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Yorodumi- EMDB-42136: PhiCb5 maturation protein with Caulobacter crescentus bNY30a pili -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42136 | |||||||||
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Title | PhiCb5 maturation protein with Caulobacter crescentus bNY30a pili | |||||||||
Map data | Caulobacter pilus binds to phiCb5 | |||||||||
Sample |
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Keywords | RNA phage / protein fibril / RECOMBINATION | |||||||||
Function / homology | Flp/Fap pilin component / Flp/Fap pilin component / Assembly protein / Phage maturation protein / virion attachment to host cell pilus / virion component / membrane / Flp family type IVb pilin / Maturation protein Function and homology information | |||||||||
Biological species | Caulobacter vibrioides (bacteria) / Caulobacter phage phiCb5 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.45 Å | |||||||||
Authors | Wang Y / Zhang J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus. Authors: Yuhang Wang / Matthew Theodore / Zhongliang Xing / Utkarsh Narsaria / Zihao Yu / Lanying Zeng / Junjie Zhang / Abstract: Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV ... Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42136.map.gz | 658.2 MB | EMDB map data format | |
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Header (meta data) | emd-42136-v30.xml emd-42136.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42136_fsc.xml | 27.5 KB | Display | FSC data file |
Images | emd_42136.png | 45.3 KB | ||
Filedesc metadata | emd-42136.cif.gz | 5.3 KB | ||
Others | emd_42136_half_map_1.map.gz emd_42136_half_map_2.map.gz | 666.6 MB 667 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42136 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42136 | HTTPS FTP |
-Validation report
Summary document | emd_42136_validation.pdf.gz | 976.8 KB | Display | EMDB validaton report |
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Full document | emd_42136_full_validation.pdf.gz | 976.3 KB | Display | |
Data in XML | emd_42136_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | emd_42136_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42136 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42136 | HTTPS FTP |
-Related structure data
Related structure data | 8ucrMC 8u2bC 8uejC C: citing same article (ref.) M: atomic model generated by this map |
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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_42136.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Caulobacter pilus binds to phiCb5 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Caulobacter pilus binds to phiCb5
File | emd_42136_half_map_1.map | ||||||||||||
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Annotation | Caulobacter pilus binds to phiCb5 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Caulobacter pilus binds to phiCb5
File | emd_42136_half_map_2.map | ||||||||||||
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Annotation | Caulobacter pilus binds to phiCb5 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : A complex of pilus and phiCb5 maturation protein
Entire | Name: A complex of pilus and phiCb5 maturation protein |
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Components |
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-Supramolecule #1: A complex of pilus and phiCb5 maturation protein
Supramolecule | Name: A complex of pilus and phiCb5 maturation protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: A complex of Caulobacter crescentus pilus and ssRNA phage phiCb5 maturation protein in buffer |
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Source (natural) | Organism: Caulobacter vibrioides (bacteria) |
Molecular weight | Theoretical: 210 KDa |
-Macromolecule #1: Maturation protein
Macromolecule | Name: Maturation protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Caulobacter phage phiCb5 (virus) |
Molecular weight | Theoretical: 40.725336 KDa |
Sequence | String: MARIRNRSSI ASSGMSTFYL FGTPIVNEEI IVRNTEWCSD VIGNPGDNPL DIHKQEWTIK PLSGQIIFGS GTYRSLQCPP EYCRGASLS HLSLPSQSGL GTTALARTNP SRPAFNLPAF IGELRDLPRM FKIAGDTMLR KGANAFLSYQ FGWKPLISDI S KALDFSAT ...String: MARIRNRSSI ASSGMSTFYL FGTPIVNEEI IVRNTEWCSD VIGNPGDNPL DIHKQEWTIK PLSGQIIFGS GTYRSLQCPP EYCRGASLS HLSLPSQSGL GTTALARTNP SRPAFNLPAF IGELRDLPRM FKIAGDTMLR KGANAFLSYQ FGWKPLISDI S KALDFSAT VRTRSDEWHR LYSNGGLKRR INLGVDIEQK KENDVVLHSS NGFVVASHTV ITVRKTWATV RWRPDAGSLP PI TKSSSEK HARALLGLGV GGLIEGAWQL MPWSWMVDWF GNVGTFLQAS NNTIGASPGL VNIMTTTTTN HQFSVKRDLS DGW IKGGDC SATVTSKARS QSSGPTITAS IPNLSGRQLS ILGALGIQRV PRHLLR UniProtKB: Maturation protein |
-Macromolecule #2: Flp family type IVb pilin
Macromolecule | Name: Flp family type IVb pilin / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: Caulobacter vibrioides (bacteria) |
Molecular weight | Theoretical: 4.37914 KDa |
Sequence | String: ATAIEYGLIV ALIAVVIVTA VTTLGTKLNL AFTKAGTAVS TAAGT UniProtKB: Flp family type IVb pilin |
-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: 20mM tris, 2mM MgCl2 | |||||||||
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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: 25.0 µm / Nominal defocus min: 5.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |