+Open data
-Basic information
Entry | Database: PDB / ID: 6qiz | ||||||
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Title | CI-2, conformation 2 | ||||||
Components | Subtilisin-chymotrypsin inhibitor-2A | ||||||
Keywords | PLANT PROTEIN / CHYMOTRYPSIN INHIBITOR 2 / hydrolase inhibitor | ||||||
Function / homology | Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / response to wounding / serine-type endopeptidase inhibitor activity / Subtilisin-chymotrypsin inhibitor-2A Function and homology information | ||||||
Biological species | Hordeum vulgare (barley) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Romero, A. / Ruiz, F.M. | ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Engineering protein assemblies with allosteric control via monomer fold-switching. Authors: Luis A Campos / Rajendra Sharma / Sara Alvira / Federico M Ruiz / Beatriz Ibarra-Molero / Mourad Sadqi / Carlos Alfonso / Germán Rivas / Jose M Sanchez-Ruiz / Antonio Romero Garrido / José ...Authors: Luis A Campos / Rajendra Sharma / Sara Alvira / Federico M Ruiz / Beatriz Ibarra-Molero / Mourad Sadqi / Carlos Alfonso / Germán Rivas / Jose M Sanchez-Ruiz / Antonio Romero Garrido / José M Valpuesta / Victor Muñoz / 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 ...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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qiz.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qiz.ent.gz | 28.7 KB | Display | PDB format |
PDBx/mmJSON format | 6qiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qiz_validation.pdf.gz | 412.6 KB | Display | wwPDB validaton report |
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Full document | 6qiz_full_validation.pdf.gz | 412.5 KB | Display | |
Data in XML | 6qiz_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 6qiz_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/6qiz ftp://data.pdbj.org/pub/pdb/validation_reports/qi/6qiz | HTTPS FTP |
-Related structure data
Related structure data | 4568C 6qiyC 2ci2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 7296.570 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 21-84 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Escherichia coli (E. coli) / References: UniProt: P01053 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% PEG 3350, 100 MM TRIS-HCL PH 8.5 AND 200 MM LITHIUM SULPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→39.58 Å / Num. obs: 9305 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 21.54 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.043 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CI2 Resolution: 1.65→39.58 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.58 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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