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- EMDB-20099: Prohead 2 of the phage T5 -

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Basic information

Entry
Database: EMDB / ID: EMD-20099
TitleProhead 2 of the phage T5
Map dataProhead 2 of the bacteriophage T5
Sample
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Major capsid protein
Keywordsprocapsid / HK97-fold / dsDNA-phage / icosahedral / VIRUS LIKE PARTICLE
Function / homologyviral scaffold / T=13 icosahedral viral capsid / Phage capsid / Phage capsid family / evasion of host immune response / viral capsid / Major capsid protein
Function and homology information
Biological speciesEscherichia phage T5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsHuet A / Duda RL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM047795 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10 OD019995 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy.
Authors: Alexis Huet / Robert L Duda / Pascale Boulanger / James F Conway /
Abstract: The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a ...The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 Å for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA.
History
DepositionApr 12, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseOct 2, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6okb
  • Surface level: 14
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6okb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20099.png

Downloads & links

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Map

FileDownload / File: emd_20099.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProhead 2 of the bacteriophage T5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 801 pix.
= 845.055 Å		1.06 Å/pix.
x 801 pix.
= 845.055 Å		1.06 Å/pix.
x 801 pix.
= 845.055 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 14.0 / Movie #1: 14
Minimum - Maximum-15.158001000000001 - 32.442999999999998
Average (Standard dev.)0.11870695 (±4.0349135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions801801801
Spacing801801801
CellA=B=C: 845.05493 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z801801801
origin x/y/z0.0000.0000.000
length x/y/z845.055845.055845.055
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS801801801
D min/max/mean-15.15832.4430.119

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Supplemental data

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Sample components

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Entire : Escherichia phage T5

EntireName: Escherichia phage T5 (virus)
Components
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: Escherichia phage T5

SupramoleculeName: Escherichia phage T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10726 / Sci species name: Escherichia phage T5 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26 MDa
Virus shellShell ID: 1 / Name: prohead 2 / Diameter: 700.0 Å / T number (triangulation number): 13

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 13 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 32.931359 KDa
SequenceString: AVNQSSSVEV SSESYETIFS QRIIRDLQKE LVVGALFEEL PMSSKILTML VEPDAGKATW VAASTYGTDT TTGEEVKGAL KEIHFSTYK LAAKSFITDE TEEDAIFSLL PLLRKRLIEA HAVSIEEAFM TGDGSGKPKG LLTLASEDSA KVVTEAKADG S VLVTAKTI ...String:
AVNQSSSVEV SSESYETIFS QRIIRDLQKE LVVGALFEEL PMSSKILTML VEPDAGKATW VAASTYGTDT TTGEEVKGAL KEIHFSTYK LAAKSFITDE TEEDAIFSLL PLLRKRLIEA HAVSIEEAFM TGDGSGKPKG LLTLASEDSA KVVTEAKADG S VLVTAKTI SKLRRKLGRH GLKLSKLVLI VSMDAYYDLL EDEEWQDVAQ VGNDSVKLQG QVGRIYGLPV VVSEYFPAKA NS AEFAVIV YKDNFVMPRQ RAVTVERERQ AGKQRDAYYV TQRVNLQRYF ANGVVSGTYA AS

UniProtKB: Major capsid protein

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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

Concentration2 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
10.0 mMTris
1.0 mMMGCl2magnesium chloride
1.0 mMCaCL2calcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 3628 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10154
Startup modelType of model: OTHER / Details: RMC
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Auto3DEM / Number images used: 8083
Initial angle assignmentType: COMMON LINE / Software - Name: Auto3DEM
Final angle assignmentType: COMMON LINE / Software - Name: Auto3DEM
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2ft1


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6okb:
Prohead 2 of the phage T5

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