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- PDB-6nj8: Encapsulin iron storage compartment from Quasibacillus thermotolerans -

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Basic information

Entry
Database: PDB / ID: 6nj8
TitleEncapsulin iron storage compartment from Quasibacillus thermotolerans
Components
  • Encapsulating protein for a DyP-type peroxidase
  • targeting peptide
KeywordsMETAL TRANSPORT / encapsulin / iron storage / IMEF / icosahedral
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / iron ion transport / intracellular iron ion homeostasis / Type 1 encapsulin shell protein
Function and homology information
Biological speciesQuasibacillus thermotolerans (bacteria)
Bacillus thermotolerans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsOrlando, B.J. / Giessen, T.W. / Chambers, M.G. / Liao, M. / Silver, P.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchLPDS 2014-05 Germany
CitationJournal: Elife / Year: 2019
Title: Large protein organelles form a new iron sequestration system with high storage capacity.
Authors: Tobias W Giessen / Benjamin J Orlando / Andrew A Verdegaal / Melissa G Chambers / Jules Gardener / David C Bell / Gabriel Birrane / Maofu Liao / Pamela A Silver /
Abstract: Iron storage proteins are essential for cellular iron homeostasis and redox balance. Ferritin proteins are the major storage units for bioavailable forms of iron. Some organisms lack ferritins, and ...Iron storage proteins are essential for cellular iron homeostasis and redox balance. Ferritin proteins are the major storage units for bioavailable forms of iron. Some organisms lack ferritins, and it is not known how they store iron. Encapsulins, a class of protein-based organelles, have recently been implicated in microbial iron and redox metabolism. Here, we report the structural and mechanistic characterization of a 42 nm two-component encapsulin-based iron storage compartment from . Using cryo-electron microscopy and x-ray crystallography, we reveal the assembly principles of a thermostable T = 4 shell topology and its catalytic ferroxidase cargo and show interactions underlying cargo-shell co-assembly. This compartment has an exceptionally large iron storage capacity storing over 23,000 iron atoms. Our results reveal a new approach for survival in diverse habitats with limited or fluctuating iron availability via an iron storage system able to store 10 to 20 times more iron than ferritin.
History
DepositionJan 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • 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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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Encapsulating protein for a DyP-type peroxidase
B: Encapsulating protein for a DyP-type peroxidase
C: Encapsulating protein for a DyP-type peroxidase
D: Encapsulating protein for a DyP-type peroxidase
E: targeting peptide
F: targeting peptide
G: targeting peptide


Theoretical massNumber of molelcules
Total (without water)131,1087
Polymers131,1087
Non-polymers00
Water0
1
A: Encapsulating protein for a DyP-type peroxidase
B: Encapsulating protein for a DyP-type peroxidase
C: Encapsulating protein for a DyP-type peroxidase
D: Encapsulating protein for a DyP-type peroxidase
E: targeting peptide
F: targeting peptide
G: targeting peptide
x 60


Theoretical massNumber of molelcules
Total (without water)7,866,498420
Polymers7,866,498420
Non-polymers00
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: Encapsulating protein for a DyP-type peroxidase
B: Encapsulating protein for a DyP-type peroxidase
C: Encapsulating protein for a DyP-type peroxidase
D: Encapsulating protein for a DyP-type peroxidase
E: targeting peptide
F: targeting peptide
G: targeting peptide
x 5


  • icosahedral pentamer
  • 656 kDa, 35 polymers
Theoretical massNumber of molelcules
Total (without water)655,54235
Polymers655,54235
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Encapsulating protein for a DyP-type peroxidase
B: Encapsulating protein for a DyP-type peroxidase
C: Encapsulating protein for a DyP-type peroxidase
D: Encapsulating protein for a DyP-type peroxidase
E: targeting peptide
F: targeting peptide
G: targeting peptide
x 6


  • icosahedral 23 hexamer
  • 787 kDa, 42 polymers
Theoretical massNumber of molelcules
Total (without water)786,65042
Polymers786,65042
Non-polymers00
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
Encapsulating protein for a DyP-type peroxidase


Mass: 32239.459 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Quasibacillus thermotolerans (bacteria)
Gene: QY95_01592 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F5HPP7
#2: Protein/peptide targeting peptide


Mass: 716.824 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thermotolerans (bacteria) / Production host: Escherichia coli (E. coli)

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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: Encapsulin iron storage compartment from Quasibacillus thermotolerans
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 9.6 MDa / Experimental value: NO
Source (natural)Organism: Bacillus thermotolerans (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 7.2 sec. / Electron dose: 44 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 601

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Processing

EM software
IDNameVersionCategory
2UCSFImage4image acquisition
7I-TASSERmodel fitting
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18995 / Symmetry type: POINT

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