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Yorodumi- EMDB-30132: Cryo-EM structure of the cargo-loaded encapsulin from Mycobacteri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30132 | |||||||||||||||
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Title | Cryo-EM structure of the cargo-loaded encapsulin from Mycobacterium smegmatis | |||||||||||||||
Map data | Non-post-processed full map after 3D-refinement generated by RELION | |||||||||||||||
Sample |
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Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||
Authors | Tang YT / Mu A / Gong HR / Wang Q / Rao ZH | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Cryo-EM structure of DyP-loaded encapsulin. Authors: Yanting Tang / An Mu / Yuying Zhang / Shan Zhou / Weiwei Wang / Yuezheng Lai / Xiaoting Zhou / Fengjiang Liu / Xiuna Yang / Hongri Gong / Quan Wang / Zihe Rao / Abstract: Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact ...Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery. | |||||||||||||||
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_30132.map.gz | 141.1 MB | EMDB map data format | |
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Header (meta data) | emd-30132-v30.xml emd-30132.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30132_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_30132.png | 126.6 KB | ||
Masks | emd_30132_msk_1.map | 178 MB | Mask map | |
Others | emd_30132_half_map_1.map.gz emd_30132_half_map_2.map.gz | 141 MB 140.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30132 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30132 | HTTPS FTP |
-Validation report
Summary document | emd_30132_validation.pdf.gz | 624.8 KB | Display | EMDB validaton report |
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Full document | emd_30132_full_validation.pdf.gz | 624.4 KB | Display | |
Data in XML | emd_30132_validation.xml.gz | 18.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30132 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30132 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30132.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Non-post-processed full map after 3D-refinement generated by RELION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 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_30132_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: First one of the half map after 3D-refinement generated by RELION
File | emd_30132_half_map_1.map | ||||||||||||
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Annotation | First one of the half map after 3D-refinement generated by RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second one of the half map after 3D-refinement generated by RELION
File | emd_30132_half_map_2.map | ||||||||||||
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Annotation | Second one of the half map after 3D-refinement generated by RELION | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Encapsulin from Mycobacterium smegmatis
Entire | Name: Encapsulin from Mycobacterium smegmatis |
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Components |
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-Supramolecule #1: Encapsulin from Mycobacterium smegmatis
Supramolecule | Name: Encapsulin from Mycobacterium smegmatis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Macromolecule #1: Cargo-loaded encapsulin
Macromolecule | Name: Cargo-loaded encapsulin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MNNLYRDLAP ITESAWAEIE LEATRTFKRH IAGRRVVDVS GPNGPTTASV STGHLLDVSP PGDGVIAHLR DAKPLVRLRV PFTVARRDID DVERGSQDSD WDPVKDAAKK LAFVEDRAIF EGYAAASIEG IRSSSSNPAL ALPDDAREIP DVIAQALSEL RLAGVDGPYS ...String: MNNLYRDLAP ITESAWAEIE LEATRTFKRH IAGRRVVDVS GPNGPTTASV STGHLLDVSP PGDGVIAHLR DAKPLVRLRV PFTVARRDID DVERGSQDSD WDPVKDAAKK LAFVEDRAIF EGYAAASIEG IRSSSSNPAL ALPDDAREIP DVIAQALSEL RLAGVDGPYS VLLSAETYTK VSETTAHGYP IREHINRLVD GEIIWAPAID GAFVLSTRGG DFDLQLGTDV SIGYLSHDAE VVHLYMEETM TFLCYTAEAS VALTP MPAP QPQPVLAPLT PAAVFLVATI DEGQEATVYD ALPDISGLVR AIGFRDPAKR LSAITSIGSD AWDRLFSGPR PAELHPFREI DGGRHHAPAT PGDLLFHLRA ESMDVCFELA TKLVEAMSGA ITIVDETHGF RFFDNRDLMG FVDGTENPDG NLAVVATQIG DEDPDFAGGC YVHVQKYLHD MASWNSLSVE EQERVIGRTK LDDIELDDDV KPANSHVALN VIEDEDGNEL KIIRHNMPFG EIGKGEFGTY YIGYSRTPSV TERMLDNMFI GDPPGNTDRI LDFSTAITGG LFFTPTVDFL DDPPPLPSED DRAEPASAPS ADPVHTDGSL GIGSLKGTR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Average exposure time: 6.4 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |