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- EMDB-3997: N2 and N3 ring of PilQ from Thermus thermophilus -

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Basic information

Database: EMDB / ID: 3997
TitleN2 and N3 ring of PilQ from Thermus thermophilus
SamplePilQ complex with 13-fold symmetry
SourceThermus thermophilus hb27 / bacteria / thermophilic
Map dataNone
Methodsingle particle reconstruction, at 7.6 Å resolution
AuthorsD'Imprima E / Vonck J / Sanchez R
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus.
Edoardo D'Imprima / Ralf Salzer / Ramachandra M Bhaskara / Ricardo Sánchez / Ilona Rose / Lennart Kirchner / Gerhard Hummer / Werner Kühlbrandt / Janet Vonck / Beate Averhoff

DateDeposition: Nov 15, 2017 / Header (metadata) release: Dec 13, 2017 / Map release: Jan 10, 2018 / Last update: Jan 17, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.0385
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0385
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_3997.map.gz (map file in CCP4 format, 136049 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
324 pix
1.63 Å/pix.
= 528.12 Å
324 pix
1.63 Å/pix.
= 528.12 Å
324 pix
1.63 Å/pix.
= 528.12 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.63 Å
Contour Level:0.0385 (by author), 0.0385 (movie #1):
Minimum - Maximum-0.041751556 - 0.09502463
Average (Standard dev.)5.8266138E-5 (0.0019338897)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 528.12 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z324324324
origin x/y/z0.0000.0000.000
length x/y/z528.120528.120528.120
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0420.0950.000

Supplemental data

Sample components

Entire PilQ complex with 13-fold symmetry

EntireName: PilQ complex with 13-fold symmetry / Number of components: 1
MassTheoretical: 1000 kDa

Component #1: protein, PilQ complex with 13-fold symmetry

ProteinName: PilQ complex with 13-fold symmetry / Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Thermus thermophilus hb27 / bacteria / thermophilic

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 8.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 70 % / Details: blotting for 8-10 seconds

Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 33 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 20000 X (nominal), 30675 X (calibrated) / Cs: 4.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter / Energy window: 18-18 eV
Specimen HolderModel: JEOL
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C13 (13 fold cyclic) / Number of projections: 2646
3D reconstructionSoftware: FREALIGN / Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF
Euler angles: The images of the subdomain containing the N2 and N3 rings after residual signal subtraction were recentered and placed in a smaller with our new program REP, followed by refinement by FREALIGN.
FSC plot (resolution assessment)

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