Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 26.02 kDa 
• Atom Count: 1813 
• Modelled Residue Count: 209 
• Deposited Residue Count: 225 
• Unique protein chains: 1

2YHC

Structure of BamD from E. coli

• DOI: 10.2210/pdb2YHC/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2011-04-28 Released: 2011-06-01 
• Deposition Author(s): Zeth, K., Albrecht, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Structural Basis of Outer Membrane Protein Biogenesis in Bacteria.

Albrecht, R., Zeth, K.

(2011) J Biol Chem 286: 27792

• PubMed: 21586578 
• DOI: 10.1074/jbc.M111.238931
• Primary Citation of Related Structures:  
  2YH9, 2YH3, 2YH5, 2YH6, 2YHC


• PubMed Abstract: 
  

In Escherichia coli, a multicomponent BAM (β-barrel assembly machinery) complex is responsible for recognition and assembly of outer membrane β-barrel proteins. The functionality of BAM in protein biogenesis is mainly orchestrated through the presence of two essential components, BamA and BamD. Here, we present crystal structures of four lipoproteins (BamB-E). Monomeric BamB and BamD proteins display scaffold architectures typically implied in transient protein interactions. BamB is a β-propeller protein comprising eight WD40 repeats. BamD shows an elongated fold on the basis of five tetratricopeptide repeats, three of which form the scaffold for protein recognition. The rod-shaped BamC protein has evolved through the gene duplication of two conserved domains known to mediate protein interactions in structurally related complexes. By contrast, the dimeric BamE is formed through a domain swap and indicates fold similarity to the β-lactamase inhibitor protein family, possibly integrating cell wall stability in BAM function. Structural and biochemical data show evidence for the specific recognition of amphipathic sequences through the tetratricopeptide repeat architecture of BamD. Collectively, our data advance the understanding of the BAM complex and highlight the functional importance of BamD in amphipathic outer membrane β-barrel protein motif recognition and protein delivery.

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Organizational Affiliation: 

Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, Tübingen 72076, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0169 LIPOPROTEIN YFIO	A	225	Escherichia coli BL21(DE3)	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12)) Explore P0AC02  Go to UniProtKB:  P0AC02

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URE	B [auth A]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.112	α = 90
b = 33.428	β = 111.41
c = 57.783	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SHARP	phasing
DM	phasing
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-28 
• Released Date: 2011-06-01 
Deposition Author(s): Zeth, K., Albrecht, R.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-08-10
  Changes: Database references, Version format compliance