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- PDB-6c53: Cryo-EM structure of the Type 1 pilus rod -

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Basic information

Entry
Database: PDB / ID: 6c53
TitleCryo-EM structure of the Type 1 pilus rod
ComponentsType-1 fimbrial protein, A chain
KeywordsPROTEIN FIBRIL / Type 1 pili / helical rod / adhesive pili
Function / homologycell adhesion involved in single-species biofilm formation / Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / identical protein binding / Type-1 fimbrial protein, A chain
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsZheng, W. / Wang, F. / Luna-Rico, A. / Francetic, O. / Hultgren, S.J. / 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: Elife / Year: 2018
Title: Functional role of the type 1 pilus rod structure in mediating host-pathogen interactions.
Authors: Caitlin N Spaulding / Henry Louis Schreiber / Weili Zheng / Karen W Dodson / Jennie E Hazen / Matt S Conover / Fengbin Wang / Pontus Svenmarker / Areli Luna-Rico / Olivera Francetic / Magnus ...Authors: Caitlin N Spaulding / Henry Louis Schreiber / Weili Zheng / Karen W Dodson / Jennie E Hazen / Matt S Conover / Fengbin Wang / Pontus Svenmarker / Areli Luna-Rico / Olivera Francetic / Magnus Andersson / Scott Hultgren / Edward H Egelman /
Abstract: Uropathogenic (UPEC), which cause urinary tract infections (UTI), utilize type 1 pili, a chaperone usher pathway (CUP) pilus, to cause UTI and colonize the gut. The pilus rod, comprised of repeating ...Uropathogenic (UPEC), which cause urinary tract infections (UTI), utilize type 1 pili, a chaperone usher pathway (CUP) pilus, to cause UTI and colonize the gut. The pilus rod, comprised of repeating FimA subunits, provides a structural scaffold for displaying the tip adhesin, FimH. We solved the 4.2 Å resolution structure of the type 1 pilus rod using cryo-electron microscopy. Residues forming the interactive surfaces that determine the mechanical properties of the rod were maintained by selection based on a global alignment of sequences. We identified mutations that did not alter pilus production in vitro but reduced the force required to unwind the rod. UPEC expressing these mutant pili were significantly attenuated in bladder infection and intestinal colonization in mice. This study elucidates an unappreciated functional role for the molecular spring-like property of type 1 pilus rods in host-pathogen interactions and carries important implications for other pilus-mediated diseases.
History
DepositionJan 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / cell / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _pdbx_audit_support.funding_organization

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Assembly

Deposited unit
A: Type-1 fimbrial protein, A chain
B: Type-1 fimbrial protein, A chain
C: Type-1 fimbrial protein, A chain
D: Type-1 fimbrial protein, A chain
E: Type-1 fimbrial protein, A chain
F: Type-1 fimbrial protein, A chain
G: Type-1 fimbrial protein, A chain
H: Type-1 fimbrial protein, A chain
I: Type-1 fimbrial protein, A chain
J: Type-1 fimbrial protein, A chain
K: Type-1 fimbrial protein, A chain


Theoretical massNumber of molelcules
Total (without water)174,18811
Polymers174,18811
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 10 / Rise per n subunits: 7.7 Å / Rotation per n subunits: 115 °)
DetailsTHE HELICAL SYMMETRY PARAMETER SHOULD BE APPLIED TO A SINGLE CHAIN OF THE MODEL, INSTEAD OF WHOLE MODEL IN COORDINATES FILE, TO ACHIEVE THE ENTIRE ASSEMBLY.

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Components

#1: Protein
Type-1 fimbrial protein, A chain / Type-1A pilin


Mass: 15835.243 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P04128

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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: Type 1 pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE / Humidity: 95 %

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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 recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: dev_2919: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN2particle selection
2EPUimage acquisition
4CTFFIND3CTF correction
7RosettaEMmodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
11SPIDERinitial Euler assignment
12SPIDERfinal Euler assignment
14SPIDER3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 115 ° / Axial rise/subunit: 7.7 Å / Axial symmetry: C1
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72627 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612177
ELECTRON MICROSCOPYf_angle_d0.92816654
ELECTRON MICROSCOPYf_dihedral_angle_d7.3417095
ELECTRON MICROSCOPYf_chiral_restr0.052079
ELECTRON MICROSCOPYf_plane_restr0.0042233

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