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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | bottom segment of the bacteriophage M13 mini variant | |||||||||
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Function / homology | ![]() viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / helical viral capsid / host cell membrane / ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Xiang Y / Jia Q | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of a bacteriophage M13 mini variant. Authors: Qi Jia / Ye Xiang / ![]() Abstract: Filamentous bacteriophages package their circular, single stranded DNA genome with the major coat protein pVIII and the minor coat proteins pIII, pVII, pVI, and pIX. Here, we report the cryo-EM ...Filamentous bacteriophages package their circular, single stranded DNA genome with the major coat protein pVIII and the minor coat proteins pIII, pVII, pVI, and pIX. Here, we report the cryo-EM structure of a ~500 Å long bacteriophage M13 mini variant. The distal ends of the mini phage are sealed by two cap-like complexes composed of the minor coat proteins. The top cap complex consists of pVII and pIX, both exhibiting a single helix structure. Arg33 of pVII and Glu29 of pIX, located on the inner surface of the cap, play a key role in recognizing the genome packaging signal. The bottom cap complex is formed by the hook-like structures of pIII and pVI, arranged in helix barrels. Most of the inner ssDNA genome adopts a double helix structure with a similar pitch to that of the A-form double-stranded DNA. These findings provide insights into the assembly of filamentous bacteriophages. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.1 KB 15.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 42.1 KB | ||
Others | ![]() ![]() | 40.7 MB 40.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ixkMC ![]() 8jwxM ![]() 8ixjC ![]() 8ixlC ![]() 8jwtC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.97 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_35794_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35794_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : bottom segment of the bacteriophage M13 mini variant
Entire | Name: bottom segment of the bacteriophage M13 mini variant |
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Components |
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-Supramolecule #1: bottom segment of the bacteriophage M13 mini variant
Supramolecule | Name: bottom segment of the bacteriophage M13 mini variant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Attachment protein G3P
Macromolecule | Name: Attachment protein G3P / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 42.573766 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: AETVESCLAK PHTENSFTNV WKDDKTLDRY ANYEGCLWNA TGVVVCTGDE TQCYGTWVPI GLAIPENEGG GSEGGGSEGG GSEGGGTKP PEYGDTPIPG YTYINPLDGT YPPGTEQNPA NPNPSLEESQ PLNTFMFQNN RFRNRQGALT VYTGTVTQGT D PVKTYYQY ...String: AETVESCLAK PHTENSFTNV WKDDKTLDRY ANYEGCLWNA TGVVVCTGDE TQCYGTWVPI GLAIPENEGG GSEGGGSEGG GSEGGGTKP PEYGDTPIPG YTYINPLDGT YPPGTEQNPA NPNPSLEESQ PLNTFMFQNN RFRNRQGALT VYTGTVTQGT D PVKTYYQY TPVSSKAMYD AYWNGKFRDC AFHSGFNEDP FVCEYQGQSS DLPQPPVNAG GGSGGGSGGG SEGGGSEGGG SE GGGSEGG GSGGGSGSGD FDYEKMANAN KGAMTENADE NALQSDAKGK LDSVATDYGA AIDGFIGDVS GLANGNGATG DFA GSNSQM AQVGDGDNSP LMNNFRQYLP SLPQSVECRP FVFGAGKPYE FSIDCDKINL FRGVFAFLLY VATFMYVFST FANI LRNKE S UniProtKB: Attachment protein G3P |
-Macromolecule #2: Capsid protein G8P
Macromolecule | Name: Capsid protein G8P / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.633036 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MKKSLVLKAS VAVATLVPML SFAAEGDDPA KAAFNSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFTS KAS UniProtKB: ![]() |
-Macromolecule #3: Head virion protein G6P
Macromolecule | Name: Head virion protein G6P / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 12.357984 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MPVLLGIPLL LRFLGFLLVT LFGYLLTFLK KGFGKIAIAI SLFLALIIGL NSILVGYLSD ISAQLPSDFV QGVQLILPSN ALPCFYVIL SVKAAIFIFD VKQKIVSYLD WDK UniProtKB: Head virion protein G6P |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |