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- PDB-8tif: Cryo-EM of mono-pilus from S. islandicus REY15A -

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Basic information

Entry
Database: PDB / ID: 8tif
TitleCryo-EM of mono-pilus from S. islandicus REY15A
ComponentsDUF973 family protein
KeywordsPROTEIN FIBRIL / helical symmetry / type iv pili / archaeal pilus / filament / quasi-equivalence
Function / homologymembrane / DUF973 family protein
Function and homology information
Biological speciesSulfolobus islandicus REY15A (acidophilic)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsEastep, G.N. / Liu, J. / Rich-New, S.T. / Egelman, E.H. / Krupovic, M. / Wang, F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: To Be Published
Title: Cryo-EM of mono-pilus from S. islandicus REY15A
Authors: Liu, J. / Eastep, G.N. / Cvirkaite-Krupovic, V. / Rich-New, S.T. / Kreutzberger, M. / Egelman, E.H. / Krupovic, M. / Wang, F.
History
DepositionJul 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF973 family protein


Theoretical massNumber of molelcules
Total (without water)14,0531
Polymers14,0531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein DUF973 family protein


Mass: 14053.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus islandicus REY15A (acidophilic)
References: UniProt: F0NG07

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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: mono-pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sulfolobus islandicus REY15A (acidophilic)
Buffer solutionpH: 4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 104.8 ° / Axial rise/subunit: 4.95 Å / Axial symmetry: C1
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78068 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00426790
ELECTRON MICROSCOPYf_angle_d0.57336690
ELECTRON MICROSCOPYf_dihedral_angle_d3.4833960
ELECTRON MICROSCOPYf_chiral_restr0.0435250
ELECTRON MICROSCOPYf_plane_restr0.0024500

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