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- PDB-6nav: Cryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus -

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Entry
Database: PDB / ID: 6nav
TitleCryo-EM reconstruction of Sulfolobus islandicus LAL14/1 Pilus
ComponentsM9UD72
KeywordsSTRUCTURAL PROTEIN / helical symmetry / archaeal pilus
Function / homologyintegral component of membrane / Uncharacterized protein
Function and homology information
Specimen sourceSulfolobus islandicus LAL14/1 (acidophilic)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsWang, F. / Cvirkaite-Krupovic, V. / Prangishvili, D. / Krupovic, M. / Egelman, E.H.
Funding supportUnited States , 1件
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesR35GM122510United States
CitationJournal: Nat Microbiol / Year: 2019
Title: An Archaeal Pilus Survives the Most Extreme Conditions Through Extensive Glycosylation
Authors: Wang, F. / Cvirkaite-Krupovic, V. / Kreutzberger, M.A.B. / Su, Z. / de Oliveira, G. / DiMaio, F. / Wall, J.S. / Prangishvili, D. / Krupovic, M. / Egelman, E.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 6, 2018 / Release: May 8, 2019Array

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Structure viewerMolecule:
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Assembly

Deposited unit
A: M9UD72
B: M9UD72
C: M9UD72
D: M9UD72
E: M9UD72
F: M9UD72
G: M9UD72
H: M9UD72
I: M9UD72
J: M9UD72
K: M9UD72
L: M9UD72
M: M9UD72
N: M9UD72
O: M9UD72
P: M9UD72
Q: M9UD72
R: M9UD72
S: M9UD72
T: M9UD72
U: M9UD72


Theoretical massNumber of molelcules
Total (without water)266,30921
Polymers266,30921
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
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TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
M9UD72


Mass: 12681.375 Da / Num. of mol.: 21 / Source method: isolated from a natural source
Source: (natural) Sulfolobus islandicus LAL14/1 (acidophilic)
References: UniProt: M9UD72

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Sulfolobus islandicus LAL14/1 Pilus / Type: COMPLEX / Entity ID: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sulfolobus islandicus LAL14/1 (acidophilic)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 2 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
Details: Images were stored containing 24 fractions, where each fraction corresponded to a dose of ~2 electrons per Angstrom^2.

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Processing

SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
EM software
IDNameCategory
1EMAN2particle selection
2EPUimage acquisition
4GctfCTF correction
12SPIDER3D reconstruction
13RELION3D reconstruction
14Rosettamodel refinement
15PHENIXmodel refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 104.97 ° / Axial rise/subunit: 4.94 Å / Axial symmetry: C1
3D reconstructionResolution: 4.1 Å / Resolution method: OTHER / Num. of particles: 181070 / Details: MODEL:MAP FSC, D99 / Symmetry type: HELICAL

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