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- EMDB-0344: CryoEM structure of Leviviridae PP7 WT coat protein dimer capsid ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0344 | |||||||||
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Title | CryoEM structure of Leviviridae PP7 WT coat protein dimer capsid (PP7PP7-WT) | |||||||||
![]() | Final map autosharp | |||||||||
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Function / homology | Bacteriophage 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![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Liangjun Z / Kopylov M / Potter CS / Carragher B / Finn MG | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 480.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12 KB 12 KB | Display Display | ![]() |
Images | ![]() | 197.8 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 518.8 KB | Display | ![]() |
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Full document | ![]() | 518.3 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n4vMC ![]() 0351C ![]() 0352C ![]() 0353C ![]() 0354C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Final map autosharp | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0733 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Pseudomonas phage PP7
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Pseudomonas phage PP7
Supramolecule | Name: 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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Host system | Organism: ![]() ![]() |
-Macromolecule #1: Coat protein
Macromolecule | Name: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 120 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.144008 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |