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Yorodumi- PDB-6e15: Handover mechanism of the growing pilus by the bacterial outer me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6.0E+15 | ||||||
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Title | Handover mechanism of the growing pilus by the bacterial outer membrane usher FimD | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / pili / chaperone / usher | ||||||
Function / homology | Function and homology information fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / chaperone-mediated protein folding ...fimbrial usher porin activity / pilus assembly / pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / chaperone-mediated protein folding / protein folding chaperone / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / cell adhesion Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||
Authors | Du, M. / Yuan, Z. / Yu, H. / Henderson, N. / Sarowar, S. / Zhao, G. / Werneburg, G.T. / Thanassi, D.G. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2018 Title: Handover mechanism of the growing pilus by the bacterial outer-membrane usher FimD. Authors: Minge Du / Zuanning Yuan / Hongjun Yu / Nadine Henderson / Samema Sarowar / Gongpu Zhao / Glenn T Werneburg / David G Thanassi / Huilin Li / Abstract: Pathogenic bacteria such as Escherichia coli assemble surface structures termed pili, or fimbriae, to mediate binding to host-cell receptors. Type 1 pili are assembled via the conserved chaperone- ...Pathogenic bacteria such as Escherichia coli assemble surface structures termed pili, or fimbriae, to mediate binding to host-cell receptors. Type 1 pili are assembled via the conserved chaperone-usher pathway. The outer-membrane usher FimD recruits pilus subunits bound by the chaperone FimC via the periplasmic N-terminal domain of the usher. Subunit translocation through the β-barrel channel of the usher occurs at the two C-terminal domains (which we label CTD1 and CTD2) of this protein. How the chaperone-subunit complex bound to the N-terminal domain is handed over to the C-terminal domains, as well as the timing of subunit polymerization into the growing pilus, have previously been unclear. Here we use cryo-electron microscopy to capture a pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH) in a conformation in which FimD is in the process of handing over the chaperone-bound end of the growing pilus to the C-terminal domains. In this structure, FimF has already polymerized with FimG, and the N-terminal domain of FimD swings over to bind CTD2; the N-terminal domain maintains contact with FimC-FimF, while at the same time permitting access to the C-terminal domains. FimD has an intrinsically disordered N-terminal tail that precedes the N-terminal domain. This N-terminal tail folds into a helical motif upon recruiting the FimC-subunit complex, but reorganizes into a loop to bind CTD2 during handover. Because both the N-terminal and C-terminal domains of FimD are bound to the end of the growing pilus, the structure further suggests a mechanism for stabilizing the assembly intermediate to prevent the pilus fibre diffusing away during the incorporation of thousands of subunits. | ||||||
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 | 6e15.cif.gz | 275.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e15.ent.gz | 222 KB | Display | PDB format |
PDBx/mmJSON format | 6e15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e15_validation.pdf.gz | 695.8 KB | Display | wwPDB validaton report |
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Full document | 6e15_full_validation.pdf.gz | 734.6 KB | Display | |
Data in XML | 6e15_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 6e15_validation.cif.gz | 75.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/6e15 ftp://data.pdbj.org/pub/pdb/validation_reports/e1/6e15 | HTTPS FTP |
-Related structure data
Related structure data | 8954MC 8953C 6e14C 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: 26716.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimC, b4316, JW4279 / Production host: Escherichia coli (E. coli) / References: UniProt: P31697 |
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#2: Protein | Mass: 96705.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: fimD_3, APZ14_00735, AW106_26365, COD30_02575, CXB56_24500, ERS085374_04437, ERS150876_04614, FORC28_5312 Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F3W955, UniProt: P30130*PLUS |
#3: Protein | Mass: 16379.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimF, b4318, JW4281 / Production host: Escherichia coli (E. coli) / References: UniProt: P08189 |
#4: Protein | Mass: 16190.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimG, b4319, JW4282 / Production host: Escherichia coli (E. coli) / References: UniProt: P08190 |
#5: Protein | Mass: 31488.260 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimH, b4320, JW4283 / Production host: Escherichia coli (E. coli) / References: UniProt: P08191 |
-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: FimDCFGH tip complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.18 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.4 |
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 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166913 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 6.2 Å | ||||||||||||||||||||||||
Refine LS restraints |
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