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- EMDB-9383: Encapsulin iron storage compartment from Quasibacillus thermotolerans -

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Basic information

Entry
Database: EMDB / ID: EMD-9383
TitleEncapsulin iron storage compartment from Quasibacillus thermotolerans
Map dataFinal EM map filtered to 3.85A with applied sharpening B-factor of -151
Sample
  • Complex: Encapsulin iron storage compartment from Quasibacillus thermotolerans
    • Protein or peptide: Encapsulating protein for a DyP-type peroxidase
    • Protein or peptide: targeting peptide
Keywordsencapsulin / iron storage / IMEF / icosahedral / METAL TRANSPORT
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 speciesBacillus thermotolerans (bacteria) / Quasibacillus thermotolerans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsOrlando BJ / Giessen TW
Funding support Germany, 1 items
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, 2019-
Header (metadata) releaseJan 23, 2019-
Map releaseAug 7, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9383.png

Downloads & links

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Map

FileDownload / File: emd_9383.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal EM map filtered to 3.85A with applied sharpening B-factor of -151
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 480 pix.
= 655.2 Å		1.37 Å/pix.
x 480 pix.
= 655.2 Å		1.37 Å/pix.
x 480 pix.
= 655.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.365 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.017820705 - 0.047575288
Average (Standard dev.)0.00001933848 (±0.0032247843)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin240240240
Dimensions480480480
Spacing480480480
CellA=B=C: 655.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3651.3651.365
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z655.200655.200655.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ344344344
MAP C/R/S123
start NC/NR/NS240240240
NC/NR/NS480480480
D min/max/mean-0.0180.0480.000

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Supplemental data

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Additional map: Final unfiltered EM map

Fileemd_9383_additional.map
AnnotationFinal unfiltered EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Encapsulin iron storage compartment from Quasibacillus thermotolerans

EntireName: Encapsulin iron storage compartment from Quasibacillus thermotolerans
Components
  • Complex: Encapsulin iron storage compartment from Quasibacillus thermotolerans
    • Protein or peptide: Encapsulating protein for a DyP-type peroxidase
    • Protein or peptide: targeting peptide

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Supramolecule #1: Encapsulin iron storage compartment from Quasibacillus thermotolerans

SupramoleculeName: Encapsulin iron storage compartment from Quasibacillus thermotolerans
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus thermotolerans (bacteria)
Molecular weightTheoretical: 9.6 MDa

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Macromolecule #1: Encapsulating protein for a DyP-type peroxidase

MacromoleculeName: Encapsulating protein for a DyP-type peroxidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Quasibacillus thermotolerans (bacteria)
Molecular weightTheoretical: 32.239459 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKSQLYPDS PLTDQDFNQL DQTVIEAARR QLVGRRFIEL YGPLGRGMQS VFNDIFMESH EAKMDFQGSF DTEVESSRRV NYTIPMLYK DFVLYWRDLE QSKALDIPID FSVAANAARD VAFLEDQMIF HGSKEFDIPG LMNVKGRLTH LIGNWYESGN A FQDIVEAR ...String:
MNKSQLYPDS PLTDQDFNQL DQTVIEAARR QLVGRRFIEL YGPLGRGMQS VFNDIFMESH EAKMDFQGSF DTEVESSRRV NYTIPMLYK DFVLYWRDLE QSKALDIPID FSVAANAARD VAFLEDQMIF HGSKEFDIPG LMNVKGRLTH LIGNWYESGN A FQDIVEAR NKLLEMNHNG PYALVLSPEL YSLLHRVHKD TNVLEIEHVR ELITAGVFQS PVLKGKSGVI VNTGRNNLDL AI SEDFETA YLGEEGMNHP FRVYETVVLR IKRPAAICTL IDPEE

UniProtKB: Type 1 encapsulin shell protein

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Macromolecule #2: targeting peptide

MacromoleculeName: targeting peptide / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus thermotolerans (bacteria)
Molecular weightTheoretical: 716.824 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TVGSLIQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 601 / Average exposure time: 7.2 sec. / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18995
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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