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- EMDB-6966: Structure of protein cage consisting of 24 eleven-membered ring p... -

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Basic information

Entry
Database: EMDB / ID: EMD-6966
TitleStructure of protein cage consisting of 24 eleven-membered ring proteins induced by addition of gold nanoparticle (GNP)
Map data
Sample
  • Complex: Designed protein cage consisting of C11-symmetric TRAP proteins assembled with gold nanoparticlesDesign
    • Protein or peptide: Transcription attenuation protein MtrB
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: 5.9 Å
AuthorsMalay AD / Miyazaki N / Biela A / Chakraborti S / Majsterkiewicz K / Kaplan CS / Hochberg GKA / Wu D / Wrobel TP / Benesch JLP ...Malay AD / Miyazaki N / Biela A / Chakraborti S / Majsterkiewicz K / Kaplan CS / Hochberg GKA / Wu D / Wrobel TP / Benesch JLP / Iwasaki K / Heddle JG / Kelemen P / Vavpetic P / Pelicon P
CitationJournal: Nature / Year: 2019
Title: An ultra-stable gold-coordinated protein cage displaying reversible assembly.
Authors: Ali D Malay / Naoyuki Miyazaki / Artur Biela / Soumyananda Chakraborti / Karolina Majsterkiewicz / Izabela Stupka / Craig S Kaplan / Agnieszka Kowalczyk / Bernard M A G Piette / Georg K A ...Authors: Ali D Malay / Naoyuki Miyazaki / Artur Biela / Soumyananda Chakraborti / Karolina Majsterkiewicz / Izabela Stupka / Craig S Kaplan / Agnieszka Kowalczyk / Bernard M A G Piette / Georg K A Hochberg / Di Wu / Tomasz P Wrobel / Adam Fineberg / Manish S Kushwah / Mitja Kelemen / Primož Vavpetič / Primož Pelicon / Philipp Kukura / Justin L P Benesch / Kenji Iwasaki / Jonathan G Heddle /
Abstract: Symmetrical protein cages have evolved to fulfil diverse roles in nature, including compartmentalization and cargo delivery, and have inspired synthetic biologists to create novel protein assemblies ...Symmetrical protein cages have evolved to fulfil diverse roles in nature, including compartmentalization and cargo delivery, and have inspired synthetic biologists to create novel protein assemblies via the precise manipulation of protein-protein interfaces. Despite the impressive array of protein cages produced in the laboratory, the design of inducible assemblies remains challenging. Here we demonstrate an ultra-stable artificial protein cage, the assembly and disassembly of which can be controlled by metal coordination at the protein-protein interfaces. The addition of a gold (I)-triphenylphosphine compound to a cysteine-substituted, 11-mer protein ring triggers supramolecular self-assembly, which generates monodisperse cage structures with masses greater than 2 MDa. The geometry of these structures is based on the Archimedean snub cube and is, to our knowledge, unprecedented. Cryo-electron microscopy confirms that the assemblies are held together by 120 S-Au-S staples between the protein oligomers, and exist in two chiral forms. The cage shows extreme chemical and thermal stability, yet it readily disassembles upon exposure to reducing agents. As well as gold, mercury(II) is also found to enable formation of the protein cage. This work establishes an approach for linking protein components into robust, higher-order structures, and expands the design space available for supramolecular assemblies to include previously unexplored geometries.
History
DepositionMay 10, 2018-
Header (metadata) releaseMar 6, 2019-
Map releaseMar 6, 2019-
UpdateMay 29, 2019-
Current statusMay 29, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6966.png

Downloads & links

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Map

FileDownload / File: emd_6966.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.74 Å
Density
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.06308363 - 0.20576885
Average (Standard dev.)0.002216382 (±0.018433945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 382.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.741.741.74
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z382.800382.800382.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0630.2060.002

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Supplemental data

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Sample components

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Entire : Designed protein cage consisting of C11-symmetric TRAP proteins a...

EntireName: Designed protein cage consisting of C11-symmetric TRAP proteins assembled with gold nanoparticlesDesign
Components
  • Complex: Designed protein cage consisting of C11-symmetric TRAP proteins assembled with gold nanoparticlesDesign
    • Protein or peptide: Transcription attenuation protein MtrB

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Supramolecule #1: Designed protein cage consisting of C11-symmetric TRAP proteins a...

SupramoleculeName: Designed protein cage consisting of C11-symmetric TRAP proteins assembled with gold nanoparticles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pET21b
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 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

Concentration0.89 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10.0 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3.0 s blotting time.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58157
FSC plot (resolution estimation)

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