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Yorodumi- EMDB-30217: Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferas... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30217 | |||||||||||||||
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Title | Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbC2-AcpM2 in complex with ethambutol | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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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) / Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.81 Å | |||||||||||||||
Authors | Zhang L / Zhao Y / Gao Y / Wang Q / Li J / Besra GS / Rao Z | |||||||||||||||
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_30217.map.gz | 167.8 MB | EMDB map data format | |
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Header (meta data) | emd-30217-v30.xml emd-30217.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
Images | emd_30217.png | 72.2 KB | ||
Masks | emd_30217_msk_1.map | 178 MB | Mask map | |
Others | emd_30217_half_map_1.map.gz emd_30217_half_map_2.map.gz | 164.8 MB 164.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30217 | HTTPS FTP |
-Validation report
Summary document | emd_30217_validation.pdf.gz | 860.9 KB | Display | EMDB validaton report |
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Full document | emd_30217_full_validation.pdf.gz | 860.5 KB | Display | |
Data in XML | emd_30217_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | emd_30217_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30217 | HTTPS FTP |
-Related structure data
Related structure data | 7bveMC 7bvcC 7bvfC 7bvgC 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_30217.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_30217_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30217_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_30217_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mycobacterium smegmatis arabinosyltransferase EmbC2-AcpM2 in comp...
Entire | Name: Mycobacterium smegmatis arabinosyltransferase EmbC2-AcpM2 in complex with ethambutol |
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Components |
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-Supramolecule #1: Mycobacterium smegmatis arabinosyltransferase EmbC2-AcpM2 in comp...
Supramolecule | Name: Mycobacterium smegmatis arabinosyltransferase EmbC2-AcpM2 in complex with ethambutol type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: EmbC
Supramolecule | Name: EmbC / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Supramolecule #3: AcpM
Supramolecule | Name: AcpM / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Macromolecule #1: Integral membrane indolylacetylinositol arabinosyltransferase EmbC
Macromolecule | Name: Integral membrane indolylacetylinositol arabinosyltransferase EmbC type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: indolylacetylinositol arabinosyltransferase |
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Source (natural) | Organism: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 116.878898 KDa |
Recombinant expression | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Sequence | String: MTGPHAAGGS NHRTARLVAI IAGLLGTLMA IATPLLPVEQ TTAELNWPQN GVWQSVDAPL IGYVATDLTV TVPCQAAAGL VGPENRNRS VLLSTVPKQA PKAIDRGLLI ERINNDLTVI VRNTPVVSAP LEQVLSPDCR YLTFTAHADK VTGEFVGLTQ G PDDDDPGE ...String: MTGPHAAGGS NHRTARLVAI IAGLLGTLMA IATPLLPVEQ TTAELNWPQN GVWQSVDAPL IGYVATDLTV TVPCQAAAGL VGPENRNRS VLLSTVPKQA PKAIDRGLLI ERINNDLTVI VRNTPVVSAP LEQVLSPDCR YLTFTAHADK VTGEFVGLTQ G PDDDDPGE AVRGERSGYD FRPQIVGVFT DLSGPAPEGL QLSATIDTRY STSPTLLKLL AMIVGVAMTV IALGALHVLD CA DGRRHKR FLPSRWWSMT PLDGLVSAML VWWHFVGANT ADDGYILTMA RVSEHAGYMA NYYRWFGTPE SPFGWYYDLL ALW AHVSTA SVWMRFPTLL MGLACWWVIS REVIPRLGAA AKHSRAAAWT AAGLFLAFWL PLNNGLRPEP IIALGILLTW CSVE RGVAT SRLLPVAVAI IIGALTLFSG PTGIAAVGAL LVAIGPLKTI VAAHVSRFGY WALLAPIAAA GTVTIFLIFR DQTLA AELQ ASSFKSAVGP SLAWFDEHIR YSRLFTTSPD GSVARRFAVL TLLLALAVSI AMTLRKGRIP GTALGPSRRI IGITII SFL AMMFTPTKWT HHFGVFAGLA GCLGALAAVA VTTTAMKSRR NRTVFGAAVL FVTALSFATV NGWWYVSNFG VPWSNSF PE FKFGFTTMLL GLSVLALLVA AWFHFSGRDV SPDRPQRRWQ RLLVAPLAVA TWALVIFEVV SLTLGMINQY PAWSVGRS N LNALTGKTCG LANDVLVEQN ANAGMLTPIG EPAGQALGAV TSLGFGPNGI PSDVSADPVM EQPGTDNFAD SDSGVVTGT EVGTEGGTTA AAGINGSRAR LPYGLNPATT PVLGSWRSGT QQPAVLRSAW YRLPDRDQAG PLLVVSAAGR FDQGEVEVQW ATDEQAAAN EPGGSITFGD VGAAPAWRNL RAPLSSIPPE ATQIRLVASD DDLAPQHWIA LTPPRIPELR TLQEVVGSSD P VMLDWLVG LAFPCQRPFD HRYGVVEVPK WRILPDRFGA EANSPVMDYL GGGPLGITEL LLRPSSVPTY LKDDWYRDWG SL QRLTPWY PDAQPARLDL GTATRSGWWS PAPLRLSHHH HHHHHHH |
-Macromolecule #2: Meromycolate extension acyl carrier protein
Macromolecule | Name: Meromycolate extension acyl carrier protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Molecular weight | Theoretical: 10.743876 KDa |
Sequence | String: MAATQEEIIA GLAEIIEEVT GIEPSEVTPE KSFVDDLDID SLSMVEIAVQ TEDKYGVKIP DEDLAGLRTV GDVVAYIQKL EEENPEAAA ALREKFAADQ |
-Macromolecule #3: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #4: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Macromolecule #5: Ethambutol
Macromolecule | Name: Ethambutol / type: ligand / ID: 5 / Number of copies: 2 / Formula: 95E |
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Molecular weight | Theoretical: 204.31 Da |
Chemical component information | ChemComp-95E: |
-Macromolecule #6: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-...
Macromolecule | Name: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide type: ligand / ID: 6 / Number of copies: 2 / Formula: PN7 |
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Molecular weight | Theoretical: 358.348 Da |
Chemical component information | ChemComp-PN7: |
-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 Component:
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Vitrification | Cryogen name: ETHANE | ||||||||
Details | The sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 78.5 K / Max: 78.6 K |
Alignment procedure | Coma free - Residual tilt: 10.0 mrad |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 5100 / 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 | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000 |
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: RIGID BODY FIT / Overall B value: 62.01 / Target criteria: correlation coefficient |
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Output model | PDB-7bve: |