PDBsum entry 2bom

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Serine protease inhibitor PDB id
Jmol PyMol
Protein chains
33 a.a.
Theoretical model
PDB id:
Name: Serine protease inhibitor
Title: Model of alzheimer's disease amyloid-beta peptide based on a RNA binding protein
Structure: Amyloid beta a4. Synonym: amyloid beta. Chain: a, b
Source: Homo sapiens
Authors: V.S.Mathura,D.Paris,G.Ait-Ghezala,A.Quadros,N.S.Patel, D.N.Kolippakkam,C.H.Volmar,M.J.Mullan
Key ref: V.S.Mathura et al. (2005). Model of Alzheimer's disease amyloid-beta peptide based on a RNA binding protein. Biochem Biophys Res Commun, 332, 585-592. PubMed id: 15896718
12-Apr-05     Release date:   14-Apr-05    
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Protein chains
Pfam   ArchSchema ?
P05067  (A4_HUMAN) -  Amyloid beta A4 protein
770 a.a.
33 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure


Biochem Biophys Res Commun 332:585-592 (2005)
PubMed id: 15896718  
Model of Alzheimer's disease amyloid-beta peptide based on a RNA binding protein.
V.S.Mathura, D.Paris, G.Ait-Ghezala, A.Quadros, N.S.Patel, D.N.Kolippakkam, C.H.Volmar, M.J.Mullan.
Although Alzheimer's Abeta peptide has been shown to form beta-sheet structure, a high-resolution molecular structure is still unavailable to date. A search for a sequence neighbor using Abeta(10-42) as the query in the Protein Data-Bank (PDB) revealed that an RNA binding protein, AF-Sm1 from Archaeoglobus fulgidus (PDB entry: 1i4k chain Z), shared 36% identical residues. Using AF-Sm1 as a template, we built a molecular model of Abeta(10-42) by applying comparative modeling methods. The model of Abeta(10-42) contains an antiparallel beta-sheet formed by residues 16-23 and 32-41. Hydrophobic surface constituted by residues 17-20 (LVFF) separates distinctly charged regions. Residues that interact with RNA in the AF-Sm1 crystal structure were found to be conserved in Abeta. Using a native gel we demonstrate for the first time that RNA can interact with Abeta and selectively retard the formation of fibrils or higher-order oligomers. We hypothesize that in a similar fashion to AF-Sm1, RNA interacts with Abeta in the beta-hairpin (beta-turn-beta) structure and prevents fibril formation.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19818105 N.S.Patel, V.S.Mathura, C.Bachmeier, D.Beaulieu-Abdelahad, V.Laporte, O.Weeks, M.Mullan, and D.Paris (2010).
Alzheimer's beta-amyloid peptide blocks vascular endothelial growth factor mediated signaling via direct interaction with VEGFR-2.
  J Neurochem, 112, 66-76.  
18266117 N.S.Patel, A.Quadros, S.Brem, M.Wotoczek-Obadia, V.S.Mathura, V.Laporte, M.Mullan, and D.Paris (2008).
Potent anti-angiogenic motifs within the Alzheimer beta-amyloid peptide.
  Amyloid, 15, 5.  
17211889 F.Dulin, I.Callebaut, N.Colloc'h, and J.P.Mornon (2007).
Sequence-based modeling of Abeta42 soluble oligomers.
  Biopolymers, 85, 422-437.  
16880933 H.Koga (2006).
Establishment of the platform for reverse chemical genetics targeting novel protein-protein interactions.
  Mol Biosyst, 2, 159-164.  
16650066 S.Parry, D.Todorova-Balvay, T.Srikrishnan, and E.Sulkowski (2005).
Thiophilic interaction chromatography of Alzheimer's beta-amyloid peptides.
  J Pept Res, 66, 99.  
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