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Yorodumi- EMDB-29675: A Vibrio cholerae viral satellite enables efficient horizontal tr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29675 | |||||||||||||||||||||
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Title | A Vibrio cholerae viral satellite enables efficient horizontal transfer by using an external scaffold to assemble hijacked coat proteins into small capsids | |||||||||||||||||||||
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Sample |
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Keywords | PLE / Procapsid / VIRUS LIKE PARTICLE | |||||||||||||||||||||
Function / homology | Major capsid protein GpE / Phage major capsid protein E / host cell cytoplasm / Putative major head protein / Phage protein Function and homology information | |||||||||||||||||||||
Biological species | Vibrio cholerae (bacteria) / Vibrio phage ICP1_2011_A (virus) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||||||||
Authors | Subramanian S / Boyd CM / Seed KD / Parent KN | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Elife / Year: 2024 Title: A viral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids. Authors: Caroline M Boyd / Sundharraman Subramanian / Drew T Dunham / Kristin N Parent / Kimberley D Seed / Abstract: Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a ...Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a satellite from , phage-inducible chromosomal island-like element (PLE), remodels the capsid it has been predicted to steal from the phage ICP1 (Netter et al., 2021). We identified that a PLE-encoded protein, TcaP, is both necessary and sufficient to form small capsids during ICP1 infection. Interestingly, we found that PLE is dependent on small capsids for efficient transduction of its genome, making it the first satellite to have this requirement. ICP1 isolates that escaped TcaP-mediated remodeling acquired substitutions in the coat protein, suggesting an interaction between these two proteins. With a procapsid-like particle (PLP) assembly platform in , we demonstrated that TcaP is a bona fide scaffold that regulates the assembly of small capsids. Further, we studied the structure of PLE PLPs using cryogenic electron microscopy and found that TcaP is an external scaffold that is functionally and somewhat structurally similar to the external scaffold, Sid, encoded by the unrelated satellite P4 (Kizziah et al., 2020). Finally, we showed that TcaP is largely conserved across PLEs. Together, these data support a model in which TcaP directs the assembly of small capsids comprised of ICP1 coat proteins, which inhibits the complete packaging of the ICP1 genome and permits more efficient packaging of replicated PLE genomes. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29675.map.gz | 251.2 MB | EMDB map data format | |
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Header (meta data) | emd-29675-v30.xml emd-29675.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29675_fsc.xml | 21.1 KB | Display | FSC data file |
Images | emd_29675.png | 206.6 KB | ||
Masks | emd_29675_msk_1.map | 824 MB | Mask map | |
Filedesc metadata | emd-29675.cif.gz | 6 KB | ||
Others | emd_29675_half_map_1.map.gz emd_29675_half_map_2.map.gz | 760.5 MB 760.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29675 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29675 | HTTPS FTP |
-Validation report
Summary document | emd_29675_validation.pdf.gz | 914.9 KB | Display | EMDB validaton report |
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Full document | emd_29675_full_validation.pdf.gz | 914.4 KB | Display | |
Data in XML | emd_29675_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | emd_29675_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29675 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29675 | HTTPS FTP |
-Related structure data
Related structure data | 8g1rMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29675.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29675_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29675_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29675_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PLE Procapsid
Entire | Name: PLE Procapsid |
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Components |
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-Supramolecule #1: PLE Procapsid
Supramolecule | Name: PLE Procapsid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vibrio cholerae (bacteria) / Strain: El Tor |
-Macromolecule #1: major head protein
Macromolecule | Name: major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio phage ICP1_2011_A (virus) |
Molecular weight | Theoretical: 38.428023 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MARMGDFGVV DYTSLMALAP RSKNFLELLG VFSESNTRYI DSRYAEFERE EKGVTKMNAM ARGGSRKYIG SEKARKEIIE VPFAPLDGV TVASEVEAFR QYGTESQTAS VEALVQRKIE HIQRSHGIYI RDCQYTALLK DKILAEDEDG NEITALAKNF S TLWGVSRK ...String: MARMGDFGVV DYTSLMALAP RSKNFLELLG VFSESNTRYI DSRYAEFERE EKGVTKMNAM ARGGSRKYIG SEKARKEIIE VPFAPLDGV TVASEVEAFR QYGTESQTAS VEALVQRKIE HIQRSHGIYI RDCQYTALLK DKILAEDEDG NEITALAKNF S TLWGVSRK TGAINTTTAV NPFSVLATKR QEIIDSMGEN NGFTSMVVLC TTRDFNAIVD HPDVRAAYEG RDGGAEYLTR RL GDAVDFQ VFTHKGVTLV EDTSGKLTDG SAYMFPLGVQ DMFQAVYAPA DSTDHVNTIS QGSYLFLNAG ENWRRDVIES EVS YACMVT RSELICDLTI TVAHHHHHH UniProtKB: Putative major head protein |
-Macromolecule #2: Serine protease
Macromolecule | Name: Serine protease / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio cholerae (bacteria) / Strain: El Tor |
Molecular weight | Theoretical: 33.231152 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MTTITTTTNN TFDLANVIAE YKAGFEQYKA DNKQYNADAY RRKIESINSD AALTNGAFNQ FAYGSQMFEG KTLQEIAESL KTMQVKDSS REDENGLIFP HVTLQLVSPT TPAQYYGLIA EAVKLGFEVC PDWRLHVGTG RNFPACRLVR QAEWYKPHNE K LMAERIAE ...String: MTTITTTTNN TFDLANVIAE YKAGFEQYKA DNKQYNADAY RRKIESINSD AALTNGAFNQ FAYGSQMFEG KTLQEIAESL KTMQVKDSS REDENGLIFP HVTLQLVSPT TPAQYYGLIA EAVKLGFEVC PDWRLHVGTG RNFPACRLVR QAEWYKPHNE K LMAERIAE AEKQEAERLK AEYFNEHRVQ AYVEQAQRKF MATQAQQAAI SLSAAISREL YASSGLSDDD LAVVAQSDVW AF NTLAPQL QEKDPNVISA ALTGAGFVKG KHKLSDGKQA TLWVKDGADV TALTLESKYI Q UniProtKB: Phage protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: 50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 10 mM MgSO4, 1 mM CaCl2 | |||||||||||||||
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.41 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |