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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: 3809
TitleThe Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod
Map data
SampleType 1 Chaperone-usher pilus:
Type-1 fimbrial protein, A chain
Function / homologyFimbrial-type adhesion domain / Adhesion domain superfamily / Fimbrial-type adhesion domain superfamily / Fimbrial protein / pilus / cell adhesion / identical protein binding / Type-1 fimbrial protein, A chain
Function and homology information
SourceEscherichia coli J96 (bacteria)
Methodhelical reconstruction / cryo EM / 4.2 Å resolution
AuthorsHospenthal MK / Costa TRD / Redzej A / Waksman G
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.
Validation ReportPDB-ID: 5oh0

SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Nov 22, 2017 / Last update: Dec 13, 2017

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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 models: PDB-5oh0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3809.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.13 Å/pix.
= 271.2 Å
240 pix
1.13 Å/pix.
= 271.2 Å
240 pix
1.13 Å/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
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.045445666 - 0.12328538
Average (Standard dev.)0.0005924707 (0.0051952004)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin000
Limit239239239
Spacing240240240
CellA=B=C: 271.2 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
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 ( map file in CCP4 format, 55297 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3809_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Type 1 Chaperone-usher pilus

EntireName: Type 1 Chaperone-usher pilus
Details: Superhelical assembly of the pilus rod subunit FimA
Number of components: 2

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Component #1: protein, Type 1 Chaperone-usher pilus

ProteinName: Type 1 Chaperone-usher pilus
Details: Superhelical assembly of the pilus rod subunit FimA
Recombinant expression: No
SourceSpecies: Escherichia coli J96 (bacteria)
Source (engineered)Expression System: Escherichia coli HB101 (bacteria)

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Component #2: protein, Type-1 fimbrial protein, A chain

ProteinName: Type-1 fimbrial protein, A chain / Recombinant expression: No
MassTheoretical: 15.835243 kDa
Source (engineered)Expression System: Escherichia coli J96 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 8.01188 Å / Delta phi: 114.992 deg.
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Input PDB model: 2JTY, 2JTY
Chain ID: 2JTY_A, 2JTY_A
Output model

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