5HPP

Crystal structure of a macrocyclic beta-sheet peptide derived from transthyretin (106-121) - (ORN)TIA(MAA)LLS(ORN)S(PHI)STTAV

• PDB DOI: https://doi.org/10.2210/pdb5HPP/pdb

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


• Deposited: 2016-01-20 Released: 2016-08-10 
• Deposition Author(s): Yoo, S., Kreutzer, A.G., Nowick, J.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Square channels formed by a peptide derived from transthyretin.

Yoo, S., Kreutzer, A.G., Truex, N.L., Nowick, J.S.

(2016) Chem Sci 7: 6946-6951

• PubMed: 28451128 
• DOI: https://doi.org/10.1039/c6sc01927g
• Primary Citation of Related Structures:  
  5HPP


• PubMed Abstract: 
  

  High-resolution structures of peptide supramolecular assemblies are key to understanding amyloid diseases and designing peptide-based materials. This paper explores the supramolecular assembly of a macrocyclic β-sheet peptide derived from transthyretin (TTR). The peptide mimics the β-hairpin formed by the β-strands G and H of TTR, which form the interface of the TTR tetramer. X-ray crystallography reveals that the peptide does not form a tetramer, but rather assembles to form square channels. The square channels are formed by extended networks of β-sheets and pack in a "tilted windows" pattern. This unexpected structure represents an emergent property of the peptide and broadens the scope of known supramolecular assemblies of β-sheets.

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Organizational Affiliation: 

Department of Chemistry , University of California , Irvine , California 92697-2025 , USA . Email: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 1.79 kDa 
• Atom Count: 129 
• Modelled Residue Count: 16 
• Deposited Residue Count: 16 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORN-THR-ILE-ALA-MAA-LEU-LEU-SER-ORN-SER-PHI-SER-THR-THR-ALA-VAL	A	16	Homo sapiens	Mutation(s): 0

Small Molecules

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

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MAA	A	L-PEPTIDE LINKING	C4 H9 N O2		ALA
ORN	A	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA
PHI	A	L-PEPTIDE LINKING	C9 H10 I N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.3	α = 90
b = 42.3	β = 90
c = 16.32	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Yoo, S., Kreutzer, A.G., Nowick, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM097562

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2017-05-17
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Advisory, Author supporting evidence
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence