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- EMDB-8812: Structure of the PulG pseudopilus -

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Basic information

Database: EMDB / ID: 8812
TitleStructure of the PulG pseudopilus
SamplePulG pseudopilus
SourceKlebsiella oxytoca / bacteria /
Map datamap of PulG filament
Methodhelical reconstruction, at 5 Å resolution
AuthorsLopez-Castilla A / Thomassin JL
CitationNat Microbiol, 2017, 2, 1686-1695

Nat Microbiol, 2017, 2, 1686-1695 Yorodumi Papers
Structure of the calcium-dependent type 2 secretion pseudopilus.
Aracelys López-Castilla / Jenny-Lee Thomassin / Benjamin Bardiaux / Weili Zheng / Mangayarkarasi Nivaskumar / Xiong Yu / Michael Nilges / Edward H Egelman / Nadia Izadi-Pruneyre / Olivera Francetic

Validation ReportPDB-ID: 5wda

SummaryFull reportAbout validation report
DateDeposition: Jul 4, 2017 / Header (metadata) release: Aug 9, 2017 / Map release: Oct 25, 2017 / Last update: Dec 13, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.056
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.056
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5wda
  • Surface level: 0.056
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5wda
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links


Fileemd_8812.map.gz (map file in CCP4 format, 8468 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.05 Å/pix.
= 315. Å
84 pix
1.05 Å/pix.
= 88.2 Å
84 pix
1.05 Å/pix.
= 88.2 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.05 Å
Contour Level:0.056 (by author), 0.056 (movie #1):
Minimum - Maximum-0.044437073 - 0.11336735
Average (Standard dev.)0.012011195 (0.02283012)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 88.2 Å / B: 88.2 Å / C: 315 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z8484300
origin x/y/z0.0000.0000.000
length x/y/z88.20088.200315.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-42-42-150
D min/max/mean-0.0440.1130.012

Supplemental data

Sample components

Entire PulG pseudopilus

EntireName: PulG pseudopilus / Number of components: 3

Component #1: cellular-component, PulG pseudopilus

Cellular-componentName: PulG pseudopilus / Recombinant expression: No
SourceSpecies: Klebsiella oxytoca / bacteria /
Source (engineered)Expression System: Escherichia coli / bacteria / /

Component #2: protein, General secretion pathway protein G

ProteinName: General secretion pathway protein G / Recombinant expression: No
MassTheoretical: 14.525482 kDa
Source (engineered)Expression System: Klebsiella oxytoca / bacteria /

Component #3: ligand, CALCIUM ION

LigandName: CALCIUM ION / Number of Copies: 25 / Recombinant expression: No
MassTheoretical: 4.007805 MDa

Experimental details

Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 10.2 Å / Delta phi: 83.2 deg.
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 1819

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: BACK PROJECTION / Software: IHRSR / Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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