6C50

Cross-alpha Amyloid-like Structure alphaAmS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Designed peptides that assemble into cross-alpha amyloid-like structures.

Zhang, S.Q.Huang, H.Yang, J.Kratochvil, H.T.Lolicato, M.Liu, Y.Shu, X.Liu, L.DeGrado, W.F.

(2018) Nat Chem Biol 14: 870-875

  • DOI: 10.1038/s41589-018-0105-5
  • Primary Citation of Related Structures:  
    6D02, 6C4X, 6C4Z, 6C4Y, 6C51, 6C50, 6C52, 6O3N

  • PubMed Abstract: 
  • Amyloids adopt 'cross-β' structures composed of long, twisted fibrils with β-strands running perpendicular to the fibril axis. Recently, a toxic peptide was proposed to form amyloid-like cross-α structures in solution, with a planar bilayer-like asse ...

    Amyloids adopt 'cross-β' structures composed of long, twisted fibrils with β-strands running perpendicular to the fibril axis. Recently, a toxic peptide was proposed to form amyloid-like cross-α structures in solution, with a planar bilayer-like assembly observed in the crystal structure. Here we crystallographically characterize designed peptides that assemble into spiraling cross-α amyloid-like structures, which resemble twisted β-amyloid fibrils. The peptides form helical dimers, stabilized by packing of small and apolar residues, and the dimers further assemble into cross-α amyloid-like fibrils with superhelical pitches ranging from 170 Å to 200 Å. When a small residue that appeared critical for packing was converted to leucine, it resulted in structural rearrangement to a helical polymer. Fluorescently tagged versions of the designed peptides form puncta in mammalian cells, which recover from photobleaching with markedly different kinetics. These structural folds could be potentially useful for directing in vivo protein assemblies with predetermined spacing and stabilities.


    Organizational Affiliation

    Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, CA, USA. william.degrado@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cross-alpha Amyloid-like Structure alphaAmS111213142122232431323334414243445152535461626364717273748182838491929394A1A2A3A4B1B2B3B4C1C2C3C4D1D2D3D4E1E2E3E4F1F2F3F4G1G2G3G4H1H2H3H4I1I2I3I4J1J2J3J4K1K2K3K4L1L2L3L4M1M2M3M4N1N2N3N4O1O2O3O4P1P2P3P4Q1Q2Q3Q4R1R2R3R4S1S2S3S4T1T2T3T4U1U2U3U4V1V2V3V4W1W2W3W4X1X2X3X4Y1Y2Y3Y4Z1Z2Z3Z4a1a2a3a4b1b2b3b4c1c2c3c4d1d2d3d4e1e2e3e4f1f2f3f4g1g2g3g4h1h2h3h4i1i2i3i4j1j2j3j4k1k2k3k4l1l2l3l4m1m2m3m4n1n2n3n4o1o2o3o4p1p2p3p4q1q2q3q4r1r2r3r4s1s2s3s4t1t2t3t4u1u2u3u4v1v2v3v4w1w2w3w4x1x2x3x427synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download CCD File 
74, G2, R3, W2, X3, q3
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
13, 14, 24, 32, 42, 43, 44, 62, 72, 81, 82, 83, 92, 93, A1, A3, A4, B3, B4, C2, D1, D2, E1, E3, E4, F3, F4, G2, G3, H1, H2, H3, I3, I4, J2, K2, L2, L3, L4, M2, N1, O1, O2, O3, P2, P3, Q2, Q3, R4, S1, S2, T2, T3, U1, U2, W4, X4, Y4, Z1, Z3, Z4, a4, b1, b4, c4, d1, d2, e1, e4, f4, g1, g4, h2, i1, i2, j1, j3, k4, m2, m3, m4, n2, o4, q1, r2, r3, s2, t1, t3, u2, u3, v3, w4, x1, x4
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.166α = 90
b = 160.159β = 109.97
c = 198.502γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-13 
  • Released Date: 2018-08-15 
  • Deposition Author(s): Liu, L., Zhang, S.Q.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR35GM122603

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-08-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence