4NW9 | pdb_00004nw9

Crystal structure of macrocycles containing Abeta17-23 (LVF(MEA)AED) and Abeta30-36 (AIIGL(ORN)V)

• PDB DOI: https://doi.org/10.2210/pdb4NW9/pdb

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


• Deposited: 2013-12-05 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: 1.66 Å
• R-Value Free: 
  0.209 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.190 (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: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.31 kDa 
• Atom Count: 1,740 
• Modeled Residue Count: 192 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic hexadecapeptide (ORN)LVF(MEA)AED(ORN)AIIGL(ORN)V	A, B, C, D, E, F, G, H, I, J, K, L	16	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	M [auth C], O [auth G], P [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	N [auth D], Q [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.209 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.22	α = 90
b = 68.22	β = 90
c = 92.99	γ = 120

Software Package:

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

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: 2017-11-22
  Changes: Advisory, Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description