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PDBsum entry 2omm

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Protein fibril PDB id
2omm
Jmol
Contents
Ligands
GLY-ASN-ASN-GLN-
GLN-ASN-TYR
Waters ×3
PDB id:
2omm
Name: Protein fibril
Title: Gnnqqny peptide corresponding to residues 7-13 of yeast prio
Structure: Gnnqqny peptide corresponding to residues 7-13 of prion sup35. Chain: a. Fragment: residues 7-13. Engineered: yes
Source: Synthetic: yes
Resolution:
2.00Å     R-factor:   0.242     R-free:   0.252
Authors: M.R.Sawaya,R.Nelson,D.Eisenberg
Key ref:
M.R.Sawaya et al. (2007). Atomic structures of amyloid cross-beta spines reveal varied steric zippers. Nature, 447, 453-457. PubMed id: 17468747 DOI: 10.1038/nature05695
Date:
22-Jan-07     Release date:   30-Jan-07    
 Headers
 References

 

 
DOI no: 10.1038/nature05695 Nature 447:453-457 (2007)
PubMed id: 17468747  
 
 
Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
M.R.Sawaya, S.Sambashivan, R.Nelson, M.I.Ivanova, S.A.Sievers, M.I.Apostol, M.J.Thompson, M.Balbirnie, J.J.Wiltzius, H.T.McFarlane, A...Madsen, C.Riekel, D.Eisenberg.
 
  ABSTRACT  
 
Amyloid fibrils formed from different proteins, each associated with a particular disease, contain a common cross-beta spine. The atomic architecture of a spine, from the fibril-forming segment GNNQQNY of the yeast prion protein Sup35, was recently revealed by X-ray microcrystallography. It is a pair of beta-sheets, with the facing side chains of the two sheets interdigitated in a dry 'steric zipper'. Here we report some 30 other segments from fibril-forming proteins that form amyloid-like fibrils, microcrystals, or usually both. These include segments from the Alzheimer's amyloid-beta and tau proteins, the PrP prion protein, insulin, islet amyloid polypeptide (IAPP), lysozyme, myoglobin, alpha-synuclein and beta(2)-microglobulin, suggesting that common structural features are shared by amyloid diseases at the molecular level. Structures of 13 of these microcrystals all reveal steric zippers, but with variations that expand the range of atomic architectures for amyloid-like fibrils and offer an atomic-level hypothesis for the basis of prion strains.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Thirteen atomic-resolution structures for peptide segments of fibril-forming proteins. See text for details of nomenclature. A two-sheet motif of each structure is depicted in projection down the needle crystal axis, showing only the top members of 10^5 stacked segments in each crystalline sheet. A dry, steric-zipper interaction is evidenced by the interdigitation of side chains between sheets. Carbon atoms are shown as purple or white, nitrogen as blue, and oxygen as red. Water molecules are shown as yellow spheres. NNQQNY also contains zinc acetate. Zippers are grouped by class (1, 2, 4, 7, 8); see text for details. Previously reported Sup35 zippers^22 belong to class 1. The three pairs of structures related by blue double-headed arrows are polymorphic pairs (forms 1 and 2; see text for details). The red arrows point to the 90° bend in the upper sheet of MVGGVV form 2.
Figure 4.
Figure 4: The eight classes of steric zippers. Two identical sheets can be classified by: the orientation of their faces (either 'face-to-face' or 'face-to-back'), the orientation of their strands (with both sheets having the same edge of the strand 'up', or one 'up' and the other 'down'), and whether the strands within the sheets are parallel or antiparallel. Both side views (left) and top views (right) show which of the six residues of the segment point into the zipper and which point outward. Green arrows show two-fold screw axes, and yellow arrows show translational symmetry. Below each class are listed protein segments that belong to that class.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 447, 453-457) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 3low 3loz
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PDB codes: 3nhc 3nhd
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PDB code: 3o79
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The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold.
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PDB code: 3cae
17483173 A.De Simone, A.Zagari, and P.Derreumaux (2007).
Structural and hydration properties of the partially unfolded states of the prion protein.
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17728226 A.M.Thackray, L.Hopkins, M.A.Klein, and R.Bujdoso (2007).
Mouse-adapted ovine scrapie prion strains are characterized by different conformers of PrPSc.
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A structural overview of the vertebrate prion proteins.
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The structural basis of yeast prion strain variants.
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Self-assembly of human latexin into amyloid-like oligomers.
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Mechanisms of amyloid plaque pathogenesis.
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Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.
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Structural basis for the recognition and cross-linking of amyloid fibrils by human apolipoprotein E.
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Molecular architecture of human prion protein amyloid: a parallel, in-register beta-structure.
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Prion strains under the magnifying glass.
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17959784 R.Giraldo (2007).
Defined DNA sequences promote the assembly of a bacterial protein into distinct amyloid nanostructures.
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Characterization of the nucleation barriers for protein aggregation and amyloid formation.
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Peptide conformation and supramolecular organization in amylin fibrils: constraints from solid-state NMR.
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Role of intermolecular forces in defining material properties of protein nanofibrils.
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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.