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- EMDB-13924: Shape-morphing of an artificial protein cage with unusual geometr... -

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Basic information

Entry
Database: EMDB / ID: EMD-13924
TitleShape-morphing of an artificial protein cage with unusual geometry induced by a single amino acid change
Map datamain map
Sample
  • Complex: artificail protein cage made out of 20 copies of TRAP ring
    • Protein or peptide: artificial protein cage made out of 20 TRAP protein rings
KeywordsTRAP / protein cage / complex / RNA BINDING PROTEIN
Function / homologyTranscription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily / DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding / Transcription attenuation protein MtrB
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.13 Å
AuthorsBiela AP / Sharma M / Kowalczyk A / Borzecka-Solarz K / Piette BMAG / Bishop J / Kukura P / Benesch J / Imamura M / Scheuring S / Heddle JG
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science Centre2016/20/W/NZ1/00095 Poland
Polish National Science Centre2019/34/A/NZ1/00196 Poland
CitationJournal: ACS Nanosci Au / Year: 2022
Title: Shape-Morphing of an Artificial Protein Cage with Unusual Geometry Induced by a Single Amino Acid Change.
Authors: Mohit Sharma / Artur P Biela / Agnieszka Kowalczyk / Kinga Borzęcka-Solarz / Bernard M A G Piette / Szymon Gaweł / Joshua Bishop / Philipp Kukura / Justin L P Benesch / Motonori Imamura / ...Authors: Mohit Sharma / Artur P Biela / Agnieszka Kowalczyk / Kinga Borzęcka-Solarz / Bernard M A G Piette / Szymon Gaweł / Joshua Bishop / Philipp Kukura / Justin L P Benesch / Motonori Imamura / Simon Scheuring / Jonathan G Heddle /
Abstract: Artificial protein cages are constructed from multiple protein subunits. The interaction between the subunits, notably the angle formed between them, controls the geometry of the resulting cage. ...Artificial protein cages are constructed from multiple protein subunits. The interaction between the subunits, notably the angle formed between them, controls the geometry of the resulting cage. Here, using the artificial protein cage, "TRAP-cage", we show that a simple alteration in the position of a single amino acid responsible for Au(I)-mediated subunit-subunit interactions in the constituent ring-shaped building blocks results in a more acute dihedral angle between them. In turn, this causes a dramatic shift in the structure from a 24-ring cage with an octahedral symmetry to a 20-ring cage with a C2 symmetry. This symmetry change is accompanied by a decrease in the number of Au(I)-mediated bonds between cysteines and a concomitant change in biophysical properties of the cage.
History
DepositionNov 30, 2021-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13924.png

Downloads & links

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Map

FileDownload / File: emd_13924.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 450 pix.
= 387. Å		0.86 Å/pix.
x 450 pix.
= 387. Å		0.86 Å/pix.
x 450 pix.
= 387. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.077
Minimum - Maximum-0.15781957 - 0.25684986
Average (Standard dev.)0.00093048264 (±0.021951739)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 387.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : artificail protein cage made out of 20 copies of TRAP ring

EntireName: artificail protein cage made out of 20 copies of TRAP ring
Components
  • Complex: artificail protein cage made out of 20 copies of TRAP ring
    • Protein or peptide: artificial protein cage made out of 20 TRAP protein rings

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Supramolecule #1: artificail protein cage made out of 20 copies of TRAP ring

SupramoleculeName: artificail protein cage made out of 20 copies of TRAP ring
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: artificial protein cage made out of 20 TRAP protein rings

MacromoleculeName: artificial protein cage made out of 20 TRAP protein rings
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYTNSDFVVI KALEDGVNVI GLTRGADTRF HHCEKLDKGE VLIAQFTEHT SAIKVRGKAY IQTSHGVIES EGKK

UniProtKB: Transcription attenuation protein MtrB

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1013 / Details: manually picked particles
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 113296
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.15.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 2.15.0) / Details: class1 - 118,270 class2 - 17,672 class3 - 21,706
FSC plot (resolution estimation)

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