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- EMDB-18904: Structure of the Co(II) triggered TRAP (S33HK35H) protein cage (l... -

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Basic information

Entry
Database: EMDB / ID: EMD-18904
TitleStructure of the Co(II) triggered TRAP (S33HK35H) protein cage (levo form)
Map datahalf map A
Sample
  • Complex: TRAP(S33HK35C) protein cage
    • Protein or peptide: Transcription attenuation protein MtrB
  • Ligand: COBALT (II) ION
KeywordsTRAP protein / protein cage / VIRUS LIKE PARTICLE
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: 2.86 Å
AuthorsBiela AP / Heddle JG
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2019/34/A/NZ1/00196 Poland
CitationJournal: Macromol Rapid Commun / Year: 2024
Title: Designed, Programmable Protein Cages Utilizing Diverse Metal Coordination Geometries Show Reversible, pH-Dependent Assembly.
Authors: Norbert Osiński / Karolina Majsterkiewicz / Zuzanna Pakosz-Stępień / Yusuke Azuma / Artur P Biela / Szymon Gaweł / Jonathan G Heddle /
Abstract: The rational design and production of a novel series of engineered protein cages are presented, which have emerged as versatile and adaptable platforms with significant applications in biomedicine. ...The rational design and production of a novel series of engineered protein cages are presented, which have emerged as versatile and adaptable platforms with significant applications in biomedicine. These protein cages are assembled from multiple protein subunits, and precise control over their interactions is crucial for regulating assembly and disassembly, such as the on-demand release of encapsulated therapeutic agents. This approach employs a homo-undecameric, ring-shaped protein scaffold with strategically positioned metal binding sites. These engineered proteins can self-assemble into highly stable cages in the presence of cobalt or zinc ions. Furthermore, the cages can be disassembled on demand by employing external triggers such as chelating agents and changes in pH. Interestingly, for certain triggers, the disassembly process is reversible, allowing the cages to reassemble upon reversal or outcompeting of triggering conditions/agents. This work offers a promising platform for the development of advanced drug delivery systems and other biomedical applications.
History
DepositionNov 16, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18904.png

Downloads & links

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Map

FileDownload / File: emd_18904.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf map A
Projections & slices

Image control

Size
Brightness
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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: 0.493
Minimum - Maximum-2.5571303 - 5.122502
Average (Standard dev.)0.027876655 (±0.27803242)
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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Half map: main map

Fileemd_18904_half_map_1.map
Annotationmain map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_18904_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TRAP(S33HK35C) protein cage

EntireName: TRAP(S33HK35C) protein cage
Components
  • Complex: TRAP(S33HK35C) protein cage
    • Protein or peptide: Transcription attenuation protein MtrB
  • Ligand: COBALT (II) ION

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Supramolecule #1: TRAP(S33HK35C) protein cage

SupramoleculeName: TRAP(S33HK35C) protein cage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 2.2 MDa

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Macromolecule #1: Transcription attenuation protein MtrB

MacromoleculeName: Transcription attenuation protein MtrB / type: protein_or_peptide / ID: 1 / Number of copies: 264 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 8.317413 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYTNSDFVVI KALEDGVNVI GLTRGADTRF HHHEHLDKGE VLIAQFTEHT SAIKVRGKAY IQTRHGVIES EGKK

UniProtKB: Transcription attenuation protein MtrB

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Macromolecule #2: COBALT (II) ION

MacromoleculeName: COBALT (II) ION / type: ligand / ID: 2 / Number of copies: 120 / Formula: CO
Molecular weightTheoretical: 58.933 Da

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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: 7.9
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
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

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 157100
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4v4f


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8r59:
Structure of the Co(II) triggered TRAP (S33HK35H) protein cage (levo form)

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