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- EMDB-60902: Cryo-EM structure of the type IVb pilus from enterotoxigenic Esch... -

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Basic information

Entry
Database: EMDB / ID: EMD-60902
TitleCryo-EM structure of the type IVb pilus from enterotoxigenic Escherichia coli
Map data
Sample
  • Complex: CFA/III major pilin, CofA
    • Protein or peptide: CFA/III pilin
  • Ligand: water
KeywordsType IV pili / colonization factor / CELL ADHESION
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)
Methodhelical reconstruction / cryo EM / Resolution: 1.78 Å
AuthorsKawahara K / Oki H / Nakamura S
Funding support Japan, 2 items
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, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60902.png

Downloads & links

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Map

FileDownload / File: emd_60902.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 400 pix.
= 300.8 Å		0.75 Å/pix.
x 400 pix.
= 300.8 Å		0.75 Å/pix.
x 400 pix.
= 300.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.051867228 - 0.24110092
Average (Standard dev.)-0.000008444755 (±0.0097644385)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60902_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpening map

Fileemd_60902_additional_1.map
Annotationsharpening map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60902_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_60902_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : CFA/III major pilin, CofA

EntireName: CFA/III major pilin, CofA
Components
  • Complex: CFA/III major pilin, CofA
    • Protein or peptide: CFA/III pilin
  • Ligand: water

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Supramolecule #1: CFA/III major pilin, CofA

SupramoleculeName: CFA/III major pilin, CofA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 31-10

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Macromolecule #1: CFA/III pilin

MacromoleculeName: CFA/III pilin / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: 31-10
Molecular weightTheoretical: 21.620418 KDa
SequenceString: MSLLEVIIVL GIIGTIAAGV VILAQRAFDS RTVSELVTNT NTIRVAMKDA YQRDGKYPDY QAPLSLTADS IKTDSTGIAV AQLVQLGKL TPDEARNGIS GDYIGIGGAI TSSGSTINKG FAMELNGLSQ EQCRSILGQV GDNWEYVAVG TSPSGSYDAL S AGAVNMLA ...String:
MSLLEVIIVL GIIGTIAAGV VILAQRAFDS RTVSELVTNT NTIRVAMKDA YQRDGKYPDY QAPLSLTADS IKTDSTGIAV AQLVQLGKL TPDEARNGIS GDYIGIGGAI TSSGSTINKG FAMELNGLSQ EQCRSILGQV GDNWEYVAVG TSPSGSYDAL S AGAVNMLA ATDNTTILRS LAANGQVSLT AEKILKTCTA TVNSITLASR

UniProtKB: CFA/III pilin

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 4175 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.77 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.014 Å
Applied symmetry - Helical parameters - Δ&Phi: 94.553 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 1.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1425921
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9iuf:
Cryo-EM structure of the type IVb pilus from enterotoxigenic Escherichia coli

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