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- PDB-9p0a: Structure of Natrinema sp. J7-2 Tafi pilus -

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Basic information

Entry
Database: PDB / ID: 9p0a
TitleStructure of Natrinema sp. J7-2 Tafi pilus
ComponentsPilin
KeywordsPROTEIN FIBRIL / Extrcellular filament / Bundling pili
Function / homologyTwin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Uncharacterized protein
Function and homology information
Biological speciesNatrinema sp. J7-2 (archaea)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSonani, R.R. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
CitationJournal: To Be Published
Title: Structure of Natrinema sp. J7-2 Tafi pilus
Authors: Sonani, R.R. / Egelman, E.H.
History
DepositionJun 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Pilin
D: Pilin
E: Pilin


Theoretical massNumber of molelcules
Total (without water)65,0863
Polymers65,0863
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Pilin


Mass: 21695.195 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Natrinema sp. J7-2 (archaea) / References: UniProt: I7CYY9
Has protein modificationN

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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: Tafi pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Natrinema sp. J7-2 (archaea)
Buffer solutionpH: 7
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -80.21 ° / Axial rise/subunit: 33.36 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: OTHER / Num. of particles: 36787 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044083
ELECTRON MICROSCOPYf_angle_d0.6945583
ELECTRON MICROSCOPYf_dihedral_angle_d7.885585
ELECTRON MICROSCOPYf_chiral_restr0.047681
ELECTRON MICROSCOPYf_plane_restr0.006756

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