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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23380 | ||||||||||||
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Title | Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S1K | ||||||||||||
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![]() | Encapsulin / Nanocompartment / VIRUS LIKE PARTICLE | ||||||||||||
Function / homology | ![]() encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / iron ion transport / intracellular iron ion homeostasis / proteolysis Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||||||||
![]() | 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 | ![]() | 204 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
Images | ![]() | 96.3 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lijMC ![]() 7liiC ![]() 7likC ![]() 7lilC ![]() 7limC ![]() 7lisC ![]() 7litC 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: 0.98 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 maratima Pore Mutant S1K
Entire | Name: Thermotoga maratima Pore Mutant S1K |
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Components |
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-Supramolecule #1: Thermotoga maratima Pore Mutant S1K
Supramolecule | Name: Thermotoga maratima Pore Mutant S1K / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Thermotoga maratima encapsulin pore mutant with H187K mutation |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1.850714 MDa |
-Macromolecule #1: Maritimacin
Macromolecule | Name: Maritimacin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on peptide bonds (peptidases) |
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Source (natural) | Organism: ![]() ![]() Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 |
Molecular weight | Theoretical: 30.507818 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 NFLKEEAGKY PLEKRVEECL RGGKIITTPR IEDALVVSER GGDFKLILGQ DLSIGYEDRE KD AVRLFIT ETFTFQVVNP EALILLKF 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 | cryo EM |
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![]() | single particle reconstruction |
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: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 60 seconds at 5 mA | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: blot 4 seconds, force 20 immediately prior to plunging into ethane. |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average exposure time: 8.0 sec. / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.8 µm / Nominal defocus min: -1.3 µm / Nominal magnification: 45000 |
Sample stage | Cooling holder cryogen: NITROGEN |
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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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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 58162 |
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) |
-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: 22.03 |
Output model | ![]() PDB-7lij: |