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- PDB-9iuf: Cryo-EM structure of the type IVb pilus from enterotoxigenic Esch... -

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Basic information

Entry
Database: PDB / ID: 9iuf
TitleCryo-EM structure of the type IVb pilus from enterotoxigenic Escherichia coli
ComponentsCFA/III pilin
KeywordsCELL ADHESION / Type IV pili / colonization factor
Function / homology
Function and homology information


extracellular organelle / pilus / membrane
Similarity search - Function
Toxin-coregulated pilus subunit TcpA / Toxin-coregulated pilus subunit TcpA / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 1.78 Å
AuthorsKawahara, K. / Oki, H. / Nakamura, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K14519 Japan
Japan Society for the Promotion of Science (JSPS)24K10218 Japan
CitationJournal: Structure / Year: 2025
Title: High-resolution cryo-EM analysis visualizes hydrated type I and IV pilus structures from enterotoxigenic Escherichia coli.
Authors: Kazuki Kawahara / Hiroya Oki / Minato Iimori / Ryuki Muramoto / Tomoya Imai / Christoph Gerle / Hideki Shigematsu / Shigeaki Matsuda / Tetsuya Iida / Shota Nakamura /
Abstract: Pathogenic bacteria utilize a variety of pilus filaments to colonize intestinal epithelia, including those synthesized by the chaperone-usher or type IV pilus assembly pathway. Despite the importance ...Pathogenic bacteria utilize a variety of pilus filaments to colonize intestinal epithelia, including those synthesized by the chaperone-usher or type IV pilus assembly pathway. Despite the importance of these filaments as potential drug and vaccine targets, their large size and dynamic nature make high-resolution structure determination challenging. Here, we used cryo-electron microscopy (cryo-EM) and whole-genome sequencing to determine the structures of type I and IV pili expressed in enterotoxigenic Escherichia coli. Well-defined cryo-EM maps at resolutions of 2.2 and 1.8 Å for type I and IV pilus, respectively, facilitated the de novo structural modeling for these filaments, revealing side-chain structures in detail. We resolved thousands of hydrated water molecules around and within the inner core of the filaments, which stabilize the otherwise metastable quaternary subunit assembly. The high-resolution structures offer novel insights into subunit-subunit interactions, and provide important clues to understand pilus assembly, stability, and flexibility.
History
DepositionJul 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CFA/III pilin
B: CFA/III pilin
C: CFA/III pilin
D: CFA/III pilin
E: CFA/III pilin
F: CFA/III pilin
G: CFA/III pilin
H: CFA/III pilin
I: CFA/III pilin
J: CFA/III pilin
K: CFA/III pilin
L: CFA/III pilin
M: CFA/III pilin
N: CFA/III pilin
O: CFA/III pilin
P: CFA/III pilin
Q: CFA/III pilin
R: CFA/III pilin


Theoretical massNumber of molelcules
Total (without water)389,16818
Polymers389,16818
Non-polymers00
Water75,2134175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
CFA/III pilin / CofA / Major pilin subunit


Mass: 21620.418 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: 31-10 / References: UniProt: Q59393
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: CFA/III major pilin, CofA / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 31-10
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 53.77 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 94.553 ° / Axial rise/subunit: 8.014 Å / Axial symmetry: C1
3D reconstructionResolution: 1.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1425921 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE

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