4NW8

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

PDB DOI: https://doi.org/10.2210/pdb4NW8/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.237
R-Value Work: 0.195
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/ja5017409
Primary Citation of 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 22.79 kDa
Atom Count: 1,703
Modelled Residue Count: 192
Deposited Residue Count: 192
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclic hexadecapeptide (ORN)LV(PHI)(MEA)AED(ORN)AIIGL(ORN)V	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	16	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain O [auth K] MOL2 format, chain N [auth D] MOL2 format, chain O [auth K]	N [auth D], O [auth K]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth D] Focus chain O [auth K] Interactions & Density Focus chain N [auth D] Focus chain O [auth K]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain P [auth K] MOL2 format, chain M [auth C] MOL2 format, chain P [auth K]	M [auth C], P [auth K]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain P [auth K] Interactions & Density Focus chain M [auth C] Focus chain P [auth K]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.237
R-Value Work: 0.195
R-Value Observed: 0.199
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.68	α = 90
b = 68.68	β = 90
c = 93.84	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-04-02

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.