4E0M

SVQIVYK segment from human Tau (305-311) displayed on 54-membered macrocycle scaffold (form I)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates

Liu, C.Zhao, M.Jiang, L.Cheng, P.N.Park, J.Sawaya, M.R.Pensalfini, A.Gou, D.Berk, A.J.Glabe, C.G.Nowick, J.Eisenberg, D.

(2012) Proc Natl Acad Sci U S A 109: 20913-20918

  • DOI: https://doi.org/10.1073/pnas.1218792109
  • Primary Citation of Related Structures:  
    4E0K, 4E0L, 4E0M, 4E0N, 4E0O

  • PubMed Abstract: 

    Although aberrant protein aggregation has been conclusively linked to dozens of devastating amyloid diseases, scientists remain puzzled about the molecular features that render amyloid fibrils or small oligomers toxic. Here, we report a previously unobserved type of amyloid fibril that tests as cytotoxic: one in which the strands of the contributing β-sheets are out of register. In all amyloid fibrils previously characterized at the molecular level, only in-register β-sheets have been observed, in which each strand makes its full complement of hydrogen bonds with the strands above and below it in the fibril. In out-of-register sheets, strands are sheared relative to one another, leaving dangling hydrogen bonds. Based on this finding, we designed out-of-register β-sheet amyloid mimics, which form both cylindrin-like oligomers and fibrils, and these mimics are cytotoxic. Structural and energetic considerations suggest that out-of-register fibrils can readily convert to toxic cylindrins. We propose that out-of-register β-sheets and their related cylindrins are part of a toxic amyloid pathway, which is distinct from the more energetically favored in-register amyloid pathway.


  • Organizational Affiliation

    UCLA-DOE Institute for Genomics and Proteomics, The Howard Hughes Medical Institute, Molecular Biology Institute and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclic pseudo-peptide SVQIVYK(ORN)EF(HAO)(4BF)K(ORN)
A, B, C, D
14N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P10636 (Homo sapiens)
Explore P10636 
Go to UniProtKB:  P10636
PHAROS:  P10636
GTEx:  ENSG00000186868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10636
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
H [auth C],
K [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E [auth B]
F [auth B]
G [auth B]
I [auth C]
J [auth C]
E [auth B],
F [auth B],
G [auth B],
I [auth C],
J [auth C],
L [auth D],
M [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
4BF
Query on 4BF
A, B, C, D
L-PEPTIDE LINKINGC9 H10 Br N O2TYR
ORN
Query on ORN
A, B, C, D
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.32α = 90
b = 25.34β = 122.19
c = 50.78γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Advisory, Data collection
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations