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- EMDB-11415: Structure of left-handed protein cage consisting of 24 eleven-mem... -

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Basic information

Entry
Database: EMDB / ID: EMD-11415
TitleStructure of left-handed protein cage consisting of 24 eleven-membered ring proteins held together by DTME cross linkers
Map dataChiralA of the DTME cross-linked TRAP cage composed with 24 TRAP rings interconected with 240 DTME molecules
Sample
  • Complex: chamically induced artificial protein cage
    • Protein or peptide: Transcription attenuation protein MtrB
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.71 Å
AuthorsBiela AP / Maskell D
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2016/20/W/NZ1/00095 Poland
CitationJournal: Sci Adv / Year: 2022
Title: Chemically induced protein cage assembly with programmable opening and cargo release.
Authors: Izabela Stupka / Yusuke Azuma / Artur P Biela / Motonori Imamura / Simon Scheuring / Elżbieta Pyza / Olga Woźnicka / Daniel P Maskell / Jonathan G Heddle /
Abstract: Engineered protein cages are promising tools that can be customized for applications in medicine and nanotechnology. A major challenge is developing a straightforward strategy for endowing cages with ...Engineered protein cages are promising tools that can be customized for applications in medicine and nanotechnology. A major challenge is developing a straightforward strategy for endowing cages with bespoke, inducible disassembly. Such cages would allow release of encapsulated cargoes at desired timing and location. Here, we achieve such programmable disassembly using protein cages, in which the subunits are held together by different molecular cross-linkers. This modular system enables cage disassembly to be controlled in a condition-dependent manner. Structural details of the resulting cages were determined using cryo–electron microscopy, which allowed observation of bridging cross-linkers at intended positions. Triggered disassembly was demonstrated by high-speed atomic force microscopy and subsequent cargo release using an encapsulated Förster resonance energy transfer pair whose signal depends on the quaternary structure of the cage.
History
DepositionJul 17, 2020-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.78
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.78
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11415.png

Downloads & links

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Map

FileDownload / File: emd_11415.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChiralA of the DTME cross-linked TRAP cage composed with 24 TRAP rings interconected with 240 DTME molecules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 220 pix.
= 379.14 Å		1.72 Å/pix.
x 220 pix.
= 379.14 Å		1.72 Å/pix.
x 220 pix.
= 379.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.78 / Movie #1: 1.78
Minimum - Maximum-0.8075255 - 3.4464118
Average (Standard dev.)0.06122052 (±0.46266714)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 379.14 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.72336363636361.72336363636361.7233636363636
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z379.140379.140379.140
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.8083.4460.061

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Supplemental data

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Mask #1

Fileemd_11415_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_11415_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_11415_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : chamically induced artificial protein cage

EntireName: chamically induced artificial protein cage
Components
  • Complex: chamically induced artificial protein cage
    • Protein or peptide: Transcription attenuation protein MtrB

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Supramolecule #1: chamically induced artificial protein cage

SupramoleculeName: chamically induced artificial protein cage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: DTME cross linked protein cage
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 2.2 MDa

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Macromolecule #1: Transcription attenuation protein MtrB

MacromoleculeName: Transcription attenuation protein MtrB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYTNSDFVVI KALEDGVNVI GLTRGADTRF HHSECLDKGE VLIAQFTEHT SAIKVRGKAY IQTSHGVIES EGKK

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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

Concentration8.9 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4942 / Average exposure time: 1.0 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000
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: 4000
Details: manual picking was followed by template creation used for automated picking afterwards
CTF correctionSoftware - Name: cryoSPARC (ver. 2.14.0)
Startup modelType of model: EMDB MAP
EMDB ID:

4443


Details: low pass filtered to 20A, EMD-4443 and EMD-4444 were used as searching models
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14.0) / Number images used: 46064
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 50000 / Software - Name: cryoSPARC (ver. 2.14.0)
FSC plot (resolution estimation)

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