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- EMDB-4655: The cryo-EM structure of bacteriophage phi29 prohead -

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Basic information

Entry
Database: EMDB / ID: EMD-4655
TitleThe cryo-EM structure of bacteriophage phi29 prohead
Map data
Sample
  • Virus: Bacillus phage phi29 (virus)
    • Protein or peptide: Major capsid protein
    • Protein or peptide: Capsid fiber protein
Keywordsbacteriophage / phi29 / prohead / VIRUS
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 speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXu J / Gui M
Funding support China, 3 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0501100 China
Ministry of Science and Technology (China)2015CB910102 China
National Natural Science Foundation of China31470721 China
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 3, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseJun 12, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qvk
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6qvk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4655.png

Downloads & links

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Map

FileDownload / File: emd_4655.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 704 pix.
= 754.688 Å		1.07 Å/pix.
x 704 pix.
= 754.688 Å		1.07 Å/pix.
x 704 pix.
= 754.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-0.42549562 - 22.243086000000002
Average (Standard dev.)0.11767079 (±0.80546385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-352-352-352
Dimensions704704704
Spacing704704704
CellA=B=C: 754.688 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0721.0721.072
M x/y/z704704704
origin x/y/z0.0000.0000.000
length x/y/z754.688754.688754.688
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-352-352-352
NC/NR/NS704704704
D min/max/mean-0.42522.2430.118

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Supplemental data

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Sample components

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Entire : Bacillus phage phi29

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

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Supramolecule #1: Bacillus phage phi29

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

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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: Bacillus phage phi29 (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

UniProtKB: Major capsid protein

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Macromolecule #2: Capsid fiber protein

MacromoleculeName: Capsid fiber protein / type: protein_or_peptide / ID: 2
Details: the residue 118-281 is adapted from crystal structure of gp8.5 (PDB entry:3QC7).
Number of copies: 165 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage phi29 (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

UniProtKB: Capsid fiber 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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: KODAK SO-163 FILM / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18230
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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