+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34680 | |||||||||
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Title | Cyanophage Pam3 capsid asymmetric unit | |||||||||
Map data | ||||||||||
Sample |
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Keywords | capsid asymmetric unit / VIRUS / VIRAL PROTEIN | |||||||||
Biological species | uncultured cyanophage (environmental samples) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
Authors | Yang F / Jiang YL / Zhou CZ | |||||||||
Funding support | China, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: Fine structure and assembly pattern of a minimal myophage Pam3. Authors: Feng Yang / Yong-Liang Jiang / Jun-Tao Zhang / Jie Zhu / Kang Du / Rong-Cheng Yu / Zi-Lu Wei / Wen-Wen Kong / Ning Cui / Wei-Fang Li / Yuxing Chen / Qiong Li / Cong-Zhao Zhou / Abstract: The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail ...The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34680.map.gz | 1.8 GB | EMDB map data format | |
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Header (meta data) | emd-34680-v30.xml emd-34680.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_34680.png | 226.7 KB | ||
Filedesc metadata | emd-34680.cif.gz | 5.3 KB | ||
Others | emd_34680_half_map_1.map.gz emd_34680_half_map_2.map.gz | 1.5 GB 1.5 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34680 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34680 | HTTPS FTP |
-Validation report
Summary document | emd_34680_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_34680_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_34680_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | emd_34680_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34680 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34680 | HTTPS FTP |
-Related structure data
Related structure data | 8hdtMC 7yfwC 7yfzC 8hdrC 8hdsC 8hdwC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34680.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.013 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34680_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34680_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : uncultured cyanophage
Entire | Name: uncultured cyanophage (environmental samples) |
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Components |
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-Supramolecule #1: uncultured cyanophage
Supramolecule | Name: uncultured cyanophage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 215796 / Sci species name: uncultured cyanophage / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Pseudanabaena mucicola (bacteria) |
-Macromolecule #1: Major capsid
Macromolecule | Name: Major capsid / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: uncultured cyanophage (environmental samples) |
Molecular weight | Theoretical: 34.143984 KDa |
Sequence | String: MNQRLMTGDA MQANFGFVTS QTAYVEAGVY RMRYPEIRYP GLIPVDYSAP EWIKTVDYYS MDGVGKAEWI ADRASDIPVV GLAMEKATT TVHLAGIGYD YGLEEVNQAI MLGMNLPGEK ANLARLVYER MVDRVAFTGD AEKDFKGLFN NGAVTAVSAT T GNWASATA ...String: MNQRLMTGDA MQANFGFVTS QTAYVEAGVY RMRYPEIRYP GLIPVDYSAP EWIKTVDYYS MDGVGKAEWI ADRASDIPVV GLAMEKATT TVHLAGIGYD YGLEEVNQAI MLGMNLPGEK ANLARLVYER MVDRVAFTGD AEKDFKGLFN NGAVTAVSAT T GNWASATA DQILADFNLG ITGLWSATNE MVYADTVLLP SAKHQIIASK RLGNEATETV LQFLQRANVY TAETGRPLTI RG MRGLNTA GAGGVSRSVF YRNSPEVLKM HIPMRHRFLP VQVVGLTYKV PGIFRLGGLD IRLPKEVRYV DGY |
-Macromolecule #2: Cement
Macromolecule | Name: Cement / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: uncultured cyanophage (environmental samples) |
Molecular weight | Theoretical: 17.210295 KDa |
Sequence | String: MAPYNETYAS DYAFAYEGMV SDIAPADIIS RTVETSAGIG FGKIVAQGTS DRGCKADVSA VSPTAPPLGI TVRSQATENL TLDKYPRYD GAAIMRKGVI WVLVTDAGGV VAGDPVWLKK SDGTFSNADV GSSGGLRLAG CRWDTSAANG ALARMRVDFD V PPVAGA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 130253 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |