+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13420 | |||||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis encapsulin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Encapsulin / icosahedral / oxidative stress response / STRUCTURAL PROTEIN | |||||||||
Function / homology | : / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / encapsulin nanocompartment / extracellular region / plasma membrane / Type 1 encapsulin shell protein Function and homology information | |||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Woodward JD | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Mycobacterium tuberculosis encapsulin Authors: Woodward JD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13420.map.gz | 288.1 MB | EMDB map data format | |
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Header (meta data) | emd-13420-v30.xml emd-13420.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13420_fsc.xml | 15.1 KB | Display | FSC data file |
Images | emd_13420.png | 209.9 KB | ||
Filedesc metadata | emd-13420.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13420 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13420 | HTTPS FTP |
-Validation report
Summary document | emd_13420_validation.pdf.gz | 707.8 KB | Display | EMDB validaton report |
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Full document | emd_13420_full_validation.pdf.gz | 707.4 KB | Display | |
Data in XML | emd_13420_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | emd_13420_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13420 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13420 | HTTPS FTP |
-Related structure data
Related structure data | 7phmMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13420.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Empty encapsulin nanocompartment
Entire | Name: Empty encapsulin nanocompartment |
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Components |
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-Supramolecule #1: Empty encapsulin nanocompartment
Supramolecule | Name: Empty encapsulin nanocompartment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 1.73 MDa |
-Macromolecule #1: 29 kDa antigen CFP29
Macromolecule | Name: 29 kDa antigen CFP29 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) / Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 29.554072 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MNNLYRDLAP VTEAAWAEIE LEAARTFKRH IAGRRVVDVS DPGGPVTAAV STGRLIDVKA PTNGVIAHLR ASKPLVRLRV PFTLSRNEI DDVERGSKDS DWEPVKEAAK KLAFVEDRTI FEGYSAASIE GIRSASSNPA LTLPEDPREI PDVISQALSE L RLAGVDGP ...String: MNNLYRDLAP VTEAAWAEIE LEAARTFKRH IAGRRVVDVS DPGGPVTAAV STGRLIDVKA PTNGVIAHLR ASKPLVRLRV PFTLSRNEI DDVERGSKDS DWEPVKEAAK KLAFVEDRTI FEGYSAASIE GIRSASSNPA LTLPEDPREI PDVISQALSE L RLAGVDGP YSVLLSADVY TKVSETSDHG YPIREHLNRL VDGDIIWAPA IDGAFVLTTR GGDFDLQLGT DVAIGYASHD TD TVRLYLQ ETLTFLCYTA EASVALSHHH HHH UniProtKB: Type 1 encapsulin shell protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL | |||||||||||||||
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Buffer | pH: 7.4 Component:
Details: Eluted in: 50mM Tris-HCl, 350mM NaCl, 10mM Imidazol, 10% v/v glycerol at pH 7.4 and diluted 1:2 in distilled water. | |||||||||||||||
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa Details: Glow-discharged using an EMS100X in air: 25 mA at 20 Pa for 30 seconds. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | C-flat 2/2 holey carbon film supported by a standard copper TEM grid and coated with an ultrathin (2-3 nm) continuous carbon film. |
-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: 14133 / Average electron dose: 45.0 e/Å2 Details: Data collected in super-resolution mode at 0.53 A/pixel and down-sampled during motion correction to 1.06 A/pixel. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
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 | Model was generated ab initio using Buccaneer within the CCPEM package and manually corrected using Coot before being refined using Isolde within ChimeraX and Phenix Real Space Refinement within the CCPEM package. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient |
Output model | PDB-7phm: |