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- EMDB-4568: Cryo-EM 3D structure of CI2eng toroidal dodecameric assembly. -

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Basic information

Entry
Database: EMDB / ID: EMD-4568
TitleCryo-EM 3D structure of CI2eng toroidal dodecameric assembly.
Map data3D reconstruction of CI2eng assembly formed in solution. Resol 8.55A
Sample
  • Complex: CI2eng modification of the chymotrypsin inhibitor 2
    • Protein or peptide: CI2eng - modification of the chymotrypsin inhibitor 2 (CI2)
Biological speciesHordeum vulgare (barley)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.55 Å
AuthorsValpuesta JM / Alvira S / Campos LA / Munoz V
Funding support Spain, 2 items
OrganizationGrant numberCountry
European Research CouncilERC-2012-ADG-323059 Spain
Spanish Ministry of Economy and CompetitivenessCSD2009-00088 Spain
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 28, 2019-
Header (metadata) releaseNov 13, 2019-
Map releaseNov 13, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.526
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.526
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4568.png

Downloads & links

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Map

FileDownload / File: emd_4568.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of CI2eng assembly formed in solution. Resol 8.55A
Voxel sizeX=Y=Z: 1.71 Å
Density
Contour LevelBy AUTHOR: 0.526 / Movie #1: 0.526
Minimum - Maximum-1.2190388 - 34.361904
Average (Standard dev.)0.20024234 (±1.4384073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 102.600006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.711.711.71
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z102.600102.600102.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean-1.21934.3620.200

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Supplemental data

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Sample components

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Entire : CI2eng modification of the chymotrypsin inhibitor 2

EntireName: CI2eng modification of the chymotrypsin inhibitor 2
Components
  • Complex: CI2eng modification of the chymotrypsin inhibitor 2
    • Protein or peptide: CI2eng - modification of the chymotrypsin inhibitor 2 (CI2)

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Supramolecule #1: CI2eng modification of the chymotrypsin inhibitor 2

SupramoleculeName: CI2eng modification of the chymotrypsin inhibitor 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Hordeum vulgare (barley) / Organ: seeds
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 80 KDa

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Macromolecule #1: CI2eng - modification of the chymotrypsin inhibitor 2 (CI2)

MacromoleculeName: CI2eng - modification of the chymotrypsin inhibitor 2 (CI2)
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare (barley)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDAKTEWPE LVGKSLEEAK KALLQDKPEA TIIVIPVGTI VTMEYRVDRV RIVVDKLDNI AEVPTVG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5 / Details: 20mM sodium borate buffer at pH 8.5
GridModel: Quantifoil R1.2/1.3 / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 2.5 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 8.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 6200
FSC plot (resolution estimation)

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