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- EMDB-3222: Structure of a Chaperone-Usher pilus reveals the molecular basis ... -

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Basic information

Entry
Database: EMDB / ID: EMD-3222
TitleStructure of a Chaperone-Usher pilus reveals the molecular basis of rod uncoilin
Map dataReconstruction of P pilus
Sample
  • Sample: P pilus
  • Protein or peptide: PapA
Keywordshelical polymer / strand donation
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / extracellular region / Pap fimbrial major pilin protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHospenthal MK / Redzej A / Dodson K / Ukleja M / Frenz B / Hultgren SJ / DiMaio F / Egelman EH / Waksman G
CitationJournal: Cell / Year: 2016
Title: Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling.
Authors: Manuela K Hospenthal / Adam Redzej / Karen Dodson / Marta Ukleja / Brandon Frenz / Catarina Rodrigues / Scott J Hultgren / Frank DiMaio / Edward H Egelman / Gabriel Waksman /
Abstract: Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher ...Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher pathway, are polymers of pilus subunits assembling into two parts: a thin, short tip fibrillum at the top, mounted on a long pilus rod. The rod adopts a helical quaternary structure and is thought to play essential roles: its formation may drive pilus extrusion by preventing backsliding of the nascent growing pilus within the secretion pore; the rod also has striking spring-like properties, being able to uncoil and recoil depending on the intensity of shear forces generated by urine flow. Here, we present an atomic model of the P pilus generated from a 3.8 Å resolution cryo-electron microscopy reconstruction. This structure provides the molecular basis for the rod's remarkable mechanical properties and illuminates its role in pilus secretion.
History
DepositionOct 28, 2015-
Header (metadata) releaseNov 11, 2015-
Map releaseJan 13, 2016-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5flu
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3222_EMD...

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Map

FileDownload / File: emd_3222.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of P pilus
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1.5
Minimum - Maximum-1.20726669 - 3.29546285
Average (Standard dev.)0.58193427 (±0.53993404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-49-49-49
Dimensions100100100
Spacing100100100
CellA=B=C: 110.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z110.000110.000110.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-49-49-49
NC/NR/NS100100100
D min/max/mean-1.2073.2950.582

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Supplemental data

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Sample components

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Entire : P pilus

EntireName: P pilus
Components
  • Sample: P pilus
  • Protein or peptide: PapA

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Supramolecule #1000: P pilus

SupramoleculeName: P pilus / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: PapA

MacromoleculeName: PapA / type: protein_or_peptide / ID: 1 / Oligomeric state: helical polymer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateJul 8, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 90 / Average electron dose: 17 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each image
Final reconstructionApplied symmetry - Helical parameters - Δz: 7.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 109.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: Spider
DetailsIHRSR

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