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Yorodumi- EMDB-30219: Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferas... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30219 | |||||||||||||||
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Title | Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with di-arabinose. | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Mycobacterium smegmatis / cell wall synthesis / drug target / ethambutol / arabinosyltransferase / EmbA / EmbB / EmbC / acyl carrier protein / arabinogalactan / lipoarabinomannan / drug resistance / TRANSFERASE | |||||||||||||||
Function / homology | Function and homology information indolylacetylinositol arabinosyltransferase / indolylacetylinositol arabinosyltransferase activity / arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / lipid A biosynthetic process / Transferases; Glycosyltransferases; Pentosyltransferases / acyl binding / acyl carrier activity / cell wall organization / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Zhang L / Zhao Y | |||||||||||||||
Funding support | China, United Kingdom, 4 items
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Citation | Journal: Science / Year: 2020 Title: Structures of cell wall arabinosyltransferases with the anti-tuberculosis drug ethambutol. Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang ...Authors: Lu Zhang / Yao Zhao / Yan Gao / Lijie Wu / Ruogu Gao / Qi Zhang / Yinan Wang / Chengyao Wu / Fangyu Wu / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Wei Zhao / Ling Qin / Xiuna Yang / Manfu Wang / Yan Zhu / Bing Zhang / Lijun Bi / Xian'en Zhang / Haitao Yang / Luke W Guddat / Wenqing Xu / Quan Wang / Jun Li / Gurdyal S Besra / Zihe Rao / Abstract: The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo- ...The arabinosyltransferases EmbA, EmbB, and EmbC are involved in cell wall synthesis and are recognized as targets for the anti-tuberculosis drug ethambutol. In this study, we determined cryo-electron microscopy and x-ray crystal structures of mycobacterial EmbA-EmbB and EmbC-EmbC complexes in the presence of their glycosyl donor and acceptor substrates and with ethambutol. These structures show how the donor and acceptor substrates bind in the active site and how ethambutol inhibits arabinosyltransferases by binding to the same site as both substrates in EmbB and EmbC. Most drug-resistant mutations are located near the ethambutol binding site. Collectively, our work provides a structural basis for understanding the biochemical function and inhibition of arabinosyltransferases and the development of new anti-tuberculosis agents. | |||||||||||||||
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_30219.map.gz | 168 MB | EMDB map data format | |
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Header (meta data) | emd-30219-v30.xml emd-30219.xml | 22.7 KB 22.7 KB | Display Display | EMDB header |
Images | emd_30219.png | 75 KB | ||
Masks | emd_30219_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-30219.cif.gz | 7.7 KB | ||
Others | emd_30219_half_map_1.map.gz emd_30219_half_map_2.map.gz | 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30219 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30219 | HTTPS FTP |
-Validation report
Summary document | emd_30219_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_30219_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_30219_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_30219_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30219 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30219 | HTTPS FTP |
-Related structure data
Related structure data | 7bvgMC 7bvcC 7bveC 7bvfC 7bvhC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30219.map.gz / Format: CCP4 / Size: 178 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: 0.82 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_30219_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30219_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_30219_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in ...
+Supramolecule #1: Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in ...
+Supramolecule #2: EmbA and EmbB
+Supramolecule #3: AcpM
+Macromolecule #1: Integral membrane indolylacetylinositol arabinosyltransferase EmbA
+Macromolecule #2: Integral membrane indolylacetylinositol arabinosyltransferase EmbB
+Macromolecule #3: Meromycolate extension acyl carrier protein
+Macromolecule #5: [(2Z,6E,10E,14Z,18E,22Z,26Z)-3,7,11,15,19,23,27,31,35,39-decameth...
+Macromolecule #6: CARDIOLIPIN
+Macromolecule #7: CALCIUM ION
+Macromolecule #8: PHOSPHATE ION
+Macromolecule #9: 4'-PHOSPHOPANTETHEINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 209894 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7bvg: |