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PDBsum entry 3cka

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protein ligands Protein-protein interface(s) links
Membrane protein PDB id
3cka
Jmol
Contents
Protein chains
315 a.a. *
Ligands
1PE ×7
Waters ×517
* Residue conservation analysis
PDB id:
3cka
Name: Membrane protein
Title: The crystal structure of ospa mutant
Structure: Outer surface protein a. Chain: a, b. Engineered: yes. Mutation: yes
Source: Borrelia burgdorferi. Lyme disease spirochete. Organism_taxid: 139. Gene: ospa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.65Å     R-factor:   0.204     R-free:   0.240
Authors: K.Makabe,M.Biancalana,V.Terechko,S.Koide
Key ref:
M.Biancalana et al. (2010). Minimalist design of water-soluble cross-{beta} architecture. Proc Natl Acad Sci U S A, 107, 3469-3474. PubMed id: 20133689 DOI: 10.1073/pnas.0912654107
Date:
14-Mar-08     Release date:   17-Mar-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q45040  (Q45040_BORBG) -  Outer surface protein A
Seq:
Struc:
273 a.a.
315 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 85 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell outer membrane   1 term 

 

 
DOI no: 10.1073/pnas.0912654107 Proc Natl Acad Sci U S A 107:3469-3474 (2010)
PubMed id: 20133689  
 
 
Minimalist design of water-soluble cross-{beta} architecture.
M.Biancalana, K.Makabe, S.Koide.
 
  ABSTRACT  
 
Demonstrated successes of protein design and engineering suggest significant potential to produce diverse protein architectures and assemblies beyond those found in nature. Here, we describe a new class of synthetic protein architecture through the successful design and atomic structures of water-soluble cross-beta proteins. The cross-beta motif is formed from the lamination of successive beta-sheet layers, and it is abundantly observed in the core of insoluble amyloid fibrils associated with protein-misfolding diseases. Despite its prominence, cross-beta has been designed only in the context of insoluble aggregates of peptides or proteins. Cross-beta's recalcitrance to protein engineering and conspicuous absence among the known atomic structures of natural proteins thus makes it a challenging target for design in a water-soluble form. Through comparative analysis of the cross-beta structures of fibril-forming peptides, we identified rows of hydrophobic residues ("ladders") running across beta-strands of each beta-sheet layer as a minimal component of the cross-beta motif. Grafting a single ladder of hydrophobic residues designed from the Alzheimer's amyloid-beta peptide onto a large beta-sheet protein formed a dimeric protein with a cross-beta architecture that remained water-soluble, as revealed by solution analysis and x-ray crystal structures. These results demonstrate that the cross-beta motif is a stable architecture in water-soluble polypeptides and can be readily designed. Our results provide a new route for accessing the cross-beta structure and expanding the scope of protein design.
 
  Selected figure(s)  
 
Figure 3.
The x-ray crystal structures of cross-β PSAMs. (A) The overall structure of the YY/LF PSAM dimer is shown in surface and cartoon representations, in two orthogonal views. Molecule A is in green and molecule B in blue. The N- and C-terminal domains are indicated. The two molecules are related by pseudo-two-fold symmetry (dashed line). (B) The arrangement of the laminated β-sheet segment of YY/LF PSAM. Residues 118–209 are shown in orthogonal orientations, with the same coloring scheme as in A. The Cα-Cα distances across the β-sheets and the positions of the YY and LF ladders are indicated. (C) Comparisons of the backbone conformations of the central β-sheet regions of the YY/KE (Orange), YY/LF (Blue), FL/LF (Magenta) PSAMs. (D) Comparisons of the cross-β PSAM dimers, showing alignments of molecule A (Left) and an orthogonal view of the entire dimer complex (Right). Proteins are shown as Cα traces, with YY/LF in blue and FL/LF in pink.
Figure 4.
The interface structures of synthetic cross-β. (A) The dimer interface of the YY/LF PSAM dimer. The dimer has been opened like a book along the axis indicated, with molecule A on the right and molecule B on the left. The red coloration indicates surfaces in the LF ladder that are buried in the interface (defined as atoms within 5 Å of the adjacent molecule). The yellow surfaces are for those atoms in the LF ladder that are not buried in the interface. All other contacts are colored orange. The insert shows how the hydrophobic ladder from subunit B (shown as stick models) overlays on the subunit A surface. (B) The dimer interface of the FL/LF PSAM dimer. The coloring scheme is the same as in A, but the red and yellow surfaces are for atoms in both hydrophobic ladders. (C) The packing of the cross-β segment of YY/LF. At left, the side chains of the YY and LF ladders are shown as spheres. For clarity, only two adjacent β-strands from molecules A and B are shown. At Center and Right are shown orthogonal representations of all side chains of the YY and LF ladders. The β-strands are shown as cartoons. The loop regions have been omitted for clarity. Side-chain carbons are colored green and blue for molecule A and molecule B, respectively. (D) The packing of the cross-β segment of FL/LF depicted in the same manner as in C.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21131979 C.Liu, M.R.Sawaya, and D.Eisenberg (2011).
β₂-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages.
  Nat Struct Mol Biol, 18, 49-55.
PDB codes: 3low 3loz
21287624 V.Babin, C.Roland, and C.Sagui (2011).
The α-sheet: a missing-in-action secondary structure?
  Proteins, 79, 937-946.  
20826442 L.S.Wolfe, M.F.Calabrese, A.Nath, D.V.Blaho, A.D.Miranker, and Y.Xiong (2010).
Protein-induced photophysical changes to the amyloid indicator dye thioflavin T.
  Proc Natl Acad Sci U S A, 107, 16863-16868.
PDB codes: 3myz 3mzt
20979077 R.Giraldo (2010).
Amyloid assemblies: protein legos at a crossroads in bottom-up synthetic biology.
  Chembiochem, 11, 2347-2357.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.