG TTAAVIPAGT FIIAIGTSFA EGSLAPKSAT R NPVKLNNF ...String: MATIAGLRGT GDWGNQERPT DFRETILWME PNGQAPLQAL MSKMSSQPTT DPEFSWWEEK LTHNRLEVKT EAAAGVTTLA VDTDQAWAC VKGDILMVES VGGLWANEIL KVVEDPTAGN ALKVARGFAG TTAAVIPAGT FIIAIGTSFA EGSLAPKSAT R NPVKLNNF CQIFKKSYEI TKTADATKAR TGSALANDKK RRMFDYYRDV EMAFIYGRKS ETVGENGKPE RTTGGLLNFI TT NRTQFGT GAGKTELTED SLIDFFANVF NYDGQGAGNQ RIAFVGNTAL TKINKLARNS PSTRINFDKQ VTQVYGMNFT RWV LPQGEI FFKTHPLFNV HPELSKAMMV LNPKGIKERV LRATKPENDI QQVGQDSIKG QWIGEFGLEV NHEETMAFAG GIA |
-Macromolecule #2: SHP of VP1
Macromolecule | Name: SHP of VP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.801501 KDa |
Sequence | String: MLVHYGKLSD MPTVVDVNTT MGTDVPEDLL EIYVGCYAAD GKTPAAGTGV LTFHGSWNGV HKRLIGTVDL AAAGEVIAYN PPLMFGGCK KLFVSYTGVG TQIVDVYVHR GE |
-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 BIOCONTINUUM (6k x 4k) / Average electron dose: 32.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.6 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 | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 441860 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |