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- EMDB-37153: Cyanophage A-1(L) sheath-tube -

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Basic information

Entry
Database: EMDB / ID: EMD-37153
TitleCyanophage A-1(L) sheath-tube
Map data
Sample
  • Virus: unclassified Caudoviricetes (virus)
    • Protein or peptide: sheath
    • Protein or peptide: tube
Keywordstail / virus / viral protein
Biological speciesunclassified Caudoviricetes (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsYu RC / Li Q / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U19A2020 China
CitationJournal: 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
DepositionAug 11, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37153.png

Downloads & links

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Map

FileDownload / File: emd_37153.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.014942685 - 0.03151598
Average (Standard dev.)0.00030891004 (±0.0019283298)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 479.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37153_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37153_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : unclassified Caudoviricetes

EntireName: unclassified Caudoviricetes (virus)
Components
  • Virus: unclassified Caudoviricetes (virus)
    • Protein or peptide: sheath
    • Protein or peptide: tube

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Supramolecule #1: unclassified Caudoviricetes

SupramoleculeName: 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
Host (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Macromolecule #1: sheath

MacromoleculeName: sheath / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 54.04541 KDa
SequenceString: MTNFLNGVNI GTPGAYAFYQ TTQSRPINVE PFRTCYMVGF ASNGVNKNVP TRISNLTDFT NVYGTSASTN SVDLFFKNSQ GFGNLYFVN VAIPTRYQIV VTAATAGSYS VTVNGVTKAI TVVGGATTTT IAADVISAIN NDTVLNKEVL ATVGGTSSTV V ITSKKPTN ...String:
MTNFLNGVNI GTPGAYAFYQ TTQSRPINVE PFRTCYMVGF ASNGVNKNVP TRISNLTDFT NVYGTSASTN SVDLFFKNSQ GFGNLYFVN VAIPTRYQIV VTAATAGSYS VTVNGVTKAI TVVGGATTTT IAADVISAIN NDTVLNKEVL ATVGGTSSTV V ITSKKPTN TTTAAVTGVI FTLTTTTGTS PSVADYVYTI NNTFDPALEA GFVIAPEAFS TFTKSDRLSI QVALENLCSA YR YQWAALI DSGAMSEISN TDRAIAEAAT YNSVQGHCSY YYPYLINLDD QQVPPSAAVA GMALYRFVID GFAEPPAGVN FPL KGVKNV AYKVTWEEQN VANPEGVNCI LNKENYGIVV WGARTLSADP NIVFISTRII LNIVINTLNR GYDFDIFNSV GGTA TVLDN IQRKTNTLLT TLYQAGLFYG QTTSEAFSVL GDASVQVPSL LQQGLVNMFI WVVPSTIIER LIINIKQTAI GDLEA TVAL DTAALQSSVE EGTATEGTAP VV

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Macromolecule #2: tube

MacromoleculeName: tube / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: unclassified Caudoviricetes (virus)
Molecular weightTheoretical: 18.55791 KDa
SequenceString:
MAVSKRPFSI NSFAVNLNIG NFVDARYWSK CSKIEKTYNT GEYSDGQSNI IYTLPGAIKY PEVVLSKAFS PGDEELINRL IAVNSDPIA WVTVFIQPMY RDGYYNVPQG GKIILEFCTV ARATPINEID TIGSNAAMFE CALNPSRIRS DGGNINWWSE P AAQVAEF

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 41062

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