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Yorodumi- EMDB-12873: Asymmetric single particle reconstruction of the Haliangium ochra... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12873 | |||||||||
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Title | Asymmetric single particle reconstruction of the Haliangium ochraceum encapsulin encapsulated ferritin complex | |||||||||
Map data | Solvent flattened B-factor sharpened map from post process | |||||||||
Sample |
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Function / homology | Function and homology information encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / intracellular iron ion homeostasis / metal ion binding Similarity search - Function | |||||||||
Biological species | Haliangium ochraceum (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Marles-Wright J / Basle A / Ross J / Clarke DJ | |||||||||
Funding support | United Kingdom, 1 items
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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: To Be Published Title: Model of Haliangium ochraceum encapsulin from icosahedral single particle reconstruction Authors: Marles-Wright J / Basle A / Clarke DJ / Ross J | |||||||||
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_12873.map.gz | 80 MB | EMDB map data format | |
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Header (meta data) | emd-12873-v30.xml emd-12873.xml | 23.7 KB 23.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12873_fsc.xml | 22 KB | Display | FSC data file |
Images | emd_12873.png | 105.3 KB | ||
Masks | emd_12873_msk_1.map | 421.9 MB | Mask map | |
Others | emd_12873_additional_1.map.gz emd_12873_half_map_1.map.gz emd_12873_half_map_2.map.gz | 336.2 MB 337.4 MB 337.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12873 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12873 | HTTPS FTP |
-Validation report
Summary document | emd_12873_validation.pdf.gz | 610.1 KB | Display | EMDB validaton report |
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Full document | emd_12873_full_validation.pdf.gz | 609.7 KB | Display | |
Data in XML | emd_12873_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | emd_12873_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12873 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12873 | HTTPS FTP |
-Related structure data
Related structure data | 7odwC 7oe2C 7oeuC C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10716 (Title: Cryo electron microscopy of single particles of the Haliangium ochraceum Encapsulin:encapsulated ferritin encapsulin nano compartment Data size: 1.7 TB Data #1: Multi-frame micrographs and particle sets for Haliangium ochraceum encapsulin:encapsulated ferritin reconstruction [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12873.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Solvent flattened B-factor sharpened map from post process | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.652 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12873_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Refine 3D map
File | emd_12873_additional_1.map | ||||||||||||
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Annotation | Refine 3D map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_12873_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_12873_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of Haliangium ochraceum encapsulin and encapsulat...
Entire | Name: Ternary complex of Haliangium ochraceum encapsulin and encapsulated ferritin proteins |
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Components |
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-Supramolecule #1: Ternary complex of Haliangium ochraceum encapsulin and encapsulat...
Supramolecule | Name: Ternary complex of Haliangium ochraceum encapsulin and encapsulated ferritin proteins type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Complex produced by co-expression in E. coli |
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Source (natural) | Organism: Haliangium ochraceum (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 1.8 MDa |
-Macromolecule #1: Haliangium ochraceum encapsulin
Macromolecule | Name: Haliangium ochraceum encapsulin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Haliangium ochraceum (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MDLLKRHLAP IVPDAWSAID EEAKEIFQGH LAGRKLVDFR GPFGWEYAAV NTGELRPIDD TPEDVDMKL RQVQPLAEVR VPFTLDVTEL DSVARGATNP DLDDVARAAE RMVEAEDSAI F HGWAQAGI KGIVDSTPHE ALAVASVSDF PRAVLSAADT LRKAGVTGPY ...String: MDLLKRHLAP IVPDAWSAID EEAKEIFQGH LAGRKLVDFR GPFGWEYAAV NTGELRPIDD TPEDVDMKL RQVQPLAEVR VPFTLDVTEL DSVARGATNP DLDDVARAAE RMVEAEDSAI F HGWAQAGI KGIVDSTPHE ALAVASVSDF PRAVLSAADT LRKAGVTGPY ALVLGPKAYD DL FAATQDG YPVAKQVQRL VVDGPLVRAN ALAGALVMSM RGGDYELTVG QDLSIGYAFH DRS KVELFV AESFTFRVLE PGAAVHLRYA |
-Macromolecule #2: Haliangium ochraceum encapsulated ferritin
Macromolecule | Name: Haliangium ochraceum encapsulated ferritin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Haliangium ochraceum (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSSEQLHEPA ELLSEETKNM HRALVTLIEE LEAVDWYQQR ADACSEPGLH DVLIHNKNEE VEHAMMTLE WIRRRSPVFD AHMRTYLFTE RPILELEEED TGSSSSVAAS PTSAPSHGSL G IGSLRQEG KED |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | |||||||||
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Buffer | pH: 8 Component:
Details: Solutions were prepared with MilliQ water and filtered using a 0.22 um filter. | |||||||||
Grid | Model: Quantifoil / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV Details: blot force -5, wait time 10 seconds and blot time of 3 seconds. | |||||||||
Details | Sample mono disperse as determined by SEC |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 8109 / Average exposure time: 1.0 sec. / Average electron dose: 40.509 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Initial fitting performed using chimera with real space refinement in Phenix. |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 86 / Target criteria: CC |