3Q7M

The crystal structure of BamB from the BAM complex in spacegroup I222


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.651 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Crystal Structure of BamB Suggests Interactions with BamA and Its Role within the BAM Complex.

Noinaj, N.Fairman, J.W.Buchanan, S.K.

(2011) J.Mol.Biol. 407: 248-260

  • DOI: 10.1016/j.jmb.2011.01.042
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Escherichia coli BamB is the largest of four lipoproteins in the β-barrel assembly machinery (BAM) complex. It interacts with the periplasmic domain of BamA, an integral outer membrane protein (OMP) essential for OMP biogenesis. Although BamB is not ...

    Escherichia coli BamB is the largest of four lipoproteins in the β-barrel assembly machinery (BAM) complex. It interacts with the periplasmic domain of BamA, an integral outer membrane protein (OMP) essential for OMP biogenesis. Although BamB is not essential, it serves an important function in the BAM complex, significantly increasing the folding efficiency of some OMPs in vivo and in vitro. To learn more about the BAM complex, we solved structures of BamB in three different crystal forms. BamB crystallized in space groups P2(1)3, I222, and P2(1)2(1)2(1), with one molecule per asymmetric unit in each case. Crystals from the space group I222 diffracted to 1. 65-Å resolution. BamB forms an eight-bladed β-propeller with a central pore and is shaped like a doughnut. A DALI search revealed that BamB shares structural homology to several eukaryotic proteins containing WD40 repeat domains, which commonly have β-propeller folds and often serve as scaffolding proteins within larger multi-protein complexes that carry out signal transduction, cell division, and chemotaxis. Using mutagenesis data from previous studies, we docked BamB onto a BamA structural model and assessed known and possible interactions between these two proteins. Our data suggest that BamB serves as a scaffolding protein within the BAM complex by optimally orienting the flexible periplasmic domain of BamA for interaction with other BAM components and chaperones. This may facilitate integration of newly synthesized OMPs into the outer membrane.


    Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-8030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipoprotein yfgL
A
376Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: bamB (yfgL)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Omp85-TpsB Outer Membrane Transporter Superfamily
Protein: 
BamB component of the Bam β-barrel assembly machine
Find proteins for P77774 (Escherichia coli (strain K12))
Go to UniProtKB:  P77774
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.651 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.163 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 50.318α = 90.00
b = 121.437β = 90.00
c = 134.291γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXmodel building
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance