6QIY | pdb_00006qiy

CI-2, conformation 1

• PDB DOI: https://doi.org/10.2210/pdb6QIY/pdb

• Classification: PLANT PROTEIN
• Organism(s): Hordeum vulgare
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-21 Released: 2019-12-25 
• Deposition Author(s): Romero, A., Ruiz, F.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.257 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Engineering protein assemblies with allosteric control via monomer fold-switching.

Campos, L.A., Sharma, R., Alvira, S., Ruiz, F.M., Ibarra-Molero, B., Sadqi, M., Alfonso, C., Rivas, G., Sanchez-Ruiz, J.M., Romero Garrido, A., Valpuesta, J.M., Munoz, V.

(2019) Nat Commun 10: 5703-5703

• PubMed: 31836707 
• DOI: https://doi.org/10.1038/s41467-019-13686-1
• Primary Citation Related Structures: 
  6QIY, 6QIZ


• PubMed Abstract: 
  

  The macromolecular machines of life use allosteric control to self-assemble, dissociate and change shape in response to signals. Despite enormous interest, the design of nanoscale allosteric assemblies has proven tremendously challenging. Here we present a proof of concept of allosteric assembly in which an engineered fold switch on the protein monomer triggers or blocks assembly. Our design is based on the hyper-stable, naturally monomeric protein CI2, a paradigm of simple two-state folding, and the toroidal arrangement with 6-fold symmetry that it only adopts in crystalline form. We engineer CI2 to enable a switch between the native and an alternate, latent fold that self-assembles onto hexagonal toroidal particles by exposing a favorable inter-monomer interface. The assembly is controlled on demand via the competing effects of temperature and a designed short peptide. These findings unveil a remarkable potential for structural metamorphosis in proteins and demonstrate key principles for engineering protein-based nanomachinery.

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Organizational Affiliation: 
• Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain.
Unidad Asociada de Nanobiotecnología IMDEA Nanociencia-CNB, Madrid, Spain.
School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK.
Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain.
Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva s/n, 18071, Granada, Spain.
Department of Bioengineering, University of California, 95343, Merced, CA, USA.
NSF-CREST Center for Cellular and Biomolecular Machines, University of California, 95343, Merced, CA, USA.
Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain. [e-mail].
Department of Bioengineering, University of California, 95343, Merced, CA, USA. [e-mail].
NSF-CREST Center for Cellular and Biomolecular Machines, University of California, 95343, Merced, CA, USA. [e-mail].
IMDEA Nanociencia, Programa de Nanobiosistemas, Faraday 9, Ciudad Universitaria Cantoblanco, 28049, Madrid, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 7.41 kDa 
• Atom Count: 592 
• Modeled Residue Count: 65 
• Deposited Residue Count: 65 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subtilisin-chymotrypsin inhibitor-2A	A	65	Hordeum vulgare	Mutation(s): 0
UniProt
Find proteins for P01053 (Hordeum vulgare) Explore P01053  Go to UniProtKB:  P01053

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.257 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.773	α = 90
b = 68.773	β = 90
c = 50.564	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Romero, A., Ruiz, F.M.

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description