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- EMDB-4677: Cryo-EM structure of the head in mature bacteriophage phi29 -

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Basic information

Entry
Database: EMDB / ID: EMD-4677
TitleCryo-EM structure of the head in mature bacteriophage phi29
Map data
Sample
  • Virus: Bacillus virus phi29
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid fiber protein
Function / homology
Function and homology information


viral capsid, fiber / viral procapsid / T=3 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell / identical protein binding
Similarity search - Function
Bacteriophage B103, Gp8, head fibre / Head fiber protein / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Capsid fiber protein / Major capsid protein
Similarity search - Component
Biological speciesBacteriophage phi-29 (virus) / Bacillus virus phi29
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXu JW / Wang DH / Gui M / Xiang Y
CitationJournal: Nat Commun / Year: 2019
Title: Structural assembly of the tailed bacteriophage ϕ29.
Authors: Jingwei Xu / Dianhong Wang / Miao Gui / Ye Xiang /
Abstract: The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile ...The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration.
History
DepositionMar 8, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateJun 12, 2019-
Current statusJun 12, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qyd
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4677.png

Downloads & links

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Map

FileDownload / File: emd_4677.map.gz / Format: CCP4 / Size: 713.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.2952 Å
Density
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-0.41824457 - 22.083573999999999
Average (Standard dev.)0.1031159 (±0.76441395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions572572572
Spacing572572572
CellA=B=C: 740.8544 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.29519930069931.29519930069931.2951993006993
M x/y/z572572572
origin x/y/z0.0000.0000.000
length x/y/z740.854740.854740.854
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS572572572
D min/max/mean-0.41822.0840.103

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Supplemental data

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Sample components

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Entire : Bacillus virus phi29

EntireName: Bacillus virus phi29
Components
  • Virus: Bacillus virus phi29
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid fiber protein

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Supramolecule #1: Bacillus virus phi29

SupramoleculeName: Bacillus virus phi29 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10756 / Sci species name: Bacillus virus phi29 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 235 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage phi-29 (virus)
Molecular weightTheoretical: 49.894906 KDa
SequenceString: MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRIG LVVIRQVSLN NPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV FEREMPNVKT LFHERNRQGF YHQTIQDDSL KTAFVSWGNF E SFVSSIIN ...String:
MRITFNDVKT SLGITESYDI VNAIRNSQGD NFKSYVPLAT ANNVAEVGAG ILINQTVQND FITSLVDRIG LVVIRQVSLN NPLKKFKKG QIPLGRTIEE IYTDITKEKQ YDAEEAEQKV FEREMPNVKT LFHERNRQGF YHQTIQDDSL KTAFVSWGNF E SFVSSIIN AIYNSAEVDE YEYMKLLVDN YYSKGLFTTV KIDEPTSSTG ALTEFVKKMR ATARKLTLPQ GSRDWNSMAV RT RSYMEDL HLIIDADLEA ELDVDVLAKA FNMNRTDFLG NVTVIDGFAS TGLEAVLVDK DWFMVYDNLH KMETVRNPRG LYW NYYYHV WQTLSVSRFA NAVAFVSGDV PAVTQVIVSP NIAAVKQGGQ QQFTAYVRAT NAKDHKVVWS VEGGSTGTAI TGDG LLSVS GNEDNQLTVK ATVDIGTEDK PKLVVGEAVV SIRPNNASGG AQA

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Macromolecule #2: Capsid fiber protein

MacromoleculeName: Capsid fiber protein / type: protein_or_peptide / ID: 2 / Number of copies: 165 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage phi-29 (virus)
Molecular weightTheoretical: 29.642361 KDa
SequenceString: MMVSFTARAK SNVMAYRLLA YSQGDDIIEI SHAAENTIPD YVAVKDVDKG DLTQVNMYPL AAWQVIAGSD IKVGDNLTTG KDGTAVPTD DPSTVFGYAV EEAQEGQLVT LVISRSKEIS IEVEDIKDAG DTGKRLLKIN TPSGARNIII ENEDAKALIN G ETTNTNKK ...String:
MMVSFTARAK SNVMAYRLLA YSQGDDIIEI SHAAENTIPD YVAVKDVDKG DLTQVNMYPL AAWQVIAGSD IKVGDNLTTG KDGTAVPTD DPSTVFGYAV EEAQEGQLVT LVISRSKEIS IEVEDIKDAG DTGKRLLKIN TPSGARNIII ENEDAKALIN G ETTNTNKK NLQDLLFSDG NVKAFLQATT TDENKTALQQ LLVSNADVLG LLSGNPTSDN KINLRTMIGA GVPYSLPAAT TT TLGGVKK GAAVTASTAT DVATAVKDLN SLITVLKNAG IISL

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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: 8
VitrificationCryogen name: ETHANE

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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) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36730

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