PDBsum entry 1b10

Prion protein

PDB id: 1b10

Contents

Protein chain

104 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Solution structure of a 142-Residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform.

Authors

T.L.James, H.Liu, N.B.Ulyanov, S.Farr-Jones, H.Zhang, D.G.Donne, K.Kaneko, D.Groth, I.Mehlhorn, S.B.Prusiner, F.E.Cohen.

Ref.

Proc Natl Acad Sci U S A, 1997, 94, 10086-10091. [DOI no: 10.1073/pnas.94.19.10086]

PubMed id

9294167

Abstract

The scrapie prion protein (PrPSc) is the major, and possibly the only, component of the infectious prion; it is generated from the cellular isoform (PrPC) by a conformational change. N-terminal truncation of PrPSc by limited proteolysis produces a protein of approximately 142 residues designated PrP 27-30, which retains infectivity. A recombinant protein (rPrP) corresponding to Syrian hamster PrP 27-30 was expressed in Escherichia coli and purified. After refolding rPrP into an alpha-helical form resembling PrPC, the structure was solved by multidimensional heteronuclear NMR, revealing many structural features of rPrP that were not found in two shorter PrP fragments studied previously. Extensive side-chain interactions for residues 113-125 characterize a hydrophobic cluster, which packs against an irregular beta-sheet, whereas residues 90-112 exhibit little defined structure. Although identifiable secondary structure is largely lacking in the N terminus of rPrP, paradoxically this N terminus increases the amount of secondary structure in the remainder of rPrP. The surface of a long helix (residues 200-227) and a structured loop (residues 165-171) form a discontinuous epitope for binding of a protein that facilitates PrPSc formation. Polymorphic residues within this epitope seem to modulate susceptibility of sheep and humans to prion disease. Conformational heterogeneity of rPrP at the N terminus may be key to the transformation of PrPC into PrPSc, whereas the discontinuous epitope near the C terminus controls this transition.

Figure 1.
Fig. 1. Secondary structure diagram for rPrP. NOE connectivities are denoted by lines, where the thickness qualitatively represents the relative intensity (weak, medium, or strong) of the NOE crosspeaks, and i designates the residue number for rPrP. d[ N](i, i+3) denotes an NOE between the -proton of residue i and the amide^ proton of residue i+3. The long-range NOE line indicates by height the relative number of NOE crosspeaks between residues i i + 4. In the consensus chemical shift index (59), contiguous up bars designate -helix and down bars designate -strand. Regions of secondary structure are depicted by helices for -helices and^ broad arrows for -strands. Hydrogen exchange was calculated from the intensity of proton NOE crosspeak between the amide and water: open circles for slow, filled for fast, and half-filled circles for medium exchange rate. No circle indicates spectral overlap or proline. The secondary structure diagram was created using the program VINCE (60).

Figure 2.
Fig. 2. NMR structure of SHa rPrP(90-231). (A) Comparison of the 15 best-scoring structures of rPrP shown with a best-fit superposition of backbone atoms for residues 113-227 (stereoview). In all figures except C, the color scheme is: disulfide between Cys179 and Cys214, yellow; sites of glycosidation in PrPC, i.e., Asn181 and Asn197, gold; hydrophobic cluster composed of residues 113-126, red; helices, pink; loops, gray; residues 129-134, green, encompassing strand S1 and residues 159-165, blue, encompassing strand S2; the arrows span residues 129-131 and 161-163, as these show a^ closer resemblance to -sheet. The structures were generated with the program DIANA (30), followed by energy minimization with AMBER 4.1 (31). Structure generation parameters are as follows: 2,401 distance restraints (intraresidue, 858; sequential (i i +1), 753; (i i +2), 195; (i i +3), 233; (i i +4), 109; and (i i + 5), 253 for amino acid i); hydrogen bond restraints, 44; distance restraint violations >0.5 Å per structure, 30; AMBER energy, 1,443 ± 111 kcal/mol. Precision of structures: atomic^ rms deviation for all backbone heavy atoms of residues 128-227, <1.9 Å. The distance restraint violations and precision in some^ molecular moities reflect the conformational heterogeneity of^ rPrP. (B) Residues 113-132 illustrating (stereoview) in one representative^ structure the interaction of the hydrophobic cluster, with van der Waals rendering of atoms in residues 113-127, with the first -strand. (C) Van der Waals surface of rPrP turned approximately 180° from A, illustrating the interaction of helix A with helix C. Helices A, B, and C are colored magenta, cyan, and gold, respectively. (D) Stereoview, using RIBBONJR, illustrating the proximity of^ helix C to the 165-171 loop and the end of helix B, where residues Gln168 and Gln172 are depicted with a low-density van der Waals rendering and helix C residues Thr215 and Gln219 are depicted with a high-density van der Waals rendering. (E) Stereoview, highlighting in white the residues corresponding to point mutations that lead to human prion diseases. Illustrations were generated with MIDASPLUS. (F) Portion of the three-dimensional 13C-NOESY spectrum corresponding to 13C planes of the unresolved Val166 methyl resonances and the Ser222 resonances (a-d) and the 15N plane showing the Tyr225 amide interaction with Val166 (e). The diagonal peaks and mirrored crosspeaks for each 1H-1H connectivity are shown. The solid lines connecting peaks designate^ NOE connectivities.