4PE2

MBP PilA1 CD160


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural and Evolutionary Analyses Show Unique Stabilization Strategies in the Type IV Pili of Clostridium difficile.

Piepenbrink, K.H.Maldarelli, G.A.Martinez de la Pena, C.F.Dingle, T.C.Mulvey, G.L.Lee, A.von Rosenvinge, E.Armstrong, G.D.Donnenberg, M.S.Sundberg, E.J.

(2015) Structure 23: 385-396

  • DOI: https://doi.org/10.1016/j.str.2014.11.018
  • Primary Citation of Related Structures:  
    4OGM, 4PE2, 4TSM

  • PubMed Abstract: 

    Type IV pili are produced by many pathogenic Gram-negative bacteria and are important for processes as diverse as twitching motility, biofilm formation, cellular adhesion, and horizontal gene transfer. However, many Gram-positive species, including Clostridium difficile, also produce type IV pili. Here, we identify the major subunit of the type IV pili of C. difficile, PilA1, and describe multiple 3D structures of PilA1, demonstrating the diversity found in three strains of C. difficile. We also model the incorporation of both PilA1 and a minor pilin, PilJ, into the pilus fiber. Although PilA1 contains no cysteine residues, and therefore cannot form the disulfide bonds found in all Gram-negative type IV pilins, it adopts unique strategies to achieve a typical pilin fold. The structures of PilA1 and PilJ exhibit similarities with the type IVb pilins from Gram-negative bacteria that suggest that the type IV pili of C. difficile are involved in microcolony formation.


  • Organizational Affiliation

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose ABC transporter periplasmic protein,Prepilin-type N-terminal cleavage/methylation domain protein516Escherichia coliClostridioides difficile CD160
This entity is chimeric
Mutation(s): 1 
Gene Names: malEBN896_3748QEW_4140
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEX9
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLI
Query on MLI

Download Ideal Coordinates CCD File 
C [auth A]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.484α = 90
b = 70.468β = 90.24
c = 117.153γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1 F32 AI 110045
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI105881

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Database references
  • Version 1.2: 2015-02-11
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 1.4: 2017-11-22
    Changes: Refinement description
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Structure summary