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Yorodumi- EMDB-41633: Type IV pilus from Pseudomonas PAO1 strain with PP7 Maturation protein -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41633 | ||||||||||||||||||||||||
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Title | Type IV pilus from Pseudomonas PAO1 strain with PP7 Maturation protein | ||||||||||||||||||||||||
Map data | Local refinement map of PP7 binding to T4P from PAO1 | ||||||||||||||||||||||||
Sample |
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Keywords | Type IV pilus / T4P / PAO1 / MEMBRANE PROTEIN | ||||||||||||||||||||||||
Function / homology | Function and homology information type IV pilus / type IV pilus-dependent motility / single-species biofilm formation on inanimate substrate / virion attachment to host cell pilus / cell adhesion involved in single-species biofilm formation / pilus / regulation of calcium-mediated signaling / virion component / host cell endoplasmic reticulum membrane / cell surface ...type IV pilus / type IV pilus-dependent motility / single-species biofilm formation on inanimate substrate / virion attachment to host cell pilus / cell adhesion involved in single-species biofilm formation / pilus / regulation of calcium-mediated signaling / virion component / host cell endoplasmic reticulum membrane / cell surface / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) / Pseudomonas phage PP7 (virus) / Pseudomonas aeruginosa PAO1 (bacteria) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.9 Å | ||||||||||||||||||||||||
Authors | Thongchol J / Zhang J / Zeng L | ||||||||||||||||||||||||
Funding support | United States, 7 items
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Citation | Journal: Science / Year: 2024 Title: Removal of type IV pili by a small RNA virus. Authors: Jirapat Thongchol / Zihao Yu / Laith Harb / Yiruo Lin / Matthias Koch / Matthew Theodore / Utkarsh Narsaria / Joshua Shaevitz / Zemer Gitai / Yinghao Wu / Junjie Zhang / Lanying Zeng / Abstract: The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through ...The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen . The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics. | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41633.map.gz | 87.4 MB | EMDB map data format | |
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Header (meta data) | emd-41633-v30.xml emd-41633.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41633_fsc.xml | 12.1 KB | Display | FSC data file |
Images | emd_41633.png | 25.2 KB | ||
Filedesc metadata | emd-41633.cif.gz | 6.2 KB | ||
Others | emd_41633_half_map_1.map.gz emd_41633_half_map_2.map.gz | 164.9 MB 164.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41633 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41633 | HTTPS FTP |
-Validation report
Summary document | emd_41633_validation.pdf.gz | 946.4 KB | Display | EMDB validaton report |
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Full document | emd_41633_full_validation.pdf.gz | 946 KB | Display | |
Data in XML | emd_41633_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | emd_41633_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41633 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41633 | HTTPS FTP |
-Related structure data
Related structure data | 8tuwMC 8tumC 8tuxC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41633.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Local refinement map of PP7 binding to T4P from PAO1 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.72 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map 1
File | emd_41633_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_41633_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type IV twitching pilus
Entire | Name: Type IV twitching pilus |
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Components |
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-Supramolecule #1: Type IV twitching pilus
Supramolecule | Name: Type IV twitching pilus / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1 |
Molecular weight | Theoretical: 240 KDa |
-Macromolecule #1: Maturation protein A
Macromolecule | Name: Maturation protein A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas phage PP7 (virus) |
Molecular weight | Theoretical: 50.763766 KDa |
Sequence | String: LEEHYYSRKT CGSGGGLSVQ RTGYPQTDPP VFKAVNSFER APLIVGDHVH SLPYWSRKIT LECTPYPFTL RWEGGVHKDG IPDKVPHPS CDPGSELVSY THSREVDCER FIGPVPSSFT DPKVTSAQWK FLEDMADMKA LADLNKSLVN LPMLYKERRE T LKMVGNRL ...String: LEEHYYSRKT CGSGGGLSVQ RTGYPQTDPP VFKAVNSFER APLIVGDHVH SLPYWSRKIT LECTPYPFTL RWEGGVHKDG IPDKVPHPS CDPGSELVSY THSREVDCER FIGPVPSSFT DPKVTSAQWK FLEDMADMKA LADLNKSLVN LPMLYKERRE T LKMVGNRL GGLVRVAHAA QDRDLKRYFK ARRKDRRKVA EEVANGHLEL IFGWLPLIGE LEGAIEYAEL PDLDFIRCHG LH TLVLQST PWDNSVDVRS YPNWERAAGT RITGSVRTRG VVESRASVRT ALRFNLETSL AGDARRLGFE PISTTYDMIP LSF VVGWFS NFDKYVRTLA PLIGVTFETG SQNRRTTCEL VGCTRFYPRT VSPPSGWFAR WKDFPDGSLS EVSGLRRTDI RSVL STLPD PDVRFHADVG LFEISAGISL LAQRYLKPLQ RLLKRKSFFY GRT UniProtKB: Maturation protein A |
-Macromolecule #2: Type IV major pilin protein PilA
Macromolecule | Name: Type IV major pilin protein PilA / type: protein_or_peptide / ID: 2 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
Molecular weight | Theoretical: 14.878889 KDa |
Recombinant expression | Organism: Pseudomonas aeruginosa PAO1 (bacteria) |
Sequence | String: FTLIELMIVV AIIGILAAIA IPQYQNYVAR SEGASALATI NPLKTTVEES LSRGIAGSKI KIGTTASTAT ETYVGVEPDA NKLGVIAVA IEDSGAGDIT FTFQTGTSSP KNATKVITLN RTADGVWACK STQDPMFTPK GCDN UniProtKB: Type IV major pilin protein PilA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 / Component - Concentration: 1.0 x / Component - Name: PBS Details: 137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4, pH 7.4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 5085 / Average electron dose: 50.85 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |