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- EMDB-8314: Architecture of a headful DNA-packaging bacterial virus at 2.89 A... -

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Basic information

Entry
Database: EMDB / ID: EMD-8314
TitleArchitecture of a headful DNA-packaging bacterial virus at 2.89 Angstrom resolution by electron cryo-microscopy
Map databacteriophage Sf6 icosahedral reconstruction
Sample
  • Virus: Shigella phage Sf6 (virus)
    • Protein or peptide: bacteriophage sf6 capsid protein gp5
Function / homologyMajor capsid protein Gp5 / P22 coat protein - gene protein 5 / Gene 5 protein
Function and homology information
Biological speciesShigella phage Sf6 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsZhao H / Li J / Jiang W / Tang L
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM090010 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structure of a headful DNA-packaging bacterial virus at 2.9 Å resolution by electron cryo-microscopy.
Authors: Haiyan Zhao / Kunpeng Li / Anna Y Lynn / Keith E Aron / Guimei Yu / Wen Jiang / Liang Tang /
Abstract: The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand ...The enormous prevalence of tailed DNA bacteriophages on this planet is enabled by highly efficient self-assembly of hundreds of protein subunits into highly stable capsids. These capsids can stand with an internal pressure as high as ∼50 atmospheres as a result of the phage DNA-packaging process. Here we report the complete atomic model of the headful DNA-packaging bacteriophage Sf6 at 2.9 Å resolution determined by electron cryo-microscopy. The structure reveals the DNA-inflated, tensed state of a robust protein shell assembled via noncovalent interactions. Remarkable global conformational polymorphism of capsid proteins, a network formed by extended N arms, mortise-and-tenon-like intercapsomer joints, and abundant β-sheet-like mainchain:mainchain intermolecular interactions, confers significant strength yet also flexibility required for capsid assembly and DNA packaging. Differential formations of the hexon and penton are mediated by a drastic α-helix-to-β-strand structural transition. The assembly scheme revealed here may be common among tailed DNA phages and herpesviruses.
History
DepositionAug 10, 2016-
Header (metadata) releaseOct 5, 2016-
Map releaseMar 22, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5l35
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5l35
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8314.png

Downloads & links

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Map

FileDownload / File: emd_8314.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbacteriophage Sf6 icosahedral reconstruction
Voxel sizeX=Y=Z: 1.01 Å
Density
Contour LevelBy AUTHOR: 6 / Movie #1: 6
Minimum - Maximum-31.98196 - 48.266804
Average (Standard dev.)0.054425415 (±2.3549652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 808.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.011.011.01
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z808.000808.000808.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS800800800
D min/max/mean-31.98248.2670.054

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Supplemental data

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Sample components

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Entire : Shigella phage Sf6

EntireName: Shigella phage Sf6 (virus)
Components
  • Virus: Shigella phage Sf6 (virus)
    • Protein or peptide: bacteriophage sf6 capsid protein gp5

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Supramolecule #1: Shigella phage Sf6

SupramoleculeName: Shigella phage Sf6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10761 / Sci species name: Shigella phage Sf6 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Shigella flexneri (bacteria) / Strain: M94
Molecular weightTheoretical: 19.5 MDa
Virus shellShell ID: 1 / Name: virus capsid / Diameter: 650.0 Å / T number (triangulation number): 7

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Macromolecule #1: bacteriophage sf6 capsid protein gp5

MacromoleculeName: bacteriophage sf6 capsid protein gp5 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Shigella phage Sf6 (virus)
SequenceString: MPNNLDSNVS QIVLKKFLPG FMSDLVLAKT VDRQLLAGEI NSSTGDSVSF KRPHQFSSLR TPTGDISGQ NKNNLISGKA TGRVGNYITV AVEYQQLEEA IKLNQLEEIL APVRQRIVTD L ETELAHFM MNNGALSLGS PNTPITKWSD VAQTASFLKD LGVNEGENYA ...String:
MPNNLDSNVS QIVLKKFLPG FMSDLVLAKT VDRQLLAGEI NSSTGDSVSF KRPHQFSSLR TPTGDISGQ NKNNLISGKA TGRVGNYITV AVEYQQLEEA IKLNQLEEIL APVRQRIVTD L ETELAHFM MNNGALSLGS PNTPITKWSD VAQTASFLKD LGVNEGENYA VMDPWSAQRL AD AQTGLHA SDQLVRTAWE NAQIPTNFGG IRALMSNGLA SRTQGAFGGT LTVKTQPTVT YNA VKDSYQ FTVTLTGATA SVTGFLKAGD QVKFTNTYWL QQQTKQALYN GATPISFTAT VTAD ANSDS GGDVTVTLSG VPIYDTTNPQ YNSVSRQVEA GDAVSVVGTA SQTMKPNLFY NKFFC GLGS IPLPKLHSID SAVATYEGFS IRVHKYADGD ANVQKMRFDL LPAYVCFNPH MGGQFF GNP

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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

Concentration15 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris
1.0 mMMgCl2magnesium chloride
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
Detailspurified Sf6 phage

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 9.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: jspr (ver. 1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr (ver. 1) / Number images used: 68000
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 46.6
Target criteria: Pseudo-crystallographic R factor and stereochemistry
Output model

PDB-5l35:
Cryo-EM structure of bacteriophage Sf6 at 2.9 Angstrom resolution

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