+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24145 | |||||||||
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Title | Structure of commercially purchased Apoferritin | |||||||||
Map data | Cryo-EM map of Apoferritin purchased commercially | |||||||||
Sample |
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Biological species | Equus ferus (tarpan) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.91 Å | |||||||||
Authors | Moser TJ / Parvate AD / Evans JE | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Cryo-EM structure of the diapause chaperone artemin. Authors: Amar D Parvate / Samantha M Powell / Jory T Brookreson / Trevor H Moser / Irina V Novikova / Mowei Zhou / James E Evans / Abstract: The protein artemin acts as both an RNA and protein chaperone and constitutes over 10% of all protein in cysts during diapause. However, its mechanistic details remain elusive since no high- ...The protein artemin acts as both an RNA and protein chaperone and constitutes over 10% of all protein in cysts during diapause. However, its mechanistic details remain elusive since no high-resolution structure of artemin exists. Here we report the full-length structure of artemin at 2.04 Å resolution. The cryo-EM map contains density for an intramolecular disulfide bond between Cys22-Cys61 and resolves the entire C-terminus extending into the core of the assembled protein cage but in a different configuration than previously hypothesized with molecular modeling. We also provide data supporting the role of C-terminal helix F towards stabilizing the dimer form that is believed to be important for its chaperoning activity. We were able to destabilize this effect by placing a tag at the C-terminus to fully pack the internal cavity and cause limited steric hindrance. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24145.map.gz | 97.1 MB | EMDB map data format | |
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Header (meta data) | emd-24145-v30.xml emd-24145.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_24145.png | 53.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24145 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24145 | HTTPS FTP |
-Validation report
Summary document | emd_24145_validation.pdf.gz | 524.5 KB | Display | EMDB validaton report |
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Full document | emd_24145_full_validation.pdf.gz | 524 KB | Display | |
Data in XML | emd_24145_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_24145_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24145 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24145 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24145.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map of Apoferritin purchased commercially | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.4108 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Apoferritin
Entire | Name: Apoferritin |
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Components |
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-Supramolecule #1: Apoferritin
Supramolecule | Name: Apoferritin / type: complex / ID: 1 / Parent: 0 Details: Commercially purchased fully assembled protein complex |
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Source (natural) | Organism: Equus ferus (tarpan) |
Molecular weight | Theoretical: 444 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 Details: Solutions made fresh and filtered with 0.22 micron filter for sterility. |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: LEICA EM GP / Details: 2 s blot. |
Details | Sample was monodisperse and suspended in TBS |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Phase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 11028 / Average exposure time: 0.5 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -1.3 µm / Nominal defocus min: -0.3 µm / Nominal magnification: 215000 |
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
Refinement | Protocol: AB INITIO MODEL |
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