1NA3 | pdb_00001na3

Design of Stable alpha-Helical Arrays from an Idealized TPR Motif

• PDB DOI: https://doi.org/10.2210/pdb1NA3/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): unidentified
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-11-26 Released: 2003-06-03 
• Deposition Author(s): Main, E., Xiong, Y., Cocco, M., D'Andrea, L., Regan, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.207 (Depositor) 
• R-Value Work: 
  0.178 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Design of Stable alpha-Helical Arrays from an Idealized TPR Motif

Main, E., Xiong, Y., Cocco, M., D'Andrea, L., Regan, L.

(2003) Structure 11: 497-508

• PubMed: 12737816 
• DOI: https://doi.org/10.1016/s0969-2126(03)00076-5
• Primary Citation Related Structures: 
  1NA0, 1NA3


• PubMed Abstract: 
  

  The tetratricopeptide repeat (TPR) is a 34-amino acid alpha-helical motif that occurs in over 300 different proteins. In the different proteins, three to sixteen or more TPR motifs occur in tandem arrays and function to mediate protein-protein interactions. The binding specificity of each TPR protein is different, although the underlying structural motif is the same. Here we describe a statistical approach to the design of an idealized TPR motif. We present the high-resolution X-ray crystal structures (to 1.55 and 1.6 A) of designed TPR proteins and describe their solution properties and stability. A detailed analysis of these structures provides an understanding of the TPR motif, how it is repeated to give helical arrays with different superhelical twists, and how a very stable framework may be constructed for future functional designs.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.35 kDa 
• Atom Count: 1,522 
• Modeled Residue Count: 172 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
designed protein CTPR2	A, B	91	unidentified	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPT	D [auth A], G [auth B]	1-methylethyl 1-thio-beta-D-galactopyranoside C9 H18 O5 S BPHPUYQFMNQIOC-NXRLNHOXSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MG	E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.207 (Depositor) 
• R-Value Work:  0.178 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.986	α = 90
b = 54.941	β = 90
c = 66.938	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-03 
Deposition Author(s): Main, E., Xiong, Y., Cocco, M., D'Andrea, L., Regan, L.

Revision History  

• Version 1.0: 2003-06-03
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Structure summary