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Yorodumi- EMDB-0344: CryoEM structure of Leviviridae PP7 WT coat protein dimer capsid ... -
+Open data
-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) | |||||||||
Map data | Final map autosharp | |||||||||
Sample |
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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 Function and homology information | |||||||||
Biological species | Pseudomonas phage PP7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Liangjun Z / Kopylov M / Potter CS / Carragher B / Finn MG | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0344.map.gz | 480.6 MB | EMDB map data format | |
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Header (meta data) | emd-0344-v30.xml emd-0344.xml | 12 KB 12 KB | Display Display | EMDB header |
Images | emd_0344.png | 197.8 KB | ||
Masks | emd_0344_msk_1.map | 512 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0344 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0344 | HTTPS FTP |
-Related structure data
Related structure data | 6n4vMC 0351C 0352C 0353C 0354C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0344.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
File | emd_0344_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Pseudomonas phage PP7
Entire | Name: Pseudomonas phage PP7 (virus) |
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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: Escherichia coli (E. coli) |
-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: Pseudomonas phage PP7 (virus) |
Molecular weight | Theoretical: 28.144008 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus min: 0.002 µm / Nominal magnification: 22500 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 35.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 0.6.5) |
Final 3D classification | Number classes: 25 / Avg.num./class: 1500 / Software - Name: RELION (ver. 3) / Details: Classified in Relion3 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 0.6.5) |
Final reconstruction | Number 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 |