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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23385 | ||||||||||||
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Title | Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G | ||||||||||||
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Function / homology | Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Andreas MP / Adamson L | ||||||||||||
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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 112.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.5 KB 15.5 KB | Display Display | ![]() |
Images | ![]() | 97.3 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7litMC ![]() 7liiC ![]() 7lijC ![]() 7likC ![]() 7lilC ![]() 7limC ![]() 7lisC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.986 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G
Entire | Name: Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G |
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Components |
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-Supramolecule #1: Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G
Supramolecule | Name: Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Thermotoga maratima encapsulin pore mutant with K182G, L190G, and deletion of amino acids K182-P189 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 1.796591 MDa |
-Macromolecule #1: Maritimacin
Macromolecule | Name: Maritimacin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 |
Molecular weight | Theoretical: 29.603766 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD ENEVVKWGLR KSLPLIELRA TFTLDLWEL DNLERGKPNV DLSSLEETVR KVAEFEDEVI FRGCEKSGVK GLLSFEERKI ECGSTPKDLL EAIVRALSIF S KDGIEGPY ...String: MEFLKRSFAP LTEKQWQEID NRAREIFKTQ LYGRKFVDVE GPYGWEYAAH PLGEVEVLSD ENEVVKWGLR KSLPLIELRA TFTLDLWEL DNLERGKPNV DLSSLEETVR KVAEFEDEVI FRGCEKSGVK GLLSFEERKI ECGSTPKDLL EAIVRALSIF S KDGIEGPY TLVINTDRWI NFLGGEKRVE ECLRGGKIIT TPRIEDALVV SERGGDFKLI LGQDLSIGYE DREKDAVRLF IT ETFTFQV VNPEALILLK F UniProtKB: Type 1 encapsulin shell protein |
-Macromolecule #2: RIBOFLAVIN
Macromolecule | Name: RIBOFLAVIN / type: ligand / ID: 2 / Number of copies: 1 / Formula: RBF |
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Molecular weight | Theoretical: 376.364 Da |
Chemical component information | ![]() ChemComp-RBF: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 2.0 mg/mL | |||||||||
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Buffer | pH: 8 Component:
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Grid | Model: C-flat-2/2 / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, wait time 30 seconds. |
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Electron microscopy
Microscope | TFS TALOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 47.84 sec. / Average electron dose: 40.0 e/Å2 |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: Initial map for refinements made from PDB entry 3DKT |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.15.0) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.15.0) |
Final reconstruction | Applied symmetry - Point group: I (icosahedral![]() |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Residue range: 1-265 / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 61.68 |
Output model | ![]() PDB-7lit: |