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- EMDB-13120: Mature capsid of bacteriophage phiRSA1 -

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Basic information

Entry
Database: EMDB / ID: EMD-13120
TitleMature capsid of bacteriophage phiRSA1
Map dataMature capsid of bacteriophage phiRSA1
Sample
  • Virus: Ralstonia solanacearum (bacteria)
    • Protein or peptide: p2 family phage major capsid protein
Keywordsbacteriophage / capsid / VIRUS
Function / homologyBacteriophage P2, capsid / Phage major capsid protein, P2 family / P2 family phage major capsid protein
Function and homology information
Biological speciesRalstonia virus RSA1 / Ralstonia solanacearum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsEffantin G / Fujiwara A
CitationJournal: 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
DepositionJun 25, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oz4
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7oz4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13120.png

Downloads & links

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Map

FileDownload / File: emd_13120.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMature capsid of bacteriophage phiRSA1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 662 pix.
= 801.02 Å		1.21 Å/pix.
x 662 pix.
= 801.02 Å		1.21 Å/pix.
x 662 pix.
= 801.02 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.02396997 - 0.025757618
Average (Standard dev.)0.00015474808 (±0.0018616295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions662662662
Spacing662662662
CellA=B=C: 801.02 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.211.211.21
M x/y/z662662662
origin x/y/z0.0000.0000.000
length x/y/z801.020801.020801.020
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS662662662
D min/max/mean-0.0240.0260.000

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Supplemental data

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Sample components

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Entire : Ralstonia solanacearum

EntireName: Ralstonia solanacearum (bacteria)
Components
  • Virus: Ralstonia solanacearum (bacteria)
    • Protein or peptide: p2 family phage major capsid protein

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Supramolecule #1: Ralstonia solanacearum

SupramoleculeName: 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
Virus shellShell ID: 1 / Name: gp8 / Diameter: 640.0 Å / T number (triangulation number): 7

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Macromolecule #1: p2 family phage major capsid protein

MacromoleculeName: p2 family phage major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia virus RSA1
Molecular weightTheoretical: 37.831531 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3399
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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