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- EMDB-8287: Cryo-EM reconstruction of Neisseria meningitidis Type IV pilus -

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Basic information

Database: EMDB / ID: 8287
TitleCryo-EM reconstruction of Neisseria meningitidis Type IV pilus
SourceNeisseria meningitidis / bacteria / ナイセリア・メニンジティディス, 髄膜炎菌
Map data3D cryo-EM reconstruction of Nm Type IV pilus
Methodhelical reconstruction, at 6 Å resolution
AuthorsKolappan S / Coureuil M / Yu X / Nassif X / Craig L / Egelman EH
CitationNat Commun, 2016, 7, 13015-13015

Nat Commun, 2016, 7, 13015-13015 Yorodumi Papers
Structure of the Neisseria meningitidis Type IV pilus.
Subramania Kolappan / Mathieu Coureuil / Xiong Yu / Xavier Nassif / Edward H Egelman / Lisa Craig

Validation ReportPDB-ID: 5kua

SummaryFull reportAbout validation report
DateDeposition: Jul 12, 2016 / Header (metadata) release: Oct 5, 2016 / Map release: Oct 12, 2016 / Last update: Feb 14, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5kua
  • Surface level: 0.45
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8287.map.gz (map file in CCP4 format, 8001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.05 Å/pix.
= 210. Å
100 pix
1.05 Å/pix.
= 105. Å
100 pix
1.05 Å/pix.
= 105. 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:0.45 (by author), 0.45 (movie #1):
Minimum - Maximum-0.39593023 - 0.9242279
Average (Standard dev.)0.073884055 (0.20737447)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 104.99999 Å / B: 104.99999 Å / C: 209.99998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z100100200
origin x/y/z0.0000.0000.000
length x/y/z105.000105.000210.000
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS-50-50-100
D min/max/mean-0.3960.9240.074

Supplemental data

Sample components

Entire pilus

EntireName: pilus / Number of components: 1

Component #1: cellular-component, pilus

Cellular-componentName: pilus / Recombinant expression: No
SourceSpecies: Neisseria meningitidis / bacteria / ナイセリア・メニンジティディス, 髄膜炎菌

Experimental details

Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 10.3 Å / Delta phi: 100.8 deg.
Sample solutionpH: 10.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 297 K / Humidity: 90 %

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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 541

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 6 Å / Resolution method: OTHER

Atomic model buiding

Output model

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