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- EMDB-10725: OP protein cage, complex 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-10725
TitleOP protein cage, complex 2
Map dataOP protein cage, complex 2
Sample
  • Complex: OP protein cage
    • Protein or peptide: OP protein cage, complex 2
Biological speciesSalmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsEdwardson TGW / Tetter S / Hilvert D
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-AdG-2012-321295 Switzerland
Human Frontier Science Program (HFSP)LT000971/2016 Switzerland
CitationJournal: Nat Commun / Year: 2020
Title: Two-tier supramolecular encapsulation of small molecules in a protein cage.
Authors: Thomas G W Edwardson / Stephan Tetter / Donald Hilvert /
Abstract: Expanding protein design to include other molecular building blocks has the potential to increase structural complexity and practical utility. Nature often employs hybrid systems, such as clathrin- ...Expanding protein design to include other molecular building blocks has the potential to increase structural complexity and practical utility. Nature often employs hybrid systems, such as clathrin-coated vesicles, lipid droplets, and lipoproteins, which combine biopolymers and lipids to transport a broader range of cargo molecules. To recapitulate the structure and function of such composite compartments, we devised a supramolecular strategy that enables porous protein cages to encapsulate poorly water-soluble small molecule cargo through templated formation of a hydrophobic surfactant-based core. These lipoprotein-like complexes protect their cargo from sequestration by serum proteins and enhance the cellular uptake of fluorescent probes and cytotoxic drugs. This design concept could be applied to other protein cages, surfactant mixtures, and cargo molecules to generate unique hybrid architectures and functional capabilities.
History
DepositionMar 3, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateNov 18, 2020-
Current statusNov 18, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0736
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0736
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10725.png

Downloads & links

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Map

FileDownload / File: emd_10725.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOP protein cage, complex 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 200 pix.
= 360. Å		1.8 Å/pix.
x 200 pix.
= 360. Å		1.8 Å/pix.
x 200 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0736 / Movie #1: 0.0736
Minimum - Maximum-0.041934736 - 0.12776837
Average (Standard dev.)0.0009391138 (±0.011009874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0420.1280.001

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Supplemental data

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Mask #1

Fileemd_10725_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10725_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10725_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OP protein cage

EntireName: OP protein cage
Components
  • Complex: OP protein cage
    • Protein or peptide: OP protein cage, complex 2

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Supramolecule #1: OP protein cage

SupramoleculeName: OP protein cage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Positively supercharged variant of the computationally designed cage protein O3-33
Source (natural)Organism: Salmonella enterica (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Macromolecule #1: OP protein cage, complex 2

MacromoleculeName: OP protein cage, complex 2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MSQAIGILEL RSIAAGMELG DAMLKSANVD LLVSKTISRG KFLLMLGGDI GAIQQAIETG TSQAGRLLVD SLVLANIHPS VLPAISGLNS VDKRQAVGIV ETRSVAACIS AADRAVKGSN VTLVRVHMAR GIGGKCYMVV AGDVSDVALA VTVASSSAGA YGRLVYASLI PRPHEAMWRQ MVEGLEHHHH HH

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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

BufferpH: 7.4 / Details: 25 mM Tris-HCl, 200 mM NaCl, 5 mM EDTA, pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 22 K / Details: blot for 12 s, 25 blot strength, before plunging.

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 127 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: -3.3 µm / Nominal defocus min: -1.8 µm / Nominal magnification: 62000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 12174
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: NONE
Details: The initial model was generated from the data themselves, with octahedral symmetry imposed.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2499
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 1461 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6fdb

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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