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- PDB-7oe2: Model of closed pentamer of the Haliangium ochraceum encapsulin f... -

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Basic information

Entry
Database: PDB / ID: 7oe2
TitleModel of closed pentamer of the Haliangium ochraceum encapsulin from symmetry expansion of icosahedral single particle reconstruction
Components
  • Haliangium ochraceum Encapsulated ferritin localisation sequence
  • Linocin_M18 bacteriocin protein
KeywordsVIRUS LIKE PARTICLE / Encapsulin / encapsulated ferritin / haliangium ochraceum
Function / homology
Function and homology information


encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / intracellular iron ion homeostasis / metal ion binding
Similarity search - Function
Ferritin-like protein / EncFtn-like / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / Ferritin-like superfamily
Similarity search - Domain/homology
Encapsulated ferritin-like protein / Type 1 encapsulin shell protein
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsMarles-Wright, J. / Basle, A. / Clarke, D.J. / Ross, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N005570/1 United Kingdom
Citation
Journal: Sci Adv / Year: 2022
Title: Pore dynamics and asymmetric cargo loading in an encapsulin nanocompartment.
Authors: Jennifer Ross / Zak McIver / Thomas Lambert / Cecilia Piergentili / Jasmine Emma Bird / Kelly J Gallagher / Faye L Cruickshank / Patrick James / Efrain Zarazúa-Arvizu / Louise E Horsfall / ...Authors: Jennifer Ross / Zak McIver / Thomas Lambert / Cecilia Piergentili / Jasmine Emma Bird / Kelly J Gallagher / Faye L Cruickshank / Patrick James / Efrain Zarazúa-Arvizu / Louise E Horsfall / Kevin J Waldron / Marcus D Wilson / C Logan Mackay / Arnaud Baslé / David J Clarke / Jon Marles-Wright /
Abstract: Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant encapsulin:encapsulated ferritin ...Encapsulins are protein nanocompartments that house various cargo enzymes, including a family of decameric ferritin-like proteins. Here, we study a recombinant encapsulin:encapsulated ferritin complex using cryo-electron microscopy and hydrogen/deuterium exchange mass spectrometry to gain insight into the structural relationship between the encapsulin shell and its protein cargo. An asymmetric single-particle reconstruction reveals four encapsulated ferritin decamers in a tetrahedral arrangement within the encapsulin nanocompartment. This leads to a symmetry mismatch between the protein cargo and the icosahedral encapsulin shell. The encapsulated ferritin decamers are offset from the interior face of the encapsulin shell. Using hydrogen/deuterium exchange mass spectrometry, we observed the dynamic behavior of the major fivefold pore in the encapsulin shell and show the pore opening via the movement of the encapsulin A-domain. These data will accelerate efforts to engineer the encapsulation of heterologous cargo proteins and to alter the permeability of the encapsulin shell via pore modifications.
#1: Journal: Biorxiv / Year: 2021
Title: Model of Haliangium ochraceum encapsulin from icosahedral single particle reconstruction
Authors: Marles-Wright, J. / Basle, A. / Clarke, D.J. / Ross, J.
History
DepositionMay 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / em_admin
Item: _citation.journal_id_ISSN / _em_admin.last_update

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Linocin_M18 bacteriocin protein
B: Linocin_M18 bacteriocin protein
C: Linocin_M18 bacteriocin protein
D: Linocin_M18 bacteriocin protein
E: Linocin_M18 bacteriocin protein
1: Haliangium ochraceum Encapsulated ferritin localisation sequence
2: Haliangium ochraceum Encapsulated ferritin localisation sequence
3: Haliangium ochraceum Encapsulated ferritin localisation sequence
4: Haliangium ochraceum Encapsulated ferritin localisation sequence
5: Haliangium ochraceum Encapsulated ferritin localisation sequence


Theoretical massNumber of molelcules
Total (without water)218,31010
Polymers218,31010
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Isolated pentameric vertex of icosahedral shell
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area14670 Å2
ΔGint-57 kcal/mol
Surface area59080 Å2
MethodPISA

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Components

#1: Protein
Linocin_M18 bacteriocin protein


Mass: 28844.598 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_3837 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0LZ74
#2: Protein
Haliangium ochraceum Encapsulated ferritin localisation sequence


Mass: 14817.368 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_3836 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0LZ73
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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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: Ternary complex of Haliangium ochraceum encapsulin and encapsulated ferritin proteins
Type: COMPLEX / Details: Complex produced by co-expression in E. coli / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)Organism: Haliangium ochraceum (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Details: Solutions were prepared with MilliQ water and filtered using a 0.22 um filter.
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium ChlorideNaCl1
220 mMHEPES1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample mono disperse as determined by SEC
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K
Details: blot force -5, wait time 10 seconds and blot time of 3 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 40.509 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8109
Image scansWidth: 11520 / Height: 8184

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1RELION3.1particle selectionmanual picking followed by auto picking based on 2D classes
2EPUimage acquisition
4CTFFIND4CTF correction
5RELION3.1CTF correctionCTFrefine
8UCSF Chimera1.1.1model fitting
10PHENIX1.18model refinement
11RELION3.1initial Euler assignmentInitial model
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionDetails: CTF correction after motion correction followed by CFT refinement after 3D Refinement.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 340403
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4734551 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 86 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: CC
Details: Initial fitting performed using chimera with real space refinement in Phenix.
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00610650
ELECTRON MICROSCOPYf_angle_d0.67514490
ELECTRON MICROSCOPYf_dihedral_angle_d5.8531490
ELECTRON MICROSCOPYf_chiral_restr0.0541640
ELECTRON MICROSCOPYf_plane_restr0.0051920

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