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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
SampleType 1 Chaperone-usher pilus
SourceEscherichia coli j96 / bacteria / image: Escherichia coli
Map data
Methodhelical reconstruction, at 4.2 Å resolution
AuthorsHospenthal MK / Costa TRD / Redzej A / Waksman G
CitationStructure, 2017, 25, 1829-1838.e4

Structure, 2017, 25, 1829-1838.e4 Yorodumi Papers
The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod.
Manuela K Hospenthal / Dawid Zyla / Tiago R D Costa / Adam Redzej / Christoph Giese / James Lillington / Rudi Glockshuber / Gabriel Waksman

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
  • Download
  • 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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Supplemental images

Downloads & links

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Map

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

Image control

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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 package.

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 / image: Escherichia coli
Source (engineered)Expression System: Escherichia coli hb101 / bacteria / image: Escherichia coli

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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 / image: Escherichia coli

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Experimental details

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Sample preparation

Specimen statehelical array
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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