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- EMDB-12526: An artificial protein cage with unusual geometry scaffolds a regu... -

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Basic information

Entry
Database: EMDB / ID: EMD-12526
TitleAn artificial protein cage with unusual geometry scaffolds a regular 3D lattice of gold nanoparticles.
Map datahalf map A
Sample
  • Complex: Supramolecular protein cage assembly with gold nano paticles lattice
    • Protein or peptide: Transcription attenuation protein MtrB
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.77 Å
AuthorsBiela AP
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: Nano Lett / Year: 2022
Title: Artificial Protein Cage with Unusual Geometry and Regularly Embedded Gold Nanoparticles.
Authors: Karolina Majsterkiewicz / Artur P Biela / Sourav Maity / Mohit Sharma / Bernard M A G Piette / Agnieszka Kowalczyk / Szymon Gaweł / Soumyananda Chakraborti / Wouter H Roos / Jonathan G Heddle /
Abstract: Artificial protein cages have great potential in a number of areas including cargo capture and delivery and as artificial vaccines. Here, we investigate an artificial protein cage whose assembly is ...Artificial protein cages have great potential in a number of areas including cargo capture and delivery and as artificial vaccines. Here, we investigate an artificial protein cage whose assembly is triggered by gold nanoparticles. Using biochemical and biophysical methods we were able to determine both the mechanical properties and the gross compositional features of the cage which, combined with mathematical models and biophysical data, allowed the structure of the cage to be predicted. The accuracy of the overall geometrical prediction was confirmed by the cryo-EM structure determined to sub-5 Å resolution. This showed the cage to be nonregular but similar to a dodecahedron, being constructed from 12 11-membered rings. Surprisingly, the structure revealed that the cage also contained a single, small gold nanoparticle at each 3-fold axis meaning that each cage acts as a synthetic framework for regular arrangement of 20 gold nanoparticles in a three-dimensional lattice.
History
DepositionMar 1, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateMay 11, 2022-
Current statusMay 11, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.41
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12526.png

Downloads & links

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Map

FileDownload / File: emd_12526.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf map A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 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: 0.41 / Movie #1: 0.41
Minimum - Maximum-0.36436516 - 3.0404563
Average (Standard dev.)0.026209798 (±0.12071204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z275.200275.200275.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.3643.0400.026

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Supplemental data

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Mask #1

Fileemd_12526_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: main map

Fileemd_12526_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_12526_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Supramolecular protein cage assembly with gold nano paticles lattice

EntireName: Supramolecular protein cage assembly with gold nano paticles lattice
Components
  • Complex: Supramolecular protein cage assembly with gold nano paticles lattice
    • Protein or peptide: Transcription attenuation protein MtrB

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Supramolecule #1: Supramolecular protein cage assembly with gold nano paticles lattice

SupramoleculeName: Supramolecular protein cage assembly with gold nano paticles lattice
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 1.6 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 KALEDGVNV I GLTRGADT RF HHSECLD KGE VLIAQF TEHT SAIKV RGKAY IQTS HGVIES EGK K

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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: 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6266 / 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 magnification: 105000
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: 1000
CTF correctionSoftware - Name: cryoSPARC (ver. 2.15.0) / Software - details: PatchCTF
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 434505
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 100 / Avg.num./class: 12000 / Software - Name: cryoSPARC (ver. 2.15.0)
FSC plot (resolution estimation)

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