PDBsum entry 2nnt

Protein fibril

PDB id: 2nnt

Contents

Protein chains

31 a.a. *

* Residue conservation analysis

PDB id:

2nnt

Name:

Protein fibril

Title:

General structural motifs of amyloid protofilaments

Structure:

Transcription elongation regulator 1. Chain: a, b, c, d. Fragment: second ww domain. Synonym: tata box-binding protein- associated factor 2s, transcription factor ca150. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: tcerg1, ca150, taf2s. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

10 models

Authors:

N.Ferguson,J.Becker,H.Tidow,S.Tremmel,T.D.Sharpe,G.Krause,J.Flinders, M.Petrovich,J.Berriman,H.Oschkinat,A.R.Fersht

Key ref:

N.Ferguson et al. (2006). General structural motifs of amyloid protofilaments. Proc Natl Acad Sci U S A, 103, 16248-16253. PubMed id: 17060612 DOI: 10.1073/pnas.0607815103

Date:

24-Oct-06 Release date: 14-Nov-06

Protein chains

O14776  (TCRG1_HUMAN) -  Transcription elongation regulator 1 from Homo sapiens

Seq: 1098 a.a.

Struc: 31 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0607815103

Proc Natl Acad Sci U S A 103:16248-16253 (2006)

PubMed id: 17060612

General structural motifs of amyloid protofilaments.

N.Ferguson, J.Becker, H.Tidow, S.Tremmel, T.D.Sharpe, G.Krause, J.Flinders, M.Petrovich, J.Berriman, H.Oschkinat, A.R.Fersht.

ABSTRACT

Human CA150, a transcriptional activator, binds to and is co-deposited with huntingtin during Huntington's disease. The second WW domain of CA150 is a three-stranded beta-sheet that folds in vitro in microseconds and forms amyloid fibers under physiological conditions. We found from exhaustive alanine scanning studies that fibrillation of this WW domain begins from its denatured conformations, and we identified a subset of residues critical for fibril formation. We used high-resolution magic-angle-spinning NMR studies on site-specific isotopically labeled fibrils to identify abundant long-range interactions between side chains. The distribution of critical residues identified by the alanine scanning and NMR spectroscopy, along with the electron microscopy data, revealed the protofilament repeat unit: a 26-residue non-native beta-hairpin. The structure we report has similarities to the hairpin formed by the A(beta)((1-40)) protofilament, yet also contains closely packed side-chains in a "steric zipper" arrangement found in the cross-beta spine formed from small peptides from the Sup35 prion protein. Fibrillation of unrelated amyloidogenic sequences shows the common feature of zippered repeat units that act as templates for fiber elongation.

Selected figure(s)

Figure 1.
Fig. 1. Cartoon of the structure of native CA150.WW2 [PDB ID code 1E0L (6)]. (A) Side chains that interact with each other in the fibrillar but not in the native state are marked in identical colors. (B) Sequence of CA150.WW2. The sequence is numbered according to the solution structure with the register of the native -strands indicated by black arrows. The first three residues (gsm) originate from the expression vector and are numbered –2, –1, and 0, respectively. Flanking residues were also present in synthetic peptides used in this study. The mutations examined in this study are shown in red.

Figure 5.
Fig. 5. Structural model of the CA150.WW2 protofilament. (A) View of the long axis of the protofilament. The strands of the parallel -sheet in the background (gray) were formed by residues 20–28, with residues 3–11 forming the -sheet in the foreground (violet). Residues N-terminal to A2 and C-terminal to T29 are not shown, because they had no detectable regular structure. Each hairpin is linked to others by backbone hydrogen bonds used as constraints (dashed lines) and buried side-chain interactions (not shown). (B) Cartoon representation of the nonnative -hairpin. The long-range interactions detected by MAS NMR and used for the structure calculations are shown by black arrows and define the interface between the -strands. Dotted arrows indicate ambiguous distance constraints that could be fitted into the structure after the calculation. Residues that eliminated or significantly decelerated fibrillation when mutated to Ala are marked in red and orange, respectively (Table 1). We could not determine the effects of mutating W8 and N22 (light gray), because the corresponding Ala variants could not be expressed in sufficient quantities for characterization. (C) One repeat unit, viewed down the fiber axis, with colors encoding atom type. It is a hairpin formed by two -strands of nonnative register linked by a flexible loop region between residues T13 and T18. The interface between strands is well packed and includes a salt bridge between E7 and R24. This interaction was not an intrinsic restraint in the model but a consequence of the periodicity dictated by the V5-R24, V5-L26, T13-T18, and T3-S28 interactions identified using solid-state MAS NMR. The width of the ordered region of the hairpin (T3-T13 = 31 Å) is consistent with the dimensions determined using EM (Fig. 3). Blue dotted lines represent the long-range interactions identified by MAS NMR, which were used as restraints in structure calculations; hydrogen bonds are indicated by dashed red lines.

Figures were selected by an automated process.