|Entry||Database: PDB / ID: 6qiy|
|Title||CI-2, conformation 1|
|Keywords||PLANT PROTEIN / CHYMOTRYPSIN INHIBITOR 2 / protease inhibitor|
|Function / homology|
Function and homology information
response to wounding / serine-type endopeptidase inhibitor activity
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Similarity search - Component
|Biological species||Hordeum vulgare (barley)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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.
|Structure viewer||Molecule: |
Downloads & links
A: Subtilisin-chymotrypsin inhibitor-2A
A: Subtilisin-chymotrypsin inhibitor-2Ax 12
|Components on special symmetry positions|
|#1: Protein|| |
Mass: 7411.657 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 20-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Escherichia coli (E. coli) / References: UniProt: P01053
|#2: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.45 Å3/Da / Density % sol: 49.76 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 |
Details: 1.4 M AMMONIUM SULPHATE AND 100 MM TRIS-HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
PH range: 8.5
|Diffraction||Mean temperature: 100 K / Serial crystal experiment: N|
|Diffraction source||Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å|
|Detector||Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 24, 2015|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1 Å / Relative weight: 1|
|Reflection||Resolution: 1.5→38.55 Å / Num. obs: 11793 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 22.61 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.02 / Net I/σ(I): 23|
|Reflection shell||Resolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.8 / % possible all: 100|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 2CI2
Resolution: 1.5→38.55 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.6
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Refinement step||Cycle: LAST / Resolution: 1.5→38.55 Å|
|Refine LS restraints|
|LS refinement shell|
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi