+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37152 | |||||||||
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Title | Cyanophage A-1(L) tail fiber | |||||||||
Map data | ||||||||||
Sample |
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Keywords | fiber / virus / viral protein | |||||||||
Biological species | unclassified Caudoviricetes (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Yu RC / Li Q / Zhou CZ | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure of the intact tail machine of Anabaena myophage A-1(L). Authors: Rong-Cheng Yu / Feng Yang / Hong-Yan Zhang / Pu Hou / Kang Du / Jie Zhu / Ning Cui / Xudong Xu / Yuxing Chen / Qiong Li / Cong-Zhao Zhou / Abstract: The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Following our recent report on the capsid structure of A-1(L), here we present the high-resolution ...The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Following our recent report on the capsid structure of A-1(L), here we present the high-resolution cryo-EM structure of its intact tail machine including the neck, tail and attached fibers. Besides the dodecameric portal, the neck contains a canonical hexamer connected to a unique pentadecamer that anchors five extended bead-chain-like neck fibers. The 1045-Å-long contractile tail is composed of a helical bundle of tape measure proteins surrounded by a layer of tube proteins and a layer of sheath proteins, ended with a five-component baseplate. The six long and six short tail fibers are folded back pairwise, each with one end anchoring to the baseplate and the distal end pointing to the capsid. Structural analysis combined with biochemical assays further enable us to identify the dual hydrolytic activities of the baseplate hub, in addition to two host receptor binding domains in the tail fibers. Moreover, the structure of the intact A-1(L) also helps us to reannotate its genome. These findings will facilitate the application of A-1(L) as a chassis cyanophage in synthetic biology. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37152.map.gz | 316.3 MB | EMDB map data format | |
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Header (meta data) | emd-37152-v30.xml emd-37152.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_37152.png | 48.8 KB | ||
Filedesc metadata | emd-37152.cif.gz | 5.5 KB | ||
Others | emd_37152_half_map_1.map.gz emd_37152_half_map_2.map.gz | 273.2 MB 272.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37152 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37152 | HTTPS FTP |
-Validation report
Summary document | emd_37152_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_37152_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_37152_validation.xml.gz | 17 KB | Display | |
Data in CIF | emd_37152_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37152 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37152 | HTTPS FTP |
-Related structure data
Related structure data | 8kecMC 8ke9C 8keaC 8keeC 8kefC 8kegC 8ts6C 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_37152.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37152_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37152_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : unclassified Caudoviricetes
Entire | Name: unclassified Caudoviricetes (virus) |
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Components |
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-Supramolecule #1: unclassified Caudoviricetes
Supramolecule | Name: unclassified Caudoviricetes / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2788787 / Sci species name: unclassified Caudoviricetes / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria) |
-Macromolecule #1: Long tail fiber
Macromolecule | Name: Long tail fiber / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: unclassified Caudoviricetes (virus) |
Molecular weight | Theoretical: 39.582539 KDa |
Sequence | String: MVRKVFNDGD ILYAEDVNII GQPFVDGQDL LGHGLKVDDN SLSDEPQNIK TRFYAWYNRF RVTVQSGLTL SVTQGSISVS GNIISFPPQ TINAIDNANS FVWIGKTDAD PAIALRVSQT LPNVCIPLAR VIAASGSVTS VTDLRDVSVD ILPPSIPDAV P VGSTIISL ...String: MVRKVFNDGD ILYAEDVNII GQPFVDGQDL LGHGLKVDDN SLSDEPQNIK TRFYAWYNRF RVTVQSGLTL SVTQGSISVS GNIISFPPQ TINAIDNANS FVWIGKTDAD PAIALRVSQT LPNVCIPLAR VIAASGSVTS VTDLRDVSVD ILPPSIPDAV P VGSTIISL IPPTAPIPAG YLELLNSSQN VSRTTYSALF VLWGTYYGNG DGSTTFGVPG TGGRFLRLGG SGLSVGDIGG SN QITIPTN ALPSHQHGIP ANTHTHSVND GGHGHTINQT PHSHSISDPG HAHGVPFGAA VDNGNNAFDT GGSPYNNGIG TTQ NQTGIS VNTANANLSI NTSSTGISIQ SASTGLTVTS NAGNGQAFQH DQPYLVFRVF VKV |
-Macromolecule #2: short tail fiber
Macromolecule | Name: short tail fiber / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: unclassified Caudoviricetes (virus) |
Molecular weight | Theoretical: 49.010348 KDa |
Sequence | String: MTNIVGRIGF LTTGKLGIKL RGVLIDESTT PNTTYLPGIE SFFNITANVL TSVSYPETET QNVTATFSIY SVDGSSNPVF PALLSFDAI VPNVASVEFD VLAPTGVVNN QLDTSALRIA KIIANDPALA QKVAGAPYPR GAYSATETYL YGEMVSYFGK N YISKSLSP ...String: MTNIVGRIGF LTTGKLGIKL RGVLIDESTT PNTTYLPGIE SFFNITANVL TSVSYPETET QNVTATFSIY SVDGSSNPVF PALLSFDAI VPNVASVEFD VLAPTGVVNN QLDTSALRIA KIIANDPALA QKVAGAPYPR GAYSATETYL YGEMVSYFGK N YISKSLSP IINILPTVTD SWYELVITLP ESVSVIATGS DTAYGTGWNG SLLVPTQNAV YDKIVTVDAA IATANTNITN LG TAKADLS YVNTQLSADQ VVLDALSSGK ADLSYVNTQL NSKANLNGAV LVNATTATPP ISDNDTSLAT TQHVRSFNHS RLA FNAFRG GQQGVPSLSY VTTTAQFNSS SVRSGWGDNF SSNRWLVGEG GTYLITVTTR FATVGGTPPT YFDALLFVGL SGSG VENFL TRSQSVYPSF GYTLSWVGIL TFNTGQNVFL NYQVNAVGGG SYSVVLEDVR FSGIQLG |
-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: 2.5 µm / Nominal defocus min: 1.5 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41062 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |