+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13120 | |||||||||
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Title | Mature capsid of bacteriophage phiRSA1 | |||||||||
Map data | Mature capsid of bacteriophage phiRSA1 | |||||||||
Sample |
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Keywords | bacteriophage / capsid / VIRUS | |||||||||
Function / homology | Bacteriophage P2, capsid / Phage major capsid protein, P2 family / p2 family phage major capsid protein Function and homology information | |||||||||
Biological species | Ralstonia virus RSA1 / Ralstonia solanacearum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Effantin G / Fujiwara A | |||||||||
Citation | Journal: Int J Mol Sci / Year: 2021 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13120.map.gz | 1012.6 MB | EMDB map data format | |
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Header (meta data) | emd-13120-v30.xml emd-13120.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13120_fsc.xml | 23.4 KB | Display | FSC data file |
Images | emd_13120.png | 185.6 KB | ||
Filedesc metadata | emd-13120.cif.gz | 4.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13120 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13120 | HTTPS FTP |
-Validation report
Summary document | emd_13120_validation.pdf.gz | 797.1 KB | Display | EMDB validaton report |
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Full document | emd_13120_full_validation.pdf.gz | 796.7 KB | Display | |
Data in XML | emd_13120_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | emd_13120_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13120 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13120 | HTTPS FTP |
-Related structure data
Related structure data | 7oz4MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13120.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
-Entire : Ralstonia solanacearum
Entire | Name: Ralstonia solanacearum (bacteria) |
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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: Ralstonia virus RSA1 |
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 UniProtKB: p2 family phage major capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |