PDBsum entry 2beg

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protein Protein-protein interface(s) links
Protein fibril PDB id
Protein chains
26 a.a. *
* Residue conservation analysis
PDB id:
Name: Protein fibril
Title: 3d structure of alzheimer's abeta(1-42) fibrils
Structure: Amyloid beta a4 protein. Chain: a, b, c, d, e. Fragment: beta-amyloid protein 42. Synonym: app, abpp, alzheimer's disease amyloid protein, cerebral vascular amyloid peptide, cvap, protease nexin-ii, pn-ii, appi. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: app. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 10 models
Authors: T.Luhrs,C.Ritter,M.Adrian,D.Riek-Loher,B.Bohrmann,H.Dobeli, D.Schubert,R.Riek
Key ref:
T.Lührs et al. (2005). 3D structure of Alzheimer's amyloid-beta(1-42) fibrils. Proc Natl Acad Sci U S A, 102, 17342-17347. PubMed id: 16293696 DOI: 10.1073/pnas.0506723102
24-Oct-05     Release date:   22-Nov-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P05067  (A4_HUMAN) -  Amyloid beta A4 protein
770 a.a.
26 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     integral to membrane   1 term 
  Biological process     nervous system development   1 term 


DOI no: 10.1073/pnas.0506723102 Proc Natl Acad Sci U S A 102:17342-17347 (2005)
PubMed id: 16293696  
3D structure of Alzheimer's amyloid-beta(1-42) fibrils.
T.Lührs, C.Ritter, M.Adrian, D.Riek-Loher, B.Bohrmann, H.Döbeli, D.Schubert, R.Riek.
Alzheimer's disease is the most fatal neurodegenerative disorder wherein the process of amyloid-beta (Abeta) amyloidogenesis appears causative. Here, we present the 3D structure of the fibrils comprising Abeta(1-42), which was obtained by using hydrogen-bonding constraints from quenched hydrogen/deuterium-exchange NMR, side-chain packing constraints from pairwise mutagenesis studies, and parallel, in-register beta-sheet arrangement from previous solid-state NMR studies. Although residues 1-17 are disordered, residues 18-42 form a beta-strand-turn-beta-strand motif that contains two intermolecular, parallel, in-register beta-sheets that are formed by residues 18-26 (beta1) and 31-42 (beta2). At least two molecules of Abeta(1-42) are required to achieve the repeating structure of a protofilament. Intermolecular side-chain contacts are formed between the odd-numbered residues of strand beta1 of the nth molecule and the even-numbered residues of strand beta2 of the (n - 1)th molecule. This interaction pattern leads to partially unpaired beta-strands at the fibrillar ends, which explains the sequence selectivity, the cooperativity, and the apparent unidirectionality of Abeta fibril growth. It also provides a structural basis for fibrillization inhibitors.
  Selected figure(s)  
Figure 2.
Fig. 2. Pairwise mutagenesis of 35LA (1-42) peptides. (A) Cartoon of intramolecular versus domain swapping-type interaction between monomers in the A (1-42) protofilament that consists of parallel, in-register -sheets exemplified by the salt bridge formed between the charged residues D23 and K28. Individual A molecules are indicated as colored bars that correspond to a cross section along the protofilament axis through the C^ atom positions of one presumed interacting pair of amino acids. The identity of each variant A peptide is indicated next to the corresponding schemes in rows 1-4. "intra" denotes the intramolecular scenario, and "inter" indicates the domain swapping-type scenario. Red diagonal crosses mark all scenarios that were considered to be incompatible with WT fibril formation. (B-J) Negative staining electron microscopy of 35LA (1-42) peptides. The variants are indicated on each image. All electron micrographs were recorded at a nominal magnification of x72,000. (Scale bar, 100 nm.
Figure 4.
Fig. 4. The 3D structure of a 35MoxA (1-42) fibril. (A and B) Ribbon diagrams of the core structure of residues 17-42 illustrating the intermolecular nature of the inter- -strand interactions. Individual molecules are colored. For example, the monomer at the odd end is shown in cyan. The -strands are indicated by arrows, nonregular secondary structure is indicated by spline curves through the C^ atom coordinates of the corresponding residues, and the bonds of side chains that constitute the core of the protofilament are shown. In B, the intermolecular salt bridge between residues D23 and K28 is indicated by dotted lines, and the two salt bridges formed by the central A (1-42) molecule are highlighted by rectangles. (C) van der Waals contact surface polarity and ribbon diagram at the odd end of the 35MoxA (1-42) protofilament comprising residues 17-42. The -sheets are indicated by cyan arrows, and nonregular secondary structure is indicated by gray spline curves. The hydrophobic, polar, negatively charged, and positively charged amino acid side chains are shown in yellow, green, red, and blue, respectively. Positively and negatively charged surface patches are shown in blue and red, respectively, and all others are shown in white. The direction of the fibril axis is indicated by an arrow pointing from even to odd. (D)(Upper) Simulation of a 35MoxA (1-42) fibril that consists of four protofilaments colored individually. Lower shows the same fibril in a noisy gray-scale image, which has been blurred corresponding to a resolution of 2 nm. In Right,a x5-magnified cross section perpendicular to the fibril axis is shown, using the same color code. Dimensions are indicated. To match the experimental twist of the protofilament of the fibril shown in E, a twist angle of 0.45° per molecule was used. (E) Two examples of cryoelectron micrographs of single 35MoxA (1-42) fibrils. (Scale bar, 50 nm.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 3cka 3eex
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PDB code: 3ni3
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16731963 A.Baumketner, S.L.Bernstein, T.Wyttenbach, N.D.Lazo, D.B.Teplow, M.T.Bowers, and J.E.Shea (2006).
Structure of the 21-30 fragment of amyloid beta-protein.
  Protein Sci, 15, 1239-1247.  
16891372 A.Huet, and P.Derreumaux (2006).
Impact of the mutation A21G (Flemish variant) on Alzheimer's beta-amyloid dimers by molecular dynamics simulations.
  Biophys J, 91, 3829-3840.  
17173479 A.Trovato, F.Chiti, A.Maritan, and F.Seno (2006).
Insight into the structure of amyloid fibrils from the analysis of globular proteins.
  PLoS Comput Biol, 2, e170.  
16555351 G.T.Dolphin, P.Dumy, and J.Garcia (2006).
Control of amyloid beta-peptide protofibril formation by a designed template assembly.
  Angew Chem Int Ed Engl, 45, 2699-2702.  
16766615 G.Wei, and J.E.Shea (2006).
Effects of solvent on the structure of the Alzheimer amyloid-beta(25-35) peptide.
  Biophys J, 91, 1638-1647.  
16765899 H.H.Tsai, K.Gunasekaran, and R.Nussinov (2006).
Sequence and structure analysis of parallel beta helices: implication for constructing amyloid structural models.
  Structure, 14, 1059-1072.  
16826550 J.Danielsson, A.Andersson, J.Jarvet, and A.Gräslund (2006).
15N relaxation study of the amyloid beta-peptide: structural propensities and persistence length.
  Magn Reson Chem, 44, S114-S121.  
17047863 J.S.Nowick (2006).
What I have learned by using chemical model systems to study biomolecular structure and interactions.
  Org Biomol Chem, 4, 3869-3885.  
16679374 J.Zheng, B.Ma, C.J.Tsai, and R.Nussinov (2006).
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35.
  Biophys J, 91, 824-833.  
17021379 J.Zheng, B.Ma, and R.Nussinov (2006).
Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure.
  Phys Biol, 3, P1-P4.  
17108084 K.Iwata, T.Fujiwara, Y.Matsuki, H.Akutsu, S.Takahashi, H.Naiki, and Y.Goto (2006).
3D structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR.
  Proc Natl Acad Sci U S A, 103, 18119-18124.
PDB code: 2e8d
17093048 K.Makabe, D.McElheny, V.Tereshko, A.Hilyard, G.Gawlak, S.Yan, A.Koide, and S.Koide (2006).
Atomic structures of peptide self-assembly mimics.
  Proc Natl Acad Sci U S A, 103, 17753-17758.
PDB codes: 2af5 2fkg 2fkj 2hkd
17060612 N.Ferguson, J.Becker, H.Tidow, S.Tremmel, T.D.Sharpe, G.Krause, J.Flinders, M.Petrovich, J.Berriman, H.Oschkinat, and A.R.Fersht (2006).
General structural motifs of amyloid protofilaments.
  Proc Natl Acad Sci U S A, 103, 16248-16253.
PDB code: 2nnt
16843895 N.Haspel, D.Zanuy, C.Alemán, H.Wolfson, and R.Nussinov (2006).
De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs.
  Structure, 14, 1137-1148.  
16563741 R.Nelson, and D.Eisenberg (2006).
Recent atomic models of amyloid fibril structure.
  Curr Opin Struct Biol, 16, 260-265.  
17122841 R.Riek (2006).
Cell biology: infectious Alzheimer's disease?
  Nature, 444, 429-431.  
16634632 T.Sato, P.Kienlen-Campard, M.Ahmed, W.Liu, H.Li, J.I.Elliott, S.Aimoto, S.N.Constantinescu, J.N.Octave, and S.O.Smith (2006).
Inhibitors of amyloid toxicity based on beta-sheet packing of Abeta40 and Abeta42.
  Biochemistry, 45, 5503-5516.  
16965061 W.Chen, N.Mousseau, and P.Derreumaux (2006).
The conformations of the amyloid-beta (21-30) fragment can be described by three families in solution.
  J Chem Phys, 125, 084911.  
17038501 W.Kim, and M.H.Hecht (2006).
Generic hydrophobic residues are sufficient to promote aggregation of the Alzheimer's Abeta42 peptide.
  Proc Natl Acad Sci U S A, 103, 15824-15829.  
16823798 Y.L.Lyubchenko, S.Sherman, L.S.Shlyakhtenko, and V.N.Uversky (2006).
Nanoimaging for protein misfolding and related diseases.
  J Cell Biochem, 99, 52-70.  
16533917 W.Guo, J.E.Shea, and R.S.Berry (2005).
The physics of the interactions governing folding and association of proteins.
  Ann N Y Acad Sci, 1066, 34-53.  
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.