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Yorodumi- PDB-7bvc: Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bvc | |||||||||||||||
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Title | Cryo-EM structure of Mycobacterium smegmatis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol | |||||||||||||||
Components |
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Keywords | TRANSFERASE / Mycobacterium smegmatis / cell wall synthesis / drug target / ethambutol / arabinosyltransferase / EmbA / EmbB / EmbC / acyl carrier protein / arabinogalactan / lipoarabinomannan / drug resistance | |||||||||||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||
Authors | Zhang, L. / Zhao, Y. / Gao, Y. / Wang, Q. / Li, J. / Besra, G.S. / Rao, Z. | |||||||||||||||
Funding support | China, United Kingdom, 4items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7bvc.cif.gz | 388.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bvc.ent.gz | 318.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bvc_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7bvc_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7bvc_validation.xml.gz | 73.7 KB | Display | |
Data in CIF | 7bvc_validation.cif.gz | 107.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/7bvc ftp://data.pdbj.org/pub/pdb/validation_reports/bv/7bvc | HTTPS FTP |
-Related structure data
Related structure data | 30216MC 7bveC 7bvfC 7bvgC 7bvhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Details | The complete assembly should be tetramer. There should be 2 molecules of AcpM, however, only one was modeled due to low density. |
-Components
-Integral membrane indolylacetylinositol arabinosyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 116561.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: embA Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R613, Transferases; Glycosyltransferases; Pentosyltransferases |
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#2: Protein | Mass: 119077.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: embB, MSMEI_6221 Production host: Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: I7GAQ2, UniProt: A0R614*PLUS, indolylacetylinositol arabinosyltransferase |
-Protein , 1 types, 1 molecules P
#3: Protein | Mass: 10743.876 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0R0B3 |
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-Non-polymers , 6 types, 8 molecules
#4: Chemical | #5: Chemical | ChemComp-F8L / [( | #6: Chemical | #7: Chemical | ChemComp-PNS / | #8: Chemical | ChemComp-PO4 / | #9: Chemical | ChemComp-95E / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was monodisperse. | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 78.6 K / Temperature (min): 78.5 K / Residual tilt: 10 mradians |
Image recording | Average exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 5100 |
-Processing
EM software |
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Image processing | Details: The selected images were normalized. | ||||||||||||||||||||||||||||||||||||
CTF correction | Details: The CTF correction was done by patch CTF correction. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1855947 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227206 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 62.01 / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.93 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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