|Entry||Database: EMDB / ID: EMD-4444|
|Title||Structure of right-handed protein cage consisting of 24 eleven-membered ring proteins held together by gold (I) bridges.|
|Sample||Designed protein cage consisting of C11-symmetric TRAP proteins coordinated by Au+1 ionsDesign:|
Transcription attenuation protein MtrB / ligand
|Function / homology||Transcription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein-like domain superfamily / Tryptophan RNA-binding attenuator protein domain / DNA-templated transcription, termination / regulation of transcription, DNA-templated / RNA binding / identical protein binding / Transcription attenuation protein MtrB|
Function and homology information
|Biological species||Geobacillus stearothermophilus (bacteria)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.7 Å|
|Authors||Malay AD / Miyazaki N / Biela AP / Iwasaki K / Heddle JG|
|Citation||Journal: 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.
|Validation Report||PDB-ID: 6rvw|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_4444.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.74 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Designed protein cage consisting of C11-symmetric TRAP proteins c...
|Entire||Name: Designed protein cage consisting of C11-symmetric TRAP proteins coordinated by Au+1 ionsDesign|
Number of components: 3
-Component #1: protein, Designed protein cage consisting of C11-symmetric TRAP p...
|Protein||Name: Designed protein cage consisting of C11-symmetric TRAP proteins coordinated by Au+1 ionsDesign|
Recombinant expression: No
|Mass||Experimental: 2.2 MDa|
|Source||Species: Geobacillus stearothermophilus (bacteria)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Vector: pET21b / Strain: BL21(DE3)|
-Component #2: protein, Transcription attenuation protein MtrB
|Protein||Name: Transcription attenuation protein MtrB / Number of Copies: 264 / Recombinant expression: No|
|Mass||Theoretical: 8.161224 kDa|
|Source||Species: Geobacillus stearothermophilus (bacteria)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
-Component #3: ligand, GOLD ION
|Ligand||Name: GOLD ION / Number of Copies: 120 / Recombinant expression: No|
|Mass||Theoretical: 0.196967 kDa|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.89 mg/mL / pH: 8|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: 3.0 s blotting time.|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 176463|
|3D reconstruction||Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF|
|FSC plot (resolution estimation)|
-Atomic model buiding
|Modeling #1||Target criteria: gradient-driven minimization of combined map and restraints target|
Refinement space: REAL
Input PDB model: 4V4F, 4V4F, 4V4F, 4V4F, 4V4F, 4V4F, 4V4F, 4V4F, 4V4F, 4V4F, 4V4F
Chain ID: AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK
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