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- PDB-7bwr: Mycobacterium smegmatis arabinosyltransferase complex EmbB2-AcpM2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bwr | |||||||||
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Title | Mycobacterium smegmatis arabinosyltransferase complex EmbB2-AcpM2 in substrate DPA bound asymmetric "active state" | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gao, R.G. / Zhang, L. / Wang, Q. / Rao, Z.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM snapshots of mycobacterial arabinosyltransferase complex EmbB-AcpM. Authors: Lu Zhang / Yao Zhao / Ruogu Gao / Jun Li / Xiuna Yang / Yan Gao / Wei Zhao / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Kajelle Kaur Besra / Wenqing Xu / Lijun Bi / Xian'en Zhang / ...Authors: Lu Zhang / Yao Zhao / Ruogu Gao / Jun Li / Xiuna Yang / Yan Gao / Wei Zhao / Sudagar S Gurcha / Natacha Veerapen / Sarah M Batt / Kajelle Kaur Besra / Wenqing Xu / Lijun Bi / Xian'en Zhang / Luke W Guddat / Haitao Yang / Quan Wang / Gurdyal S Besra / Zihe Rao / ![]() ![]() ![]() Abstract: Inhibition of Mycobacterium tuberculosis (Mtb) cell wall assembly is an established strategy for anti-TB chemotherapy. Arabinosyltransferase EmbB, which catalyzes the transfer of arabinose from the ...Inhibition of Mycobacterium tuberculosis (Mtb) cell wall assembly is an established strategy for anti-TB chemotherapy. Arabinosyltransferase EmbB, which catalyzes the transfer of arabinose from the donor decaprenyl-phosphate-arabinose (DPA) to its arabinosyl acceptor is an essential enzyme for Mtb cell wall synthesis. Analysis of drug resistance mutations suggests that EmbB is the main target of the front-line anti-TB drug, ethambutol. Herein, we report the cryo-EM structures of Mycobacterium smegmatis EmbB in its "resting state" and DPA-bound "active state". EmbB is a fifteen-transmembrane-spanning protein, assembled as a dimer. Each protomer has an associated acyl-carrier-protein (AcpM) on their cytoplasmic surface. Conformational changes upon DPA binding indicate an asymmetric movement within the EmbB dimer during catalysis. Functional studies have identified critical residues in substrate recognition and catalysis, and demonstrated that ethambutol inhibits transferase activity of EmbB by competing with DPA. The structures represent the first step directed towards a rational approach for anti-TB drug discovery. | |||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 346 KB | Display | ![]() |
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PDB format | ![]() | 267.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30234MC ![]() 7bx8C 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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Components
#1: Protein | Mass: 116870.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: embB, MSMEI_6221 Production host: ![]() References: UniProt: I7GAQ2, UniProt: A0R614*PLUS, ![]() #2: Protein | Mass: 10743.876 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: acpM, MSMEG_4326, MSMEI_4226 Production host: ![]() References: UniProt: A0R0B3 #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-F8L / [( | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Mycobacterial Arabinosyltransferase Complex EmbB2-AcpM2 Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 254 kDa/nm / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
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![]() |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Classification: refinement | ||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: NONE | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125899 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.88 Å2 / Biso mean: 94.9808 Å2 / Biso min: 20 Å2 |