Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 176.35 kDa 
• Atom Count: 11732 
• Residue Count: 1554 
• Unique protein chains: 5

4J3O

Crystal structure of the FimD usher traversed by the pilus tip complex assembly composed of FimC:FimF:FimG:FimH

• DOI: 10.2210/pdb4J3O/pdb

• Classification: CELL ADHESION/CHAPERONE/MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-06 Released: 2013-04-10 
• Deposition Author(s): Geibel, S., Waksman, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.299 
• R-Value Work: 0.248 
• R-Value Observed: 0.250 

Literature

Structural and energetic basis of folded-protein transport by the FimD usher.

Geibel, S., Procko, E., Hultgren, S.J., Baker, D., Waksman, G.

(2013) Nature 496: 243-246

• PubMed: 23579681 
• DOI: 10.1038/nature12007
• Primary Citation of Related Structures:  
  4J3O


• PubMed Abstract: 
  

Type 1 pili, produced by uropathogenic Escherichia coli, are multisubunit fibres crucial in recognition of and adhesion to host tissues. During pilus biogenesis, subunits are recruited to an outer membrane assembly platform, the FimD usher, which catalyses their polymerization and mediates pilus secretion. The recent determination of the crystal structure of an initiation complex provided insight into the initiation step of pilus biogenesis resulting in pore activation, but very little is known about the elongation steps that follow. Here, to address this question, we determine the structure of an elongation complex in which the tip complex assembly composed of FimC, FimF, FimG and FimH passes through FimD. This structure demonstrates the conformational changes required to prevent backsliding of the nascent pilus through the FimD pore and also reveals unexpected properties of the usher pore. We show that the circular binding interface between the pore lumen and the folded substrate participates in transport by defining a low-energy pathway along which the nascent pilus polymer is guided during secretion.

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Organizational Affiliation: 

Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein FimG	G	144	Escherichia coli K-12	Mutation(s): 0  Gene Names: fimG, b4319, JW4282
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group:  Beta-Barrel Membrane Proteins: Monomeric/Dimeric	Protein:  P pilus FimD usher in complex with FimC:FimF:FimG:FimH
Find proteins for P08190 (Escherichia coli (strain K12)) Explore P08190  Go to UniProtKB:  P08190

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein FimH	H	279	Escherichia coli K-12	Mutation(s): 0  Gene Names: fimH, b4320, JW4283
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group:  Beta-Barrel Membrane Proteins: Monomeric/Dimeric	Protein:  P pilus FimD usher in complex with FimC:FimF:FimG:FimH
Find proteins for P08191 (Escherichia coli (strain K12)) Explore P08191  Go to UniProtKB:  P08191

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein FimC	C	211	Escherichia coli K-12	Mutation(s): 0  Gene Names: fimC, b4316, JW4279
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group:  Beta-Barrel Membrane Proteins: Monomeric/Dimeric	Protein:  P pilus FimD usher in complex with FimC:FimF:FimG:FimH
Find proteins for P31697 (Escherichia coli (strain K12)) Explore P31697  Go to UniProtKB:  P31697

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein FimF	F	154	Escherichia coli K-12	Mutation(s): 0  Gene Names: fimF, b4318, JW4281
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group:  Beta-Barrel Membrane Proteins: Monomeric/Dimeric	Protein:  P pilus FimD usher in complex with FimC:FimF:FimG:FimH
Find proteins for P08189 (Escherichia coli (strain K12)) Explore P08189  Go to UniProtKB:  P08189

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane usher protein FimD	D	843	Escherichia coli K-12	Mutation(s): 0  Gene Names: fimD, b4317, JW5780
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group:  Beta-Barrel Membrane Proteins: Monomeric/Dimeric	Protein:  P pilus FimD usher in complex with FimC:FimF:FimG:FimH
Find proteins for P30130 (Escherichia coli (strain K12)) Explore P30130  Go to UniProtKB:  P30130

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.299 
• R-Value Work: 0.248 
• R-Value Observed: 0.250 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.36	α = 90
b = 122.36	β = 90
c = 328.46	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-06 
• Released Date: 2013-04-10 
Deposition Author(s): Geibel, S., Waksman, G.

Revision History 

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2013-04-24
  Changes: Database references