5ZFR

Crystal structure of PilB, an extension ATPase motor of Type IV pilus, from Geobacter sulfurreducens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into the mechanism of Type IVa pilus extension and retraction ATPase motors

Solanki, V.Kapoor, S.Thakur, K.G.

(2018) FEBS J 285: 3402-3421

  • DOI: https://doi.org/10.1111/febs.14619
  • Primary Citation of Related Structures:  
    5ZFQ, 5ZFR

  • PubMed Abstract: 

    Type IVa pili are bacterial appendages involved in diverse physiological processes, including electron transfer in Geobacter sulfurreducens. ATP hydrolysis coupled with conformational changes powers the extension (PilB) and retraction (PilT) motors in the pilus machinery. We report the unliganded crystal structures of the core ATPase domain of PilB and PilT-4 from G. sulfurreducens at 3.1 and 2.6 Å resolution, respectively. PilB structure revealed three distinct conformations, that is, open, closed, and open' which were previously proposed to be mediated by ATP/ADP binding. PilT-4 subunits, on the other hand, were observed in the closed state conformation. We further report that both PilB and PilT-4 hexamers have two high-affinity ATP-binding sites. Comparative structural analysis and solution data presented here supports the "symmetric rotary model" for these ATPase motors. Our data further suggest that pores of these motors rotate either clockwise or counterclockwise to facilitate assembly or disassembly of right-handed or left-handed pilus.


  • Organizational Affiliation

    Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV pilus biogenesis ATPase PilB
A, B, C
582Geobacter sulfurreducens PCAMutation(s): 0 
Gene Names: pilBGSU1491
UniProt
Find proteins for Q74D28 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA))
Explore Q74D28 
Go to UniProtKB:  Q74D28
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ74D28
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.219 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.301α = 90
b = 176.301β = 90
c = 138.561γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Council of Scientific and Industrial ResearchIndia--
Department of BiotechnologyIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description