+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35794 | |||||||||
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Title | bottom segment of the bacteriophage M13 mini variant | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Viral coat protein / M13 / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information viral extrusion / virion attachment to host cell pilus / adhesion receptor-mediated virion attachment to host cell / helical viral capsid / host cell membrane / virion component / viral capsid / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / host cell plasma membrane / membrane Similarity search - Function | |||||||||
Biological species | Inovirus M13 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Xiang Y / Jia Q | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nat Commun / Year: 2023 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 | emd_35794.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-35794-v30.xml emd-35794.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35794_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_35794.png | 42.1 KB | ||
Others | emd_35794_half_map_1.map.gz emd_35794_half_map_2.map.gz | 40.7 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35794 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35794 | HTTPS FTP |
-Validation report
Summary document | emd_35794_validation.pdf.gz | 757.4 KB | Display | EMDB validaton report |
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Full document | emd_35794_full_validation.pdf.gz | 757 KB | Display | |
Data in XML | emd_35794_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | emd_35794_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35794 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35794 | HTTPS FTP |
-Related structure data
Related structure data | 8ixkMC 8jwxM 8ixjC 8ixlC 8jwtC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35794.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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 |
-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: Inovirus M13 |
-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: Inovirus M13 |
Molecular weight | Theoretical: 42.573766 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Inovirus M13 |
Molecular weight | Theoretical: 7.633036 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKSLVLKAS VAVATLVPML SFAAEGDDPA KAAFNSLQAS ATEYIGYAWA MVVVIVGATI GIKLFKKFTS KAS UniProtKB: Capsid protein G8P |
-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: Inovirus M13 |
Molecular weight | Theoretical: 12.357984 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPVLLGIPLL LRFLGFLLVT LFGYLLTFLK KGFGKIAIAI SLFLALIIGL NSILVGYLSD ISAQLPSDFV QGVQLILPSN ALPCFYVIL SVKAAIFIFD VKQKIVSYLD WDK UniProtKB: Head virion protein G6P |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |