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- EMDB-0397: Cryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus -

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Basic information

Database: EMDB / ID: EMD-0397
TitleCryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus
Map data
SampleSulfolobus islandicus LAL14/1 Pilus:
Function / homologyintegral component of membrane / Uncharacterized protein
Function and homology information
SourceSulfolobus islandicus LAL14/1 (acidophilic)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang F / Cvirkaite-Krupovic V / Prangishvili D / Krupovic M / Egelman EH
CitationJournal: Nat Microbiol / Year: 2019
Title: An Archaeal Pilus Survives the Most Extreme Conditions Through Extensive Glycosylation
Authors: Wang F / Cvirkaite-Krupovic V / Kreutzberger MAB / Su Z / de Oliveira G / DiMaio F / Wall JS / Prangishvili D / Krupovic M / Egelman EH
Validation ReportPDB-ID: 6nav

SummaryFull reportAbout validation report
DateDeposition: Dec 6, 2018 / Header (metadata) release: Jan 23, 2019 / Map release: May 8, 2019 / Update: May 8, 2019

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.127
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nav
  • Surface level: 0.127
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6nav
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_0397.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 384 pix.
= 537.6 Å
1.4 Å/pix.
x 384 pix.
= 537.6 Å
1.4 Å/pix.
x 384 pix.
= 537.6 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Contour LevelBy AUTHOR: 0.127 / Movie #1: 0.127
Minimum - Maximum-0.15029839 - 0.3493753
Average (Standard dev.)0.00035732737 (±0.0065073087)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
MAP C/R/S123
start NC/NR/NS-192-192-192
D min/max/mean-0.1500.3490.000

Supplemental data

Sample components

Entire Sulfolobus islandicus LAL14/1 Pilus

EntireName: Sulfolobus islandicus LAL14/1 Pilus / Number of components: 2

Component #1: protein, Sulfolobus islandicus LAL14/1 Pilus

ProteinName: Sulfolobus islandicus LAL14/1 Pilus / Recombinant expression: No
SourceSpecies: Sulfolobus islandicus LAL14/1 (acidophilic)

Component #2: protein, M9UD72

ProteinName: M9UD72 / Number of Copies: 21 / Recombinant expression: No
MassTheoretical: 12.681375 kDa
SourceSpecies: Sulfolobus islandicus LAL14/1 (acidophilic)

Experimental details

Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4.94 Å / Delta phi: 104.97 %deg;
Sample solutionpH: 6
VitrificationCryogen name: ETHANE / 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: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

Image acquisition

Image acquisitionDetails: Images were stored containing 24 fractions, where each fraction corresponded to a dose of ~2 electrons per Angstrom^2.

Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: SPIDER, RELION / Resolution: 4.1 Å / Resolution method: OTHER / Details: MODEL:MAP FSC, D99

Atomic model buiding

Output model

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