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- PDB-9fxs: Cryo-EM structure of the type 1 pilus complex including pilus rod... -

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Basic information

Entry
Database: PDB / ID: 9fxs
TitleCryo-EM structure of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement
Components
  • Chaperone protein FimC
  • Fimbrin-like protein FimI
  • Outer membrane usher protein FimD
KeywordsMEMBRANE PROTEIN / rod / pilus / usher / termination
Function / homology
Function and homology information


fimbrial usher porin activity / pilus assembly / cell adhesion involved in single-species biofilm formation / pilus / : / protein folding chaperone / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. ...Outer membrane usher protein / Fimbrial membrane usher, conserved site / PapC, N-terminal domain / PapC, N-terminal domain superfamily / Outer membrane usher protein FimD, plug domain / PapC-like, C-terminal domain superfamily / Outer membrane usher protein / PapC C-terminal domain / PapC N-terminal domain / Fimbrial biogenesis outer membrane usher protein signature. / PapC-like, C-terminal domain / Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Outer membrane usher protein FimD / Chaperone protein FimC / Fimbrin-like protein FimI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBachmann, P. / Afanasyev, P. / Boehringer, D. / Glockshuber, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_201234 Switzerland
CitationJournal: To Be Published
Title: Cryo-EM structure of the type 1 pilus complex including pilus rod and FimI-bound assembly platform after incorporation of two FimI subunits - Local refinement
Authors: Bachmann, P. / Afanasyev, P. / Boehringer, D. / Glockshuber, R.
History
DepositionJul 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 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

Downloads & links

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Assembly

Deposited unit
B: Fimbrin-like protein FimI
C: Chaperone protein FimC
D: Outer membrane usher protein FimD
I: Fimbrin-like protein FimI


Theoretical massNumber of molelcules
Total (without water)151,1864
Polymers151,1864
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 Fimbrin-like protein FimI


Mass: 17189.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimI, b4315, JW5779 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39264
#2: Protein Chaperone protein FimC


Mass: 23714.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimC, b4316, JW4279 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31697
#3: Protein Outer membrane usher protein FimD


Mass: 93092.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fimD, b4317, JW5780 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: P30130
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FimDHGFAnIChis complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)/Tuner
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.6 sec. / Electron dose: 68 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21.1_5286model refinement
3EPUimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41257 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 124.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00168712
ELECTRON MICROSCOPYf_angle_d0.39811836
ELECTRON MICROSCOPYf_chiral_restr0.03981312
ELECTRON MICROSCOPYf_plane_restr0.00281549
ELECTRON MICROSCOPYf_dihedral_angle_d3.14121201

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