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- EMDB-8423: High affinity anchoring of the decoration protein pb10 onto the b... -

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Basic information

Entry
Database: EMDB / ID: EMD-8423
TitleHigh affinity anchoring of the decoration protein pb10 onto the bacteriophage T5 capsid
Map dataEmpty expanded capsid of bacteriophage T5 without the decoration protein
Sample
  • Virus: Enterobacteria phage T5 (virus)
Biological speciesEnterobacteria phage T5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 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 5, 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: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8423.png

Downloads & links

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Map

FileDownload / File: emd_8423.map.gz / Format: CCP4 / Size: 474 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEmpty expanded capsid of bacteriophage T5 without the decoration protein
Voxel sizeX=Y=Z: 2.14 Å
Density
Contour LevelBy AUTHOR: 6. / Movie #1: 6
Minimum - Maximum-6.7652707 - 22.827423
Average (Standard dev.)0.0046043587 (±2.3287013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-249-249-249
Dimensions499499499
Spacing499499499
CellA=B=C: 1067.8601 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.142.142.14
M x/y/z499499499
origin x/y/z0.0000.0000.000
length x/y/z1067.8601067.8601067.860
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-249-249-249
NC/NR/NS499499499
D min/max/mean-6.76522.8270.005

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Supplemental data

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Sample components

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Entire : Enterobacteria phage T5

EntireName: Enterobacteria phage T5 (virus)
Components
  • Virus: Enterobacteria phage T5 (virus)

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Supramolecule #1: Enterobacteria phage T5

SupramoleculeName: Enterobacteria phage T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: from AMN5 amber mutant strain - mutation in the terminase.
NCBI-ID: 10726 / Sci species name: Enterobacteria phage T5 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: E.Coli (others)
Virus shellShell ID: 1 / Name: capsid / 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 - Concentration: 10.0 mM / Component - Name: tris
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 TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14.0 µm / Number real images: 5171 / Average exposure time: 2.0 sec. / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 28919
CTF correctionSoftware - Name: CTFFIND3
Initial angle assignmentType: COMMON LINE / Software - Name: Auto3DEM
Final angle assignmentType: COMMON LINE / Software - Name: Auto3DEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3DEM / Number images used: 26027
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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