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Yorodumi- EMDB-18031: Cryo-EM structure of the DyP peroxidase-loaded encapsulin nanocom... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18031 | |||||||||
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Title | Cryo-EM structure of the DyP peroxidase-loaded encapsulin nanocompartment from Mycobacterium tuberculosis with icosahedral symmetry imposed. | |||||||||
Map data | The 2.7 A resolution cryo-EM reconstruction of Mycobacterium tuberculosis encapsulin containing DyP peroxidase | |||||||||
Sample |
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Keywords | Encapsulin / cfp29 / nanocompartment / VIRUS LIKE PARTICLE | |||||||||
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: 2.7 Å | |||||||||
Authors | Willmore R / Woodward JD | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: To Be Published Title: The 2.7 A resolution cryo-EM reconstruction of Mycobacterium tuberculosis encapsulin nanocompartment containing DyP peroxidase. Authors: Willmore R / Woodward JD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18031.map.gz | 228.3 MB | EMDB map data format | |
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Header (meta data) | emd-18031-v30.xml emd-18031.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18031_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_18031.png | 61 KB | ||
Filedesc metadata | emd-18031.cif.gz | 5.8 KB | ||
Others | emd_18031_half_map_1.map.gz emd_18031_half_map_2.map.gz | 193.7 MB 193.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18031 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18031 | HTTPS FTP |
-Validation report
Summary document | emd_18031_validation.pdf.gz | 928.6 KB | Display | EMDB validaton report |
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Full document | emd_18031_full_validation.pdf.gz | 928.1 KB | Display | |
Data in XML | emd_18031_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_18031_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18031 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18031 | HTTPS FTP |
-Related structure data
Related structure data | 8pysMC 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_18031.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | The 2.7 A resolution cryo-EM reconstruction of Mycobacterium tuberculosis encapsulin containing DyP peroxidase | ||||||||||||||||||||||||||||||||||||
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
-Half map: Half map 1
File | emd_18031_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_18031_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : DyP cargo loaded encapsulin nanocompartment
Entire | Name: DyP cargo loaded encapsulin nanocompartment |
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Components |
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-Supramolecule #1: DyP cargo loaded encapsulin nanocompartment
Supramolecule | Name: DyP cargo loaded encapsulin nanocompartment / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 1 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) |
Molecular weight | Theoretical: 29.554072 KDa |
Recombinant expression | Organism: Escherichia coli DH5[alpha] (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
Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||||||||
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6204 / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Protocol: RIGID BODY FIT / Overall B value: 26.39 / Target criteria: Cross-correlation coefficient |
Output model | PDB-8pys: |