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- PDB-6qiy: CI-2, conformation 1 -

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Basic information

Entry
Database: PDB / ID: 6qiy
TitleCI-2, conformation 1
ComponentsSubtilisin-chymotrypsin inhibitor-2A
KeywordsPLANT PROTEIN / CHYMOTRYPSIN INHIBITOR 2 / protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / response to wounding
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
Subtilisin-chymotrypsin inhibitor-2A
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRomero, A. / Ruiz, F.M.
CitationJournal: 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
DepositionJan 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilisin-chymotrypsin inhibitor-2A


Theoretical massNumber of molelcules
Total (without water)7,4121
Polymers7,4121
Non-polymers00
Water1,17165
1
A: Subtilisin-chymotrypsin inhibitor-2A
x 12


Theoretical massNumber of molelcules
Total (without water)88,94012
Polymers88,94012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
crystal symmetry operation10_555-y,-x,-z1
crystal symmetry operation11_555-x+y,y,-z1
crystal symmetry operation12_555x,x-y,-z1
Buried area19520 Å2
ΔGint-95 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.773, 68.773, 50.564
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-144-

HOH

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Components

#1: Protein Subtilisin-chymotrypsin inhibitor-2A / CI-2A


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIX(1.10_2155: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CI2

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
RfactorNum. reflection% reflection
Rfree0.257 578 4.92 %
Rwork0.211 --
obs0.213 11750 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms521 0 0 65 586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006535
X-RAY DIFFRACTIONf_angle_d0.863727
X-RAY DIFFRACTIONf_dihedral_angle_d17.627339
X-RAY DIFFRACTIONf_chiral_restr0.0688
X-RAY DIFFRACTIONf_plane_restr0.00693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.65110.35011410.32062704X-RAY DIFFRACTION99
1.6511-1.890.26411360.24422741X-RAY DIFFRACTION100
1.89-2.38110.24931480.24082771X-RAY DIFFRACTION99
2.3811-38.5590.25021530.18822956X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.48630.35430.51398.08250.31662.4338-0.0962-0.08610.3170.1217-0.2157-0.8611-0.16280.16150.3230.22120.0163-0.03990.24720.03520.284821.807916.316214.1938
22.4341.1246-1.46485.03020.75841.3438-0.04380.55990.1535-0.8291-0.09030.8349-0.1472-0.25750.04990.35670.03-0.12340.32810.03350.45259.724118.20758.5052
33.7201-1.60050.56687.56310.32232.65990.02420.0566-0.1926-0.2435-0.01920.34110.2-0.16480.010.18370.00470.00540.19540.00390.238314.594810.427611.6179
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 25 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 26 THROUGH 47 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 48 THROUGH 66 )

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