5VF1

X-ray Crystallographic Structure of a Giant Double-Walled Peptide Nanotube Formed by a Macrocyclic Beta-Sheet Containing ABeta16-22

• PDB DOI: https://doi.org/10.2210/pdb5VF1/pdb

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


• Deposited: 2017-04-06 Released: 2017-06-21 
• Deposition Author(s): Chen, K.H., Corro, K.A., Le, S.P., Nowick, J.S.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.273 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 

Literature

X-ray Crystallographic Structure of a Giant Double-Walled Peptide Nanotube Formed by a Macrocyclic beta-Sheet Containing A beta 16-22.

Chen, K.H., Corro, K.A., Le, S.P., Nowick, J.S.

(2017) J Am Chem Soc 139: 8102-8105

• PubMed: 28598147 
• DOI: https://doi.org/10.1021/jacs.7b03890
• Primary Citation of Related Structures:  
  5VF1


• PubMed Abstract: 
  

  This paper describes the supramolecular assembly of a macrocyclic β-sheet containing residues 16-22 of the β-amyloid peptide, Aβ. X-ray crystallography reveals that the macrocyclic β-sheet assembles to form double-walled nanotubes, with an inner diameter of 7 nm and outer diameter of 11 nm. The inner wall is composed of an extended network of hydrogen-bonded dimers. The outer wall is composed of a separate extended network of β-barrel-like tetramers. These large peptide nanotubes pack into a hexagonal lattice that resembles a honeycomb. The complexity and size of the peptide nanotubes rivals some of the largest tubular biomolecular assemblies, such as GroEL and microtubules. These observations demonstrate that small amyloidogenic sequences can be used to build large nanostructures.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 144-mer - A144 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.35 kDa 
• Atom Count: 865 
• Modelled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ORN-LYS-LEU-VAL-PHI-PHE-ALA-GLU-ORN-GLU-ALA-PHE-MEA-VAL-LEU-LYS	A, B, C, D, E, F	16	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEA	A, B, C, D, E, F	L-PEPTIDE LINKING	C10 H13 N O2		PHE
ORN	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA
PHI	A, B, C, D, E, F	L-PEPTIDE LINKING	C9 H10 I N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.273 
• R-Value Work: 0.219 
• R-Value Observed: 0.224 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.22	α = 90
b = 121.22	β = 90
c = 29.958	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
CrystalClear	data collection
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Chen, K.H., Corro, K.A., Le, S.P., Nowick, J.S.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1507840

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Advisory, Author supporting evidence
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence