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- PDB-7lis: Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S5D -

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Basic information

Entry
Database: PDB / ID: 7lis
TitleThermotoga maritima Encapsulin Nanocompartment Pore Mutant S5D
ComponentsMaritimacin
KeywordsVIRUS LIKE PARTICLE / Encapsulin / Nanocompartment
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / iron ion transport / intracellular iron ion homeostasis / proteolysis
Similarity search - Function
Type 1 encapsulin shell protein / Encapsulating protein for peroxidase
Similarity search - Domain/homology
RIBOFLAVIN / Type 1 encapsulin shell protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsAndreas, M.P. / Adamson, L. / Tasneem, N. / Close, W. / Giessen, T. / Lau, Y.H.
Funding support Australia, United States, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE190100624 Australia
Other privateWRF2020 Australia
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133325 United States
CitationJournal: 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
DepositionJan 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-23384
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Maritimacin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4682
Polymers30,0911
Non-polymers3761
Water0
1
A: Maritimacin
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,828,059120
Polymers1,805,47760
Non-polymers22,58260
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Maritimacin
hetero molecules
x 5


  • icosahedral pentamer
  • 152 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)152,33810
Polymers150,4565
Non-polymers1,8825
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Maritimacin
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 183 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)182,80612
Polymers180,5486
Non-polymers2,2586
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Maritimacin / Thermotoga bacteriocin / Encapsulin Nanocompartment Pore


Mass: 30091.287 Da / Num. of mol.: 1 / Mutation: E184D,P189D, Del(185-188)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0785 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9WZP2, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N4O6
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Thermotoga maritima Encapsulin Nanocompartment Pore Mutant S5D
Type: COMPLEX
Details: Thermotoga maratima encapsulin pore mutant with E184D, P189D, and deletion of amino acids A185-Y188
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1.825782 MDa / Experimental value: NO
Source (natural)Organism: Thermotoga maritima MSB8 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium ChlorideNaClSodium chloride1
220 mMTrisC4H11NO31
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/2
VitrificationInstrument: 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

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -2500 nm / Nominal defocus min: -1000 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 47.84 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1cryoSPARC2.15.0particle selection
2Leginonimage acquisition
4cryoSPARC2.15.0CTF correction
7UCSF Chimeramodel fitting
8Coot0.9model fitting
10cryoSPARC2.15.0initial Euler assignment
11cryoSPARC2.15.0final Euler assignment
13cryoSPARC2.15.03D reconstruction
14PHENIX1.18.2-3874-000model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33416 / Symmetry type: POINT
Atomic model buildingB value: 51.86 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 3DKT

3dkt


Pdb chain-ID: A / Pdb chain residue range: 1-265

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