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- EMDB-0344: CryoEM structure of Leviviridae PP7 WT coat protein dimer capsid ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0344
TitleCryoEM structure of Leviviridae PP7 WT coat protein dimer capsid (PP7PP7-WT)
Map dataFinal map autosharp
Sample
  • Virus: Pseudomonas phage PP7 (virus)
    • Protein or peptide: Coat protein
KeywordsT4 / icosahedral / PP7 / biotechnology / vaccine / drug delivery / VIRUS LIKE PARTICLE
Function / homologyBacteriophage PP7, coat / Phage PP7 coat protein / Bacteriophage RNA-type, capsid / T=3 icosahedral viral capsid / regulation of translation / RNA binding / identical protein binding / Capsid protein
Function and homology information
Biological speciesPseudomonas phage PP7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiangjun Z / Kopylov M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM103310 United States
CitationJournal: ACS Nano / Year: 2019
Title: Engineering the PP7 Virus Capsid as a Peptide Display Platform.
Authors: Liangjun Zhao / Mykhailo Kopylov / Clinton S Potter / Bridget Carragher / M G Finn /
Abstract: As self-assembling polyvalent nanoscale structures that can tolerate substantial genetic and chemical modification, virus-like particles are useful in a variety of fields. Here we describe the ...As self-assembling polyvalent nanoscale structures that can tolerate substantial genetic and chemical modification, virus-like particles are useful in a variety of fields. Here we describe the genetic modification and structural characterization of the Leviviridae PP7 capsid protein as a platform for the presentation of functional polypeptides. This particle was shown to tolerate the display of sequences from 1 kDa (a cell penetrating peptide) to 14 kDa (the Fc-binding double Z-domain) on its exterior surface as C-terminal genetic fusions to the coat protein. In addition, a dimeric construct allowed the presentation of exogenous loops between capsid monomers and the simultaneous presentation of two different peptides at different positions on the icosahedral structure. The PP7 particle is thereby significantly more tolerant of these types of polypeptide additions than Qβ and MS2, the other Leviviridae-derived VLPs in common use.
History
DepositionNov 20, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseApr 3, 2019-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.496
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.496
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6n4v
  • Surface level: 0.496
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6n4v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0344.png

Downloads & links

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Map

FileDownload / File: emd_0344.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map autosharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 549.53 Å		1.07 Å/pix.
x 512 pix.
= 549.53 Å		1.07 Å/pix.
x 512 pix.
= 549.53 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0733 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.496 / Movie #1: 0.496
Minimum - Maximum-1.4895145 - 3.6047127
Average (Standard dev.)-0.0037346743 (±0.14880326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 549.5296 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.073300781251.073300781251.07330078125
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z549.530549.530549.530
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-1.4903.605-0.004

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Supplemental data

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Mask #1

Fileemd_0344_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pseudomonas phage PP7

EntireName: Pseudomonas phage PP7 (virus)
Components
  • Virus: Pseudomonas phage PP7 (virus)
    • Protein or peptide: Coat protein

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Supramolecule #1: Pseudomonas phage PP7

SupramoleculeName: Pseudomonas phage PP7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12023 / Sci species name: Pseudomonas phage PP7 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 120 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage PP7 (virus)
Molecular weightTheoretical: 28.144008 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SKTIVLSVGE ATRTLTEIQS TADRQIFEEK VGPLVGRLRL TASLRQNGAK TAYRVNLKLD QADVVDCSTS VCGELPKVRY TQVWSHDVT IVANSTEASR KSLYDLTKSL VATSQVEDLV VNLVPLGRAY GGSKTIVLSV GEATRTLTEI QSTADRQIFE E KVGPLVGR ...String:
SKTIVLSVGE ATRTLTEIQS TADRQIFEEK VGPLVGRLRL TASLRQNGAK TAYRVNLKLD QADVVDCSTS VCGELPKVRY TQVWSHDVT IVANSTEASR KSLYDLTKSL VATSQVEDLV VNLVPLGRAY GGSKTIVLSV GEATRTLTEI QSTADRQIFE E KVGPLVGR LRLTASLRQN GAKTAYRVNL KLDQADVVDC STSVCGELPK VRYTQVWSHD VTIVANSTEA SRKSLYDLTK SL VATSQVE DLVVNLVPLG R

UniProtKB: 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

Concentration1 mg/mL
BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 0.002 µm / Nominal magnification: 22500
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 5 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.6.5) / Number images used: 33224
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 0.6.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 0.6.5)
Final 3D classificationNumber classes: 25 / Avg.num./class: 1500 / Software - Name: RELION (ver. 3) / Details: Classified in Relion3

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