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- EMDB-34680: Cyanophage Pam3 capsid asymmetric unit -

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Basic information

Entry
Database: EMDB / ID: EMD-34680
TitleCyanophage Pam3 capsid asymmetric unit
Map data
Sample
  • Virus: uncultured cyanophage (environmental samples)
    • Protein or peptide: Major capsid
    • Protein or peptide: Cement
Keywordscapsid asymmetric unit / VIRUS / VIRAL PROTEIN
Biological speciesuncultured cyanophage (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsYang F / Jiang YL / Zhou CZ
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: 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
DepositionNov 6, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34680.png

Downloads & links

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Map

FileDownload / File: emd_34680.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 800 pix.
= 810.4 Å		1.01 Å/pix.
x 800 pix.
= 810.4 Å		1.01 Å/pix.
x 800 pix.
= 810.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.013 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.06045936 - 0.093227565
Average (Standard dev.)0.0005374361 (±0.0058759423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 810.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34680_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34680_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : uncultured cyanophage

EntireName: uncultured cyanophage (environmental samples)
Components
  • Virus: uncultured cyanophage (environmental samples)
    • Protein or peptide: Major capsid
    • Protein or peptide: Cement

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Supramolecule #1: uncultured cyanophage

SupramoleculeName: 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
Host (natural)Organism: Pseudanabaena mucicola (bacteria)

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Macromolecule #1: Major capsid

MacromoleculeName: Major capsid / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 34.143984 KDa
SequenceString: 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

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Macromolecule #2: Cement

MacromoleculeName: Cement / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 17.210295 KDa
SequenceString:
MAPYNETYAS DYAFAYEGMV SDIAPADIIS RTVETSAGIG FGKIVAQGTS DRGCKADVSA VSPTAPPLGI TVRSQATENL TLDKYPRYD GAAIMRKGVI WVLVTDAGGV VAGDPVWLKK SDGTFSNADV GSSGGLRLAG CRWDTSAANG ALARMRVDFD V PPVAGA

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.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 assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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