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- PDB-7bvf: Cryo-EM structure of Mycobacterium tuberculosis arabinosyltransfe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bvf | |||||||||||||||
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Title | Cryo-EM structure of Mycobacterium tuberculosis arabinosyltransferase EmbA-EmbB-AcpM2 in complex with ethambutol | |||||||||||||||
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![]() | TRANSFERASE / Mycobacterium tuberculosis / cell wall synthesis / drug target / ethambutol / arabinosyltransferase / EmbA / EmbB / EmbC / acyl carrier protein / arabinogalactan / lipoarabinomannan / drug resistance | |||||||||||||||
Function / homology | ![]() arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / cell wall / lipid A biosynthetic process / plasma membrane => GO:0005886 / Transferases; Glycosyltransferases; Pentosyltransferases / acyl binding / acyl carrier activity / cell wall organization / membrane => GO:0016020 ...arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / cell wall / lipid A biosynthetic process / plasma membrane => GO:0005886 / Transferases; Glycosyltransferases; Pentosyltransferases / acyl binding / acyl carrier activity / cell wall organization / membrane => GO:0016020 / response to antibiotic / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||||||||
![]() | Zhang, L. / Zhao, Y. / Gao, Y. / Wang, Q. / Li, J. / Besra, G.S. / Rao, Z. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 394.7 KB | Display | ![]() |
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PDB format | ![]() | 308.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30218MC ![]() 7bvcC ![]() 7bveC ![]() 7bvgC ![]() 7bvhC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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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. |
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Components
-Probable arabinosyltransferase ... , 2 types, 2 molecules BA
#1: Protein | Mass: 120332.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: embB, Rv3795, MTCY13D12.29 Production host: ![]() References: UniProt: P9WNL7, Transferases; Glycosyltransferases; Pentosyltransferases |
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#2: Protein | Mass: 116789.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: embA, Rv3794, MTCY13D12.28 Production host: ![]() References: UniProt: P9WNL9, Transferases; Glycosyltransferases; Pentosyltransferases |
-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) ![]() References: UniProt: A0R0B3 |
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-Non-polymers , 4 types, 5 molecules ![](data/chem/img/CA.gif)
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#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-95E / |
#6: Chemical | ChemComp-DSL / |
#7: Chemical |
-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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
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 |
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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: ![]() | ||||||||||||||||||||||||||||
Electron lens | Mode: BRIGHT FIELD / 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 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 521803 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.28 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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