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Open data
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Basic information
Entry | Database: PDB / ID: 7lit | ||||||||||||
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Title | Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G | ||||||||||||
![]() | Maritimacin | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Andreas, M.P. / Adamson, L. / Tasneem, N. / Close, W. / Giessen, T. / Lau, Y.H. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Pore structure controls stability and molecular flux in engineered protein cages. Authors: Lachlan S R Adamson / Nuren Tasneem / Michael P Andreas / William Close / Eric N Jenner / Taylor N Szyszka / Reginald Young / Li Chen Cheah / Alexander Norman / Hugo I MacDermott-Opeskin / ...Authors: Lachlan S R Adamson / Nuren Tasneem / Michael P Andreas / William Close / Eric N Jenner / Taylor N Szyszka / Reginald Young / Li Chen Cheah / Alexander Norman / Hugo I MacDermott-Opeskin / Megan L O'Mara / Frank Sainsbury / Tobias W Giessen / Yu Heng Lau / ![]() ![]() Abstract: Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of ...Protein cages are a common architectural motif used by living organisms to compartmentalize and control biochemical reactions. While engineered protein cages have featured in the construction of nanoreactors and synthetic organelles, relatively little is known about the underlying molecular parameters that govern stability and flux through their pores. In this work, we systematically designed 24 variants of the encapsulin cage, featuring pores of different sizes and charges. Twelve pore variants were successfully assembled and purified, including eight designs with exceptional thermal stability. While negatively charged mutations were better tolerated, we were able to form stable assemblies covering a full range of pore sizes and charges, as observed in seven new cryo-EM structures at 2.5- to 3.6-Å resolution. Molecular dynamics simulations and stopped-flow experiments revealed the importance of considering both pore size and charge, together with flexibility and rate-determining steps, when designing protein cages for controlling molecular flux. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.6 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 23385MC ![]() 7liiC ![]() 7lijC ![]() 7likC ![]() 7lilC ![]() 7limC ![]() 7lisC 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
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Symmetry | Point symmetry: (Schoenflies symbol![]() ![]() |
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Components
#1: Protein | Mass: 29603.766 Da / Num. of mol.: 1 / Mutation: K182G, L190G, Del(182-189) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0785 / Production host: ![]() ![]() ![]() References: UniProt: Q9WZP2, ![]() |
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#2: Chemical | ChemComp-RBF / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G Type: COMPLEX Details: Thermotoga maratima encapsulin pore mutant with K182G, L190G, and deletion of amino acids K182-P189 Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Value: 1.796591 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | |||||||||||||||
Source (recombinant) | Organism: ![]() ![]() ![]() | |||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||
Specimen support | Grid type: C-flat-2/2 | |||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: blot force 0, wait time 30 seconds |
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Electron microscopy imaging
Microscopy | Model: TFS TALOS |
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Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 47.84 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90905 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 61.68 / Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3DKT Pdb chain-ID: A / Accession code: 3DKT / Pdb chain residue range: 1-265 / Source name: PDB / Type: experimental model |