4WC8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: https://doi.org/10.1021/jacs.5b01673
  • Primary Citation of Related Structures:  
    4P4V, 4P4W, 4P4X, 4P4Y, 4P4Z, 4WC8, 4X0S

  • 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 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   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
A, E, I, J, K
A, E, I, J, K, L
16synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
B, C, D, F, G
B, C, D, F, G, H
16synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth I]
BA [auth I]
EA [auth J]
FA [auth J]
GA [auth K]
AA [auth I],
BA [auth I],
EA [auth J],
FA [auth J],
GA [auth K],
M [auth A],
N [auth A],
O [auth A],
S [auth C],
T [auth E],
U [auth E],
W [auth G],
Y [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth I]
DA [auth I]
HA [auth K]
P [auth B]
Q [auth B]
CA [auth I],
DA [auth I],
HA [auth K],
P [auth B],
Q [auth B],
R [auth B],
V [auth F],
X [auth G],
Z [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
MAA
Query on MAA
A, E, I, J, K
A, E, I, J, K, L
L-PEPTIDE LINKINGC4 H9 N O2ALA
ORN
Query on ORN
A, E, I, J, K
A, E, I, J, K, L
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A, E, I, J, K
A, E, I, J, K, L
L-PEPTIDE LINKINGC9 H10 I N O2PHE
MLE
Query on MLE
B, C, D, F, G
B, C, D, F, G, H
L-PEPTIDE LINKINGC7 H15 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.174 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.048α = 90
b = 58.048β = 90
c = 112.954γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 2.0: 2023-12-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy