+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23385 | ||||||||||||
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Title | Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S7G | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Encapsulin / Nanocompartment / VIRUS LIKE PARTICLE | ||||||||||||
Function / homology | Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / iron ion transport / intracellular iron ion homeostasis / proteolysis / Type 1 encapsulin shell protein Function and homology information | ||||||||||||
Biological species | Thermotoga maritima MSB8 (bacteria) / Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.53 Å | ||||||||||||
Authors | Andreas MP / Adamson L | ||||||||||||
Funding support | Australia, United States, 3 items
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Citation | Journal: Sci Adv / Year: 2022 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23385.map.gz | 112.7 MB | EMDB map data format | |
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Header (meta data) | emd-23385-v30.xml emd-23385.xml | 15.5 KB 15.5 KB | Display Display | EMDB header |
Images | emd_23385.png | 97.3 KB | ||
Filedesc metadata | emd-23385.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23385 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23385 | HTTPS FTP |
-Validation report
Summary document | emd_23385_validation.pdf.gz | 705.3 KB | Display | EMDB validaton report |
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Full document | emd_23385_full_validation.pdf.gz | 704.9 KB | Display | |
Data in XML | emd_23385_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | emd_23385_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23385 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23385 | HTTPS FTP |
-Related structure data
Related structure data | 7litMC 7liiC 7lijC 7likC 7lilC 7limC 7lisC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23385.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-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: Thermotoga maritima MSB8 (bacteria) |
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: Hydrolases; Acting on peptide bonds (peptidases) |
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Source (natural) | Organism: Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 |
Molecular weight | Theoretical: 29.603766 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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. |
-Electron microscopy
Microscope | TFS TALOS |
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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 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
-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: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 90905 |
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: 61.68 |
Output model | PDB-7lit: |