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Yorodumi- PDB-7lhg: Cryo-EM structure of E. coli P pilus tip assembly intermediate Pa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lhg | |||||||||
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Title | Cryo-EM structure of E. coli P pilus tip assembly intermediate PapC-PapD-PapK-PapG in the first conformation | |||||||||
Components |
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Keywords | CHAPERONE / Cryo-EM / Uropathogenic Escherichia coli / chaperone-usher / P pilus | |||||||||
Function / homology | Function and homology information cell adhesion involved in single-species biofilm formation / pilus / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space / carbohydrate binding / cell adhesion / extracellular region Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Du, M. / Yuan, Z. / Werneburg, G. / Henderson, N. / Chauhan, H. / Kovach, A. / Zhao, G. / Johl, J. / Li, H. / Thanassi, D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Processive dynamics of the usher assembly platform during uropathogenic Escherichia coli P pilus biogenesis. Authors: Minge Du / Zuanning Yuan / Glenn T Werneburg / Nadine S Henderson / Hemil Chauhan / Amanda Kovach / Gongpu Zhao / Jessica Johl / Huilin Li / David G Thanassi / Abstract: Uropathogenic Escherichia coli assemble surface structures termed pili or fimbriae to initiate infection of the urinary tract. P pili facilitate bacterial colonization of the kidney and ...Uropathogenic Escherichia coli assemble surface structures termed pili or fimbriae to initiate infection of the urinary tract. P pili facilitate bacterial colonization of the kidney and pyelonephritis. P pili are assembled through the conserved chaperone-usher pathway. Much of the structural and functional understanding of the chaperone-usher pathway has been gained through investigations of type 1 pili, which promote binding to the bladder and cystitis. In contrast, the structural basis for P pilus biogenesis at the usher has remained elusive. This is in part due to the flexible and variable-length P pilus tip fiber, creating structural heterogeneity, and difficulties isolating stable P pilus assembly intermediates. Here, we circumvent these hindrances and determine cryo-electron microscopy structures of the activated PapC usher in the process of secreting two- and three-subunit P pilus assembly intermediates, revealing processive steps in P pilus biogenesis and capturing new conformational dynamics of the usher assembly machine. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lhg.cif.gz | 269.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lhg.ent.gz | 212.6 KB | Display | PDB format |
PDBx/mmJSON format | 7lhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/7lhg ftp://data.pdbj.org/pub/pdb/validation_reports/lh/7lhg | HTTPS FTP |
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-Related structure data
Related structure data | 23339MC 7lhhC 7lhiC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 88746.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papC, GE554_23855, HJR83_004260 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A773A954 |
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#2: Protein | Mass: 26833.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papD / Production host: Escherichia coli (E. coli) / References: UniProt: P15319 |
#3: Protein | Mass: 18895.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papK / Production host: Escherichia coli (E. coli) / References: UniProt: P62532 |
#4: Protein | Mass: 37620.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: papG-II, HJS42_005082 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A798R8B8 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: PapCDKG / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227396 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT |