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- EMDB-18907: Structure of the Zn(II) triggered TRAP (S33HK35H) protein cage (d... -

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Basic information

Entry
Database: EMDB / ID: EMD-18907
TitleStructure of the Zn(II) triggered TRAP (S33HK35H) protein cage (dextro form)
Map datamain map
Sample
  • Complex: Zn(II) triggered TRAP (S33HK35H) protein cage
    • Protein or peptide: TRAP protein - Transcription attenuation protein
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: 4.31 Å
AuthorsBiela AP
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_18907.png

Downloads & links

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Map

FileDownload / File: emd_18907.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 500 pix.
= 430. Å		0.86 Å/pix.
x 500 pix.
= 430. Å		0.86 Å/pix.
x 500 pix.
= 430. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.377
Minimum - Maximum-0.28478402 - 1.283084
Average (Standard dev.)0.012092055 (±0.10708574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 430.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_18907_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_18907_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Zn(II) triggered TRAP (S33HK35H) protein cage

EntireName: Zn(II) triggered TRAP (S33HK35H) protein cage
Components
  • Complex: Zn(II) triggered TRAP (S33HK35H) protein cage
    • Protein or peptide: TRAP protein - Transcription attenuation protein

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Supramolecule #1: Zn(II) triggered TRAP (S33HK35H) protein cage

SupramoleculeName: Zn(II) triggered TRAP (S33HK35H) protein cage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 2.2 MDa

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Macromolecule #1: TRAP protein - Transcription attenuation protein

MacromoleculeName: TRAP protein - Transcription attenuation protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
SequenceString:
MYTNSDFVVI KALEDGVNVI GLTRGADTRF HHHEHLDKGE VLIAQFTEHT SAIKVRGKAY IQTRHGVIES 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: 7.9
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) / Resolution.type: BY AUTHOR / Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12136
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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