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- EMDB-31080: Cyanophage Pam1 tail machine -

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Basic information

Entry
Database: EMDB / ID: EMD-31080
TitleCyanophage Pam1 tail machine
Map data
Sample
  • Complex: Pam1
    • Protein or peptide: Needle head proteins
    • Protein or peptide: Tailspike head-binding domain
KeywordsNeedle head proteins and tailspike head-binding proteins / VIRAL PROTEIN
Biological speciesunidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 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: 0.0334
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0334
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7eeq
  • Surface level: 0.0334
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7eeq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31080.png

Downloads & links

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Map

FileDownload / File: emd_31080.map.gz / Format: CCP4 / Size: 178 MB / 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 360 pix.
= 364.68 Å		1.01 Å/pix.
x 360 pix.
= 364.68 Å		1.01 Å/pix.
x 360 pix.
= 364.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.013 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0334 / Movie #1: 0.0334
Minimum - Maximum-0.04310951 - 0.10322636
Average (Standard dev.)0.002945137 (±0.007622199)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 364.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0131.0131.013
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z364.680364.680364.680
α/β/γ90.00090.00090.000
start NX/NY/NZ336210602
NX/NY/NZ227193139
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0430.1030.003

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Supplemental data

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Sample components

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Entire : Pam1

EntireName: Pam1
Components
  • Complex: Pam1
    • Protein or peptide: Needle head proteins
    • Protein or peptide: Tailspike head-binding domain

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Supramolecule #1: Pam1

SupramoleculeName: Pam1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: unidentified (others)

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Macromolecule #1: Needle head proteins

MacromoleculeName: Needle head proteins / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 48.534621 KDa
SequenceString: MKIPYGLGAY TRNRGNLPPL ELINLFVEKS DSQGVILQSR KALVEVADVG AGPVRATFQK DGVFGGDRFT LSGDEFYRGA TLLGTVAGG GQARIVSNGL EVLVNAGGLV YSYNGTNFIN AGFPEAAATT IAFTGRYFIG LSAGTGEWYF SAVNNGRSWD A LDFATAEN ...String:
MKIPYGLGAY TRNRGNLPPL ELINLFVEKS DSQGVILQSR KALVEVADVG AGPVRATFQK DGVFGGDRFT LSGDEFYRGA TLLGTVAGG GQARIVSNGL EVLVNAGGLV YSYNGTNFIN AGFPEAAATT IAFTGRYFIG LSAGTGEWYF SAVNNGRSWD A LDFATAEN EPDALLDVLV LDGVLVFFGT ESIEFWGFTG DADLPYSPIQ QRVFEQGIYA TGCAVRVDNS FYWVGKDKIV YR NGDVPQA VSDDGIVEKA EGSTNLTLFV LEDERHKFVC LRGDDFTHPH DVTTGQWCEF KSYGRTNFRA TADFGDDETG KIW AWGGYD DEGIIERLFM AGAALEEATQ IDNIRLTCEV GTTPNLVGIY TDPTLEMRFS YDAGNTWEDW EAETLGAQGK YRQR VEWRA LGMFDDPGAL FQFRITDPVS FRLSDVQANA ATGGRQR

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Macromolecule #2: Tailspike head-binding domain

MacromoleculeName: Tailspike head-binding domain / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 10.782913 KDa
SequenceString:
MAAELHITPS RATSSNGLNL DGAKWFFYQT GTTTPQSVYT TAALSVAHSN PVVADAAGKF PAIYFDTTLE YRGVLKTADE ATTIYDIDP INSGILSVLG TSS

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

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Image processing

Particle selectionNumber selected: 20704
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 20700
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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