Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus

Bardiaux, Benjamin; Amorim, Gisele Cardoso de; Rico, Areli Luna; Zheng, Weili; Guilvout, Ingrid; Jollivet, Camille; Nilges, Michaël; Egelman, Edward H.; Izadi-Pruneyre, Nadia; Francetić, Olivera

doi:10.1016/j.str.2019.03.021

Cited by 39 publications

(52 citation statements)

References 80 publications

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“…6C. For prepilin peptidase-dependent pilin (Bardiaux et al, 2019), which is another one of eight unusual eUMF value, the main plot ( Fig. 6B) was found to be just like the pattern of hist1h2ab.…”

Section: Distribution Plotmentioning

confidence: 76%

Repertoire of morphable proteins in an organism

Izumi

Saho

Kutomi

et al. 2020

PeerJ

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All living organisms have evolved to contain a set of proteins with variable physical and chemical properties. Efforts in the field of structural biology have contributed to uncovering the shape and the variability of each component. However, quantification of the variability has been performed mostly by multiple pair-wise comparisons. A set of experimental coordinates for a given protein can be used to define the "morphness/unmorphness". To understand the evolved repertoire in an organism, here we show the results of global analysis of more than a thousand Escherichia coli proteins, by the recently introduced method, distance scoring analysis (DSA). By collecting a new index "UnMorphness Factor" (UMF), proposed in this study and determined from DSA for each of the proteins, the lowest and the highest boundaries of the experimentally observable structural variation are comprehensibly defined. The distribution plot of UMFs obtained for E. coli represents the first view of a substantial fraction of non-redundant proteome set of an organism, demonstrating how rigid and flexible components are balanced. The present analysis extends to evaluate the growing data from single particle cryo-electron microscopy, providing valuable information on effective interpretation to structural changes of proteins and the supramolecular complexes.

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Section: Distribution Plotmentioning

confidence: 76%

Repertoire of morphable proteins in an organism

Izumi

Saho

Kutomi

et al. 2020

PeerJ

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“…For prepilin peptidase-dependent pilin (PPDD) 16 , which is another one of seven unusual eUMF value, the main plot ( Fig. 6b) was found to be just like the pattern of hist1h2ab.…”

Section: Cryo-em Structure Analysismentioning

confidence: 86%

Repertoire of morphable proteins in an organism

Izumi

Saho

Kutomi

et al. 2019

Preprint

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All living organisms have evolved to contain a set of proteins with variable physical and chemical properties. Efforts in the field of structural biology have contributed to uncovering the shape and the variability of each component. A set of experimental coordinates for a given protein can be used to define the "morphness/unmorphness". Here we show the results of global analysis of more than a thousand E. coli proteins, demonstrating that it would be a comprehensive method of understanding the evolved repertoire in an organism. By collecting "UnMorphness Factor" (UMF) determined for each of the proteins, the lowest and the highest boundaries of the experimentally observable structural variation are understood. The distribution of UMFs obtained for an organism is expected to represent how rigid and flexible components are balanced. The present analysis extends to evaluate the growing data from single particle cryoelectron microscopy, providing valuable information on effective interpretation to structural changes of proteins and the supramolecular complexes. The data and the method presented here also conform to FAIR data principles, having potential significance to advance the field of structural and molecular cell biology.

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“…T. thermophilus demonstrated the presence of narrow (4.5 nm) and wide (7 nm) pili 389 53 . In Figure 7D, the EcT4aP cryoEM structure (yellow) is fit into our VcPilQ structure (in grey) 52 . The gate region with diameters of 25 Å at the lower gate and 391 36 Å in the upper gate clashes with the pilus (Figures 4A and 7D).…”

Section: Outer Membrane-spanning Domain 312mentioning

confidence: 99%

“…CryoEM structures of several Type IVa Pili (T4aP) have been solved from N. 384 meningitidis (NmT4aP, 6 Å resolution, 6 to 7 nm diameter), N. gonorrhoeae 385 (NgT4aP, 5 Å resolution, 6 nm diameter), E. coli (EHEC strain, EcT4aP, 8 386 Å resolution, 6 nm diameter), and P. aeruginosa (PaT4aP, 8 Å resolution, 5 nm 387 diameter)[50][51][52] . Additionally, a recent preprint on bioRxiv studying Type IV pili in 388…”

mentioning

confidence: 99%