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- EMDB-31078: Cyanophage Pam1 capsid asymmetric unit -

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Basic information

Entry
Database: EMDB / ID: EMD-31078
TitleCyanophage Pam1 capsid asymmetric unit
Map dataAn asymmetric unit of Pam1 capsid.Cutting out using phenix Map box program.
SamplePam1 != unidentified

Pam1

  • Virus: unidentified (others)
    • Protein or peptide: Major capsid proteins
    • Protein or peptide: Cement (decoration) proteins
KeywordsMajor capsid and cement proteins / VIRUS
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsZhang JT / Jiang YL
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: Structure / Year: 2022
Title: Structure and assembly pattern of a freshwater short-tailed cyanophage Pam1.
Authors: Jun-Tao Zhang / Feng Yang / Kang Du / Wei-Fang Li / Yuxing Chen / Yong-Liang Jiang / Qiong Li / Cong-Zhao Zhou /
Abstract: Despite previous structural analyses of bacteriophages, quite little is known about the structures and assembly patterns of cyanophages. Using cryo-EM combined with crystallography, we solve the near- ...Despite previous structural analyses of bacteriophages, quite little is known about the structures and assembly patterns of cyanophages. Using cryo-EM combined with crystallography, we solve the near-atomic-resolution structure of a freshwater short-tailed cyanophage, Pam1, which comprises a 400-Å-long tail and an icosahedral capsid of 650 Å in diameter. The outer capsid surface is reinforced by trimeric cement proteins with a β-sandwich fold, which structurally resemble the distal motif of Pam1's tailspike, suggesting its potential role in host recognition. At the portal vertex, the dodecameric portal and connected adaptor, followed by a hexameric needle head, form a DNA ejection channel, which is sealed by a trimeric needle. Moreover, we identify a right-handed rifling pattern that might help DNA to revolve along the wall of the ejection channel. Our study reveals the precise assembly pattern of a cyanophage and lays the foundation to support its practical biotechnological and environmental applications.
History
DepositionMar 19, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0285
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7eel
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7eel
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31078.png

Downloads & links

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Map

FileDownload / File: emd_31078.map.gz / Format: CCP4 / Size: 23.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAn asymmetric unit of Pam1 capsid.Cutting out using phenix Map box program.
Voxel sizeX=Y=Z: 1.013 Å
Density
Contour LevelBy AUTHOR: 0.0285 / Movie #1: 0.022
Minimum - Maximum-0.058751106 - 0.09510435
Average (Standard dev.)0.00049589283 (±0.005638261)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin210602336
Dimensions193139227
Spacing227193139
CellA: 229.951 Å / B: 195.509 Å / C: 140.807 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0131.0131.013
M x/y/z227193139
origin x/y/z0.0000.0000.000
length x/y/z229.951195.509140.807
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S321
start NC/NR/NS602210336
NC/NR/NS139193227
D min/max/mean-0.0590.0950.000

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Supplemental data

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Sample components

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Entire : Pam1

EntireName: Pam1
Components
  • Virus: unidentified (others)
    • Protein or peptide: Major capsid proteins
    • Protein or peptide: Cement (decoration) proteins

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Supramolecule #1: unidentified

SupramoleculeName: unidentified / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 32644 / Sci species name: unidentified / 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 proteins

MacromoleculeName: Major capsid proteins / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 39.379066 KDa
SequenceString: MADFSLATAS QRKEWSNKAH MEYVRRSRFA PYIRNTENSI FQGYSDLEKR AGDTLNIPLF YKLGGAPVTG DTPIVGNETP LDNYNCGVP VALRGKGVAI TKNQTFRTEI DVMNAAKQSL TRYFGELLRD DIIEALGSVV TTGDTTVNYG SASAANRNAF S AANPDRLF ...String:
MADFSLATAS QRKEWSNKAH MEYVRRSRFA PYIRNTENSI FQGYSDLEKR AGDTLNIPLF YKLGGAPVTG DTPIVGNETP LDNYNCGVP VALRGKGVAI TKNQTFRTEI DVMNAAKQSL TRYFGELLRD DIIEALGSVV TTGDTTVNYG SASAANRNAF S AANPDRLF FGSISGYSAT WATGLGNVDA AETCTAARVG VMKRLAMSAS PAITPMQVDD DEGREYFVAF HGSRTFRDLK GD TAMLNAN REARPRDVSS NPLLQDGDLI YEGVIHREVP EIDAWAAANG FNTAGAGSAP IRPVFLCGTQ SVFLAYAQRP QAG TEKSDI PALNRRMTVG MDEIIGVKKA AFNGKQHGVV MGFFGAAGD

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Macromolecule #2: Cement (decoration) proteins

MacromoleculeName: Cement (decoration) proteins / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 13.831203 KDa
SequenceString:
MPATNSAQAR LAAPGHGFGG NVKVSYGSVA FTGTITTADA ATVCNLPVGA IVLGVTLESD DLDTNATPTI TLNVGDAGSA TRYFSASTV AQAGTSSSAP ATTGLLWTVT EGNTAVRIAV ANNAATSADG SVRVAVTYYL P

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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

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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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
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: 21210
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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