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- EMDB-4681: The cryo-EM structure of the head of the genome empited bacteriop... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4681 | ||||||||||||
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Title | The cryo-EM structure of the head of the genome empited bacteriophage phi29 | ||||||||||||
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![]() | bacteriophage / phi29 / genome emptied virion / VIRUS | ||||||||||||
Function / homology | ![]() 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 | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
![]() | Xu J / Wang D | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 69.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.3 KB 11.3 KB | Display Display | ![]() |
Images | ![]() | 73.3 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qz0MC ![]() 4655C ![]() 4662C ![]() 4677C ![]() 4678C ![]() 4679C ![]() 4680C ![]() 4682C ![]() 4683C ![]() 4684C ![]() 4685C ![]() 6qvkC ![]() 6qx7C ![]() 6qydC ![]() 6qyjC ![]() 6qymC ![]() 6qyyC ![]() 6qyzC ![]() 6qz9C ![]() 6qzfC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Bacillus phage phi29
Entire | Name: ![]() ![]() |
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Components |
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-Supramolecule #1: Bacillus phage phi29
Supramolecule | Name: 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
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 235 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 49.894906 KDa |
Sequence | String: 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 |
-Macromolecule #2: Capsid fiber protein
Macromolecule | Name: Capsid fiber protein / type: protein_or_peptide / ID: 2 Details: the residues from 117 to 281 is derived from crystal structure of head fiber protein (PDB entry: 3QC7) Number of copies: 165 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 29.642361 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44059 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |