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- PDB-6qiz: CI-2, conformation 2 -

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Basic information

Entry
Database: PDB / ID: 6qiz
TitleCI-2, conformation 2
ComponentsSubtilisin-chymotrypsin inhibitor-2A
KeywordsPLANT PROTEIN / CHYMOTRYPSIN INHIBITOR 2 / hydrolase inhibitor
Function / homologyProteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / serine-type endopeptidase inhibitor activity / response to wounding / Subtilisin-chymotrypsin inhibitor-2A
Function and homology information
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)7,2971
Polymers7,2971
Non-polymers00
Water1,74797
1
A: Subtilisin-chymotrypsin inhibitor-2A
x 12


Theoretical massNumber of molelcules
Total (without water)87,55912
Polymers87,55912
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 area40550 Å2
ΔGint-260 kcal/mol
Surface area34010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.550, 68.550, 53.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

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


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.65→1.71 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.6 / % 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: 1.65→39.58 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.32
RfactorNum. reflection% reflection
Rfree0.22 473 5.08 %
Rwork0.184 --
obs0.186 9305 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms513 0 0 97 610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006539
X-RAY DIFFRACTIONf_angle_d0.862736
X-RAY DIFFRACTIONf_dihedral_angle_d14.046346
X-RAY DIFFRACTIONf_chiral_restr0.0690
X-RAY DIFFRACTIONf_plane_restr0.00594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6514-1.89040.29661470.24552868X-RAY DIFFRACTION100
1.8904-2.38170.241600.20022882X-RAY DIFFRACTION100
2.3817-39.58890.19921660.16723082X-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)
15.57341.66460.06434.6057-1.15363.3001-0.13070.1811-0.4904-0.1638-0.045-0.12870.21360.02930.15780.18120.01380.02540.1628-0.0440.2008-3.0269-27.122-15.6285
20.85810.866-1.41791.4008-1.81662.62660.0896-0.14890.04090.3030.0432-0.1795-0.21740.0963-0.11440.21250.0086-0.00260.1887-0.04090.2697-8.2293-18.7554-6.381
32.1222-2.551-1.05578.46082.73831.9276-0.02950.03090.1676-0.087-0.0028-0.1019-0.02210.10390.03080.1913-0.0045-0.00020.15170.00370.1671-14.6014-10.289612.398
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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