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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13120 | |||||||||
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Title | Mature capsid of bacteriophage phiRSA1 | |||||||||
![]() | Mature capsid of bacteriophage phiRSA1 | |||||||||
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Function / homology | Bacteriophage P2, capsid / Phage major capsid protein, P2 family / p2 family phage major capsid protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Effantin G / Fujiwara A / Kawsaki T / Yamada T / Schoehn G | |||||||||
![]() | ![]() Title: High Resolution Structure of the Mature Capsid of Bacteriophage ϕRSA1 by Cryo-Electron Microscopy. Authors: Grégory Effantin / Akiko Fujiwara / Takeru Kawasaki / Takashi Yamada / Guy Schoehn / ![]() ![]() Abstract: The ϕRSA1 bacteriophage has been isolated from , a gram negative bacteria having a significant economic impact on many important crops. We solved the three-dimensional structure of the ϕRSA1 mature ...The ϕRSA1 bacteriophage has been isolated from , a gram negative bacteria having a significant economic impact on many important crops. We solved the three-dimensional structure of the ϕRSA1 mature capsid to 3.9 Å resolution by cryo-electron microscopy. The capsid shell, that contains the 39 kbp of dsDNA genome, has an icosahedral symmetry characterized by an unusual triangulation number of T = 7, . The ϕRSA1 capsid is composed solely of the polymerization of the major capsid protein, gp8, which exhibits the typical "Johnson" fold first characterized in bacteriophage HK97. As opposed to the latter, the ϕRSA1 mature capsid is not stabilized by covalent crosslinking between its subunits, nor by the addition of a decoration protein. We further describe the molecular interactions occurring between the subunits of the ϕRSA1 capsid and their relationships with the other known bacteriophages. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1012.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9 KB 9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 23.4 KB | Display | ![]() |
Images | ![]() | 185.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 409.8 KB | Display | ![]() |
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Full document | ![]() | 409.4 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oz4MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mature capsid of bacteriophage phiRSA1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Ralstonia solanacearum
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Ralstonia solanacearum
Supramolecule | Name: Ralstonia solanacearum / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 305 / Sci species name: Ralstonia solanacearum / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Virus shell | Shell ID: 1 / Name: gp8 / Diameter: 640.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: p2 family phage major capsid protein
Macromolecule | Name: p2 family phage major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 37.831531 KDa |
Sequence | String: MRNDTRRLFA AYKAAIAKLN GVERVDEKFS VAPSVQQKLE TKVQESSDFL KSINFYGVPE QEGEKIGLGV SGPVASTTDT TQQDRETSD ISTMDGRRYR CEQTNSDTHI TYQKLDAWAK FADFQTRIRD AIIKRQALDR IMIGFNGVSR AATSDRVANP M LQDVNKGW ...String: MRNDTRRLFA AYKAAIAKLN GVERVDEKFS VAPSVQQKLE TKVQESSDFL KSINFYGVPE QEGEKIGLGV SGPVASTTDT TQQDRETSD ISTMDGRRYR CEQTNSDTHI TYQKLDAWAK FADFQTRIRD AIIKRQALDR IMIGFNGVSR AATSDRVANP M LQDVNKGW LQNLREQAPQ RVMKEGKAAA GKITVGGAGA DYGNLDALVY DITNHLVEPW YAEDPDLVVV CGRNLLSDKY FP LVNRDRD PVQQIAADLI ISQKRIGNLP AIRVPYFPAN GLLVTRLDNL SIYYQEGGRR RTILDNAKRD RIENYESSND AYV IEDLAC AAMAENIALA AAA |
-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: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |