4P4Z

Octomer formed by a macrocyclic peptide derived from beta-2-microglobulin (63-69) - (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK

  • Classification: DE NOVO PROTEIN

  • Deposited: 2014-03-13 Released: 2015-05-06 
  • Deposition Author(s): Spencer, R.K., Nowick, J.S.
  • Funding Organization(s): National Science Foundation (United States) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray Crystallographic Structures of Oligomers of Peptides Derived from beta 2-Microglobulin.

Spencer, R.K.Kreutzer, A.G.Salveson, P.J.Li, H.Nowick, J.S.

(2015) J.Am.Chem.Soc. 137: 6304-6311

  • DOI: 10.1021/jacs.5b01673
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Amyloid diseases such as Alzheimer's disease, Parkinson's disease, and type II diabetes share common features of toxic soluble protein oligomers. There are no structures at atomic resolution of oligomers formed by full-length amyloidogenic peptides a ...

    Amyloid diseases such as Alzheimer's disease, Parkinson's disease, and type II diabetes share common features of toxic soluble protein oligomers. There are no structures at atomic resolution of oligomers formed by full-length amyloidogenic peptides and proteins, and only a few structures of oligomers formed by peptide fragments. The paucity of structural information provides a fundamental roadblock to understanding the pathology of amyloid diseases and developing preventions or therapies. Here, we present the X-ray crystallographic structures of three families of oligomers formed by macrocyclic peptides containing a heptapeptide sequence derived from the amyloidogenic E chain of β2-microglobulin (β2m). Each macrocyclic peptide contains the heptapeptide sequence β2m63-69 and a second heptapeptide sequence containing an N-methyl amino acid. These peptides form β-sheets that further associate into hexamers, octamers, and dodecamers: the hexamers are trimers of dimers; the octamers are tetramers of dimers; and the dodecamers contain two trimer subunits surrounded by three pairs of β-sheets. These structures illustrate a common theme in which dimer and trimer subunits further associate to form a hydrophobic core. The seven X-ray crystallographic structures not only illustrate a range of oligomers that a single amyloidogenic peptide sequence can form, but also how mutation can alter the size and topology of the oligomers. A cocrystallization experiment in which a dodecamer-forming peptide recruits a hexamer-forming peptide to form mixed dodecamers demonstrates that one species can dictate the oligomerization of another. These findings should also be relevant to the formation of oligomers of full-length peptides and proteins in amyloid diseases.


    Organizational Affiliation

    Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIC HEXADECAPEPTIDE (ORN)YLL(PHI)YTE(ORN)KVT(MVA)TVK
A, B, C, D, E, F, G, H, I, J, K, L
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, D, F, L
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B, E, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ORN
Query on ORN
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC9 H10 I N O2PHE
MVA
Query on MVA
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC6 H13 N O2VAL
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.31 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.151 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 63.310α = 90.00
b = 63.310β = 90.00
c = 126.710γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE-1112188

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-13
    Type: Database references
  • Version 1.2: 2015-06-03
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy