3UFI

Crystal structure of a putative cell adhesion protein (BACOVA_04980) from Bacteroides ovatus ATCC 8483 at 2.18 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

A Distinct Type of Pilus from the Human Microbiome.

Xu, Q.Shoji, M.Shibata, S.Naito, M.Sato, K.Elsliger, M.A.Grant, J.C.Axelrod, H.L.Chiu, H.J.Farr, C.L.Jaroszewski, L.Knuth, M.W.Deacon, A.M.Godzik, A.Lesley, S.A.Curtis, M.A.Nakayama, K.Wilson, I.A.

(2016) Cell 165: 690-703

  • DOI: https://doi.org/10.1016/j.cell.2016.03.016
  • Primary Citation of Related Structures:  
    3LIU, 3PAY, 3R4R, 3SY6, 3T2L, 3UFI, 3UP6, 4DGU, 4EPS, 4GPV, 4H40, 4JG5, 4JRF, 4K4K, 4Q98, 4QB7, 4QDG, 4RDB, 5CAG

  • PubMed Abstract: 

    Pili are proteinaceous polymers of linked pilins that protrude from the cell surface of many bacteria and often mediate adherence and virulence. We investigated a set of 20 Bacteroidia pilins from the human microbiome whose structures and mechanism of assembly were unknown. Crystal structures and biochemical data revealed a diverse protein superfamily with a common Greek-key β sandwich fold with two transthyretin-like repeats that polymerize into a pilus through a strand-exchange mechanism. The assembly mechanism of the central, structural pilins involves proteinase-assisted removal of their N-terminal β strand, creating an extended hydrophobic groove that binds the C-terminal donor strands of the incoming pilin. Accessory pilins at the tip and base have unique structural features specific to their location, allowing initiation or termination of the assembly. The Bacteroidia pilus, therefore, has a biogenesis mechanism that is distinct from other known pili and likely represents a different type of bacterial pilus.


  • Organizational Affiliation

    Joint Center for Structural Genomics, http://www.jcsg.org; SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA 94025, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hypothetical protein BACOVA_04980297Bacteroides ovatus ATCC 8483Mutation(s): 0 
Gene Names: BACOVA_04980
UniProt
Find proteins for A7M4D9 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153))
Explore A7M4D9 
Go to UniProtKB:  A7M4D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7M4D9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 63
  • Diffraction Data: https://doi.org/10.18430/M33UFI
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.66α = 90
b = 176.66β = 90
c = 51.171γ = 120
Software Package:
Software NamePurpose
MolProbitymodel building
PDB_EXTRACTdata extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNTrefinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Structure summary
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 1.4: 2020-04-22
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-02-01
    Changes: Database references, Derived calculations