9QHC | pdb_00009qhc

Crystal structure of 8-repeat CTPR protein with eliminated coordination sites

• PDB DOI: https://doi.org/10.2210/pdb9QHC/pdb

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


• Deposited: 2025-03-14 Released: 2025-10-22 
• Deposition Author(s): Liutkus, M., Rojas, A.L., Cortajarena, A.L.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free: 
  0.338 (Depositor), 0.341 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Rational Crystal Contact Engineering for Programmable Self-Assembled Protein Architectures.

Liutkus, M., Rojas, A.L., Cortajarena, A.L.

(2025) Angew Chem Int Ed Engl : e202516635-e202516635

• PubMed: 41077847 
• DOI: https://doi.org/10.1002/anie.202516635
• Primary Citation of Related Structures:  
  9QHB, 9QHC


• PubMed Abstract: 
  

  Ordered protein-based assemblies are increasingly desirable for materials science, but the design of new materials remains challenging and requires considerable effort. Crystal lattice contact modulation enables rapid rational design of an assortment of structurally diverse constructs with crystalline order. Targeted disruption of crystal contacts and directional growth pre-biasing allows for restricting crystal lattice growth in selected directions, resulting in lower-dimension assemblies with parent crystal structural features. Two-dimensional crystals, one-dimensional fibres, flexible ribbons, and single-walled nanotubes based on tetratricopeptide repeat proteins were constructed from reengineered 3D crystal lattices. The large library of available crystal structures provides an abundance of engineering targets, promising to make crystal contact engineering a rapid and attractive approach for the design of ordered supramolecular protein assemblies.

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Organizational Affiliation: 
• Centre for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance, Paseo de Miramón 194, San Sebastian, 20014, Spain.
Centre for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance, Building 801 A, Bizkaia Science & Technology Park, Derio, 48160, Spain.
Ikerbasque, Basque Foundation for Science, Bilbao, 48009, Spain.

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: 68.7 kDa 
• Atom Count: 4,654 
• Modeled Residue Count: 552 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered tetratricopeptide repeat protein	A, B	292	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA	C [auth A], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.88 Å
• R-Value Free:  0.338 (Depositor), 0.341 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.26	α = 90
b = 134.185	β = 90
c = 78.096	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Liutkus, M., Rojas, A.L., Cortajarena, A.L.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	863170

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release