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- PDB-5flu: Structure of a Chaperone-Usher pilus reveals the molecular basis ... -

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Basic information

Entry
Database: PDB / ID: 5flu
TitleStructure of a Chaperone-Usher pilus reveals the molecular basis of rod uncoilin
ComponentsPAP FIMBRIAL MAJOR PILIN PROTEIN
KeywordsSTRUCTURAL PROTEIN / HELICAL POLYMER / STRAND DONATION
Function / homology
Function and homology information


pilus / cell adhesion / extracellular region
Similarity search - Function
Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pap fimbrial major pilin protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHospenthal, M.K. / Redzej, A. / Dodson, K. / Ukleja, M. / Frenz, B. / Hultgren, S.J. / DiMaio, F. / Egelman, E.H. / Waksman, G.
CitationJournal: Cell / Year: 2016
Title: Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling.
Authors: Manuela K Hospenthal / Adam Redzej / Karen Dodson / Marta Ukleja / Brandon Frenz / Catarina Rodrigues / Scott J Hultgren / Frank DiMaio / Edward H Egelman / Gabriel Waksman /
Abstract: Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher ...Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher pathway, are polymers of pilus subunits assembling into two parts: a thin, short tip fibrillum at the top, mounted on a long pilus rod. The rod adopts a helical quaternary structure and is thought to play essential roles: its formation may drive pilus extrusion by preventing backsliding of the nascent growing pilus within the secretion pore; the rod also has striking spring-like properties, being able to uncoil and recoil depending on the intensity of shear forces generated by urine flow. Here, we present an atomic model of the P pilus generated from a 3.8 Å resolution cryo-electron microscopy reconstruction. This structure provides the molecular basis for the rod's remarkable mechanical properties and illuminates its role in pilus secretion.
History
DepositionOct 28, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Oct 3, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • EMDB-3222
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Assembly

Deposited unit
A: PAP FIMBRIAL MAJOR PILIN PROTEIN
B: PAP FIMBRIAL MAJOR PILIN PROTEIN
C: PAP FIMBRIAL MAJOR PILIN PROTEIN
D: PAP FIMBRIAL MAJOR PILIN PROTEIN
E: PAP FIMBRIAL MAJOR PILIN PROTEIN
F: PAP FIMBRIAL MAJOR PILIN PROTEIN
G: PAP FIMBRIAL MAJOR PILIN PROTEIN
H: PAP FIMBRIAL MAJOR PILIN PROTEIN
I: PAP FIMBRIAL MAJOR PILIN PROTEIN
J: PAP FIMBRIAL MAJOR PILIN PROTEIN
K: PAP FIMBRIAL MAJOR PILIN PROTEIN
L: PAP FIMBRIAL MAJOR PILIN PROTEIN
M: PAP FIMBRIAL MAJOR PILIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)215,38813
Polymers215,38813
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein
PAP FIMBRIAL MAJOR PILIN PROTEIN / PAP PILI / PAPA


Mass: 16568.346 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04127
Has protein modificationY

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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: P PILUS / Type: COMPLEX
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 8, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 17 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 90

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: EACH IMAGE
3D reconstructionMethod: IHRSR / Resolution: 3.8 Å / Num. of particles: 56341 / Nominal pixel size: 1.1 Å / Actual pixel size: 1.1 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3222. (DEPOSITION ID: 13990).
Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--EM
RefinementHighest resolution: 3.8 Å
Refinement stepCycle: LAST / Highest resolution: 3.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15132 0 0 0 15132

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