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- EMDB-3809: The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Us... -

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Basic information

Entry
Database: EMDB / ID: EMD-3809
TitleThe Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod
Map data
Sample
  • Complex: Type 1 Chaperone-usher pilus
    • Protein or peptide: Type-1 fimbrial protein, A chain
Keywordsbacterial pilus / chaperone-usher pilus / PROTEIN FIBRIL
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / cell adhesion / identical protein binding
Similarity search - Function
Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
Type-1 fimbrial protein, A chain
Similarity search - Component
Biological speciesEscherichia coli J96 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHospenthal MK / Costa TRD / Redzej A / Waksman G
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)018434 United Kingdom
CitationJournal: Structure / Year: 2017
Title: The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod.
Authors: Manuela K Hospenthal / Dawid Zyla / Tiago R D Costa / Adam Redzej / Christoph Giese / James Lillington / Rudi Glockshuber / Gabriel Waksman /
Abstract: Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play ...Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play important roles during urinary tract colonization, mediating attachment to the bladder and kidney, respectively. The biomechanical properties of the helical pilus rods allow them to reversibly uncoil in response to flow-induced forces, allowing UPEC to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2-Å resolution cryo-EM structure of the type 1 pilus rod, which together with the previous P pilus rod structure rationalizes the remarkable "spring-like" properties of chaperone-usher pili. The cryo-EM structure of the type 1 pilus rod differs in its helical parameters from the structure determined previously by a hybrid approach. We provide evidence that these structural differences originate from different quaternary structures of pili assembled in vivo and in vitro.
History
DepositionJul 13, 2017-
Header (metadata) releaseAug 16, 2017-
Map releaseNov 22, 2017-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5oh0
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5oh0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3809.png

Downloads & links

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Map

FileDownload / File: emd_3809.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 240 pix.
= 271.2 Å		1.13 Å/pix.
x 240 pix.
= 271.2 Å		1.13 Å/pix.
x 240 pix.
= 271.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.045445666 - 0.12328538
Average (Standard dev.)0.0005924707 (±0.0051952004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 271.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z271.200271.200271.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0450.1230.001

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Supplemental data

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Mask #1

Fileemd_3809_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type 1 Chaperone-usher pilus

EntireName: Type 1 Chaperone-usher pilus
Components
  • Complex: Type 1 Chaperone-usher pilus
    • Protein or peptide: Type-1 fimbrial protein, A chain

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Supramolecule #1: Type 1 Chaperone-usher pilus

SupramoleculeName: Type 1 Chaperone-usher pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Superhelical assembly of the pilus rod subunit FimA
Source (natural)Organism: Escherichia coli J96 (bacteria)

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Macromolecule #1: Type-1 fimbrial protein, A chain

MacromoleculeName: Type-1 fimbrial protein, A chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli J96 (bacteria)
Molecular weightTheoretical: 15.835243 KDa
Recombinant expressionOrganism: Escherichia coli HB101 (bacteria)
SequenceString:
AATTVNGGTV HFKGEVVNAA CAVDAGSVDQ TVQLGQVRTA SLAQEGATSS AVGFNIQLND CDTNVASKAA VAFLGTAIDA GHTNVLALQ SSAAGSATNV GVQILDRTGA ALTLDGATFS SETTLNNGTN TIPFQARYFA TGAATPGAAN ADATFKVQYQ

UniProtKB: Type-1 fimbrial protein, A chain

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5 / Component:
ConcentrationName
20.0 mMTris
150.0 mMNaCl
GridModel: Quantifoil 1.2/1.3 400 mesh grid / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.01188 Å
Applied symmetry - Helical parameters - Δ&Phi: 114.992 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 115510
Segment selectionNumber selected: 115545 / Software - Name: RELION (ver. 2.0)
Startup modelType of model: OTHER / Details: solid cylinder (diameter 100 Angstrom)
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model
PDB IDChain

2jty

chain_id: A, residue_range: 20-159, source_name: PDB, initial_model_type: experimental model

2jty

chain_id: A, residue_range: 172-182, source_name: PDB, initial_model_type: experimental model
Output model

PDB-5oh0:
The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod

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