4WC8

Heterogeneous dodecamer formed from macrocycles containing a sequence from beta-2-microglobulin(63-69).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.908 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
A, E, I, J, K, L
16Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
B, C, D, F, G, H
16Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C, E, G, H, I, J, K
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, F, G, H, I, K
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
MLE
Query on MLE
B, C, D, F, G, H
L-PEPTIDE LINKINGC7 H15 N O2LEU
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
MAA
Query on MAA
A, E, I, J, K, L
L-peptide linkingC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.908 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.048α = 90.00
b = 58.048β = 90.00
c = 112.954γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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