5UHR

Crystal structure of (Cit)LANFLV heptapeptide segment from islet amyloid polypeptide (IAPP) incorporated into a macrocyclic beta-sheet template

• PDB DOI: https://doi.org/10.2210/pdb5UHR/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2017-01-11 Released: 2017-07-12 
• Deposition Author(s): Wang, Y., Kreutzer, A.G., Nowick, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.265 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 

Literature

A Tetramer Derived from Islet Amyloid Polypeptide.

Wang, Y., Kreutzer, A.G., Truex, N.L., Nowick, J.S.

(2017) J Org Chem 82: 7905-7912

• PubMed: 28661686 
• DOI: https://doi.org/10.1021/acs.joc.7b01116
• Primary Citation of Related Structures:  
  5UHR


• PubMed Abstract: 
  

  Aggregation of the islet amyloid polypeptide (IAPP) to form fibrils and oligomers is important in the progression of type 2 diabetes. This article describes X-ray crystallographic and solution-state NMR studies of peptides derived from residues 11-17 of IAPP that assemble to form tetramers. Incorporation of residues 11-17 of IAPP (RLANFLV) into a macrocyclic β-sheet peptide results in a monomeric peptide that does not self-assemble to form oligomers. Mutation of Arg ₁₁ to the uncharged isostere citrulline gives peptide homologues that assemble to form tetramers in both the crystal state and in aqueous solution. The tetramers consist of hydrogen-bonded dimers that sandwich together through hydrophobic interactions. The tetramers share several features with structures reported for IAPP fibrils and demonstrate the importance of hydrogen bonding and hydrophobic interactions in the oligomerization of IAPP-derived peptides.

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Organizational Affiliation: 

Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.41 kDa 
• Atom Count: 540 
• Modelled Residue Count: 56 
• Deposited Residue Count: 56 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORN-CIR-LEU-ALA-ASN-PHE-LEU-VAL-ORN-ILE-LYS-HAO-LYS-A8E	A, B, C, D	14	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A8E	A, B, C, D	L-PEPTIDE LINKING	C5 H8 Br N O2		VAL
CIR	A, B, C, D	L-PEPTIDE LINKING	C6 H13 N3 O3		ARG
ORN	A, B, C, D	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.265 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.876	α = 90
b = 33.876	β = 90
c = 99.054	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Wang, Y., Kreutzer, A.G., Nowick, J.S.

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Data collection
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations