4NTR | pdb_00004ntr

Crystal structure of macrocycles containing Abeta 17-23 (LVFFAED) and Abeta 30-36 (AII(SAR)L(ORN)V)

• PDB DOI: https://doi.org/10.2210/pdb4NTR/pdb

• Classification: de novo protein, protein binding
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2013-12-02 Released: 2014-04-02 
• Deposition Author(s): Spencer, R.K., Li, H., Nowick, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

X-ray crystallographic structures of trimers and higher-order oligomeric assemblies of a peptide derived from A beta (17-36).

Spencer, R.K., Li, H., Nowick, J.S.

(2014) J Am Chem Soc 136: 5595-5598

• PubMed: 24669800 
• DOI: https://doi.org/10.1021/ja5017409
• Primary Citation Related Structures: 
  4NTP, 4NTR, 4NW8, 4NW9


• PubMed Abstract: 
  

  A peptide derived from Aβ17-36 crystallizes to form trimers that further associate to form higher-order oligomers. The trimers consist of three highly twisted β-hairpins in a triangular arrangement. Two trimers associate face-to-face in the crystal lattice to form a hexamer; four trimers in a tetrahedral arrangement about a central cavity form a dodecamer. These structures provide a working model for the structures of oligomers associated with neurodegeneration in Alzheimer's disease.

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Organizational Affiliation: 
• Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 16-mer - A16 

Local Symmetry: Dihedral - D3  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Dihedral - D3  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.56 kDa 
• Atom Count: 2,239 
• Modeled Residue Count: 256 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic hexadecapeptide (ORN)LVFFAED(ORN)AII(SAR)L(ORN)V	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	16	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	Q [auth A], T [auth C], U [auth C], V [auth D], W [auth E], X [auth G], Y [auth H], Z [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	AA [auth M], R [auth A], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ORN	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA
SAR	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	PEPTIDE LINKING	C3 H7 N O2		GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68	α = 90
b = 68	β = 90
c = 169.26	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Spencer, R.K., Li, H., Nowick, J.S.

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-05-14
  Changes: Database references
• Version 1.2: 2014-07-09
  Changes: Database references
• Version 1.3: 2023-09-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description