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- EMDB-8419: High affinity anchoring of the decoration protein pb10 onto the b... -

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Basic information

Entry
Database: EMDB / ID: EMD-8419
TitleHigh affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid
Map datadecorated empty expanded capsid of bacteriophage T5
SampleHigh affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid != Escherichia phage T5

High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid

  • Virus: Escherichia phage T5 (virus)
Function / homologyviral scaffold / T=13 icosahedral viral capsid / : / Phage capsid / Phage capsid family / symbiont-mediated 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: 9.0 Å
AuthorsConway J / Huet A
CitationJournal: Sci Rep / Year: 2017
Title: High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid.
Authors: Emeline Vernhes / Madalena Renouard / Bernard Gilquin / Philippe Cuniasse / Dominique Durand / Patrick England / Sylviane Hoos / Alexis Huet / James F Conway / Anatoly Glukhov / Vladimir ...Authors: Emeline Vernhes / Madalena Renouard / Bernard Gilquin / Philippe Cuniasse / Dominique Durand / Patrick England / Sylviane Hoos / Alexis Huet / James F Conway / Anatoly Glukhov / Vladimir Ksenzenko / Eric Jacquet / Naïma Nhiri / Sophie Zinn-Justin / Pascale Boulanger /
Abstract: Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function ...Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. The decoration protein pb10 of phage T5 binds at the centre of the 120 hexamers formed by the major capsid protein. Here we determined the 3D structure of pb10 and investigated its capsid-binding properties using NMR, SAXS, cryoEM and SPR. Pb10 consists of an α-helical capsid-binding domain and an Ig-like domain exposed to the solvent. It binds to the T5 capsid with a remarkably high affinity and its binding kinetics is characterized by a very slow dissociation rate. We propose that the conformational exchange events observed in the capsid-binding domain enable rearrangements upon binding that contribute to the quasi-irreversibility of the pb10-capsid interaction. Moreover we show that pb10 binding is a highly cooperative process, which favours immediate rebinding of newly dissociated pb10 to the 120 hexamers of the capsid protein. In extreme conditions, pb10 protects the phage from releasing its genome. We conclude that pb10 may function to reinforce the capsid thus favouring phage survival in harsh environments.
History
DepositionOct 4, 2016-
Header (metadata) releaseNov 16, 2016-
Map releaseFeb 22, 2017-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 10
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5tjt
  • Surface level: 10
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5tjt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8419.png

Downloads & links

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Map

FileDownload / File: emd_8419.map.gz / Format: CCP4 / Size: 479.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdecorated empty expanded capsid of bacteriophage T5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.74 Å/pix.
x 501 pix.
= 1372.74 Å		2.74 Å/pix.
x 501 pix.
= 1372.74 Å		2.74 Å/pix.
x 501 pix.
= 1372.74 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10. / Movie #1: 10
Minimum - Maximum-10.389001 - 32.442999999999998
Average (Standard dev.)-0.050304458 (±2.5765135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-250-250-250
Dimensions501501501
Spacing501501501
CellA=B=C: 1372.74 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.742.742.74
M x/y/z501501501
origin x/y/z0.0000.0000.000
length x/y/z1372.7401372.7401372.740
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-250-250-250
NC/NR/NS501501501
D min/max/mean-10.38932.443-0.050

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Supplemental data

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Sample components

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Entire : High affinity anchoring of the decoration protein pb10 onto the b...

EntireName: High affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid
Components
  • Virus: Escherichia phage T5 (virus)

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Supramolecule #1: Escherichia phage T5

SupramoleculeName: Escherichia phage T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / 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: E.Coli (others)
Virus shellShell ID: 1 / Name: expanded head / Diameter: 900.0 Å / T number (triangulation number): 13

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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

Concentration1 mg/mL
BufferpH: 7.6
Component:
ConcentrationNameFormula
10.0 mMTris
100.0 mMNaCl
1.0 mMCa2+
1.0 mMMg
GridMaterial: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number real images: 1939 / Average exposure time: 1.0 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.16 µm / Nominal defocus min: 1.27 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Detailsthe images were binned by 2
Particle selectionNumber selected: 2651
CTF correctionSoftware - Name: CTFFIND3
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3DEM / Number images used: 1856
Initial angle assignmentType: COMMON LINE / Software - Name: Auto3dem (ppft)
Final angle assignmentType: COMMON LINE / Software - Name: Auto3dem (PO2R)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5tjt:
T5 bacteriophage major capsid protein - one PB8 hexon

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