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- PDB-6rvv: Structure of left-handed protein cage consisting of 24 eleven-mem... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rvv | ||||||||||||||||||
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Title | Structure of left-handed protein cage consisting of 24 eleven-membered ring proteins held together by gold (I) bridges. | ||||||||||||||||||
![]() | Transcription attenuation protein MtrB | ||||||||||||||||||
![]() | RNA BINDING PROTEIN / TRAP / protein cage / gold binding / snub cube | ||||||||||||||||||
Function / homology | ![]() DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
![]() | Malay, A.D. / Miyazaki, N. / Biela, A.P. / Iwasaki, K. / Heddle, J.G. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 2.3 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4443MC ![]() 4444C ![]() 6966C ![]() 6rvwC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 8161.224 Da / Num. of mol.: 264 / Mutation: K35C, R64S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mtrB / Production host: ![]() ![]() #2: Chemical | ChemComp-AU / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: LH TRAP protein cage / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 2.16 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.89 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3.0 s blotting time |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Width: 4096 / Height: 4096 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82125 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Target criteria: gradient-driven minimization of combined map and restraints target | ||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Accession code: 4V4F / Initial refinement model-ID: 1 / PDB-ID: 4V4F / Source name: PDB / Type: experimental model
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