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Open data
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Basic information
Entry | Database: PDB / ID: 8jes | ||||||
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Title | Cryo-EM structure of DltB homo-tetramer | ||||||
![]() | Teichoic acid D-alanyltransferase | ||||||
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Function / homology | ![]() lipoteichoic acid biosynthetic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, P. / Liu, Z. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural insights into the transporting and catalyzing mechanism of DltB in LTA D-alanylation. Authors: Pingfeng Zhang / Zheng Liu / ![]() Abstract: DltB, a model member of the Membrane-Bound O-AcylTransferase (MBOAT) superfamily, plays a crucial role in D-alanylation of the lipoteichoic acid (LTA), a significant component of the cell wall of ...DltB, a model member of the Membrane-Bound O-AcylTransferase (MBOAT) superfamily, plays a crucial role in D-alanylation of the lipoteichoic acid (LTA), a significant component of the cell wall of gram-positive bacteria. This process stabilizes the cell wall structure, influences bacterial virulence, and modulates the host immune response. Despite its significance, the role of DltB is not well understood. Through biochemical analysis and cryo-EM imaging, we discover that Streptococcus thermophilus DltB forms a homo-tetramer on the cell membrane. We further visualize DltB in an apo form, in complex with DltC, and in complex with its inhibitor amsacrine (m-AMSA). Each tetramer features a central hole. The C-tunnel of each protomer faces the intratetramer interface and provides access to the periphery membrane. Each protomer binds a DltC without changing the tetrameric organization. A phosphatidylglycerol (PG) molecule in the substrate-binding site may serve as an LTA carrier. The inhibitor m-AMSA bound to the L-tunnel of each protomer blocks the active site. The tetrameric organization of DltB provides a scaffold for catalyzing D-alanyl transfer and regulating the channel opening and closing. Our findings unveil DltB's dual function in the D-alanylation pathway, and provide insight for targeting DltB as a anti-virulence antibiotic. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 474.4 KB | Display | ![]() |
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PDB format | ![]() | 321.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 36194MC ![]() 8jemC ![]() 8jf2C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 51780.027 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: LMG 18311 / Gene: dltB, stu0762 / Production host: ![]() ![]() ![]() References: UniProt: Q5M4V4, ![]() #2: Chemical | ChemComp-PGT / ( ![]() #3: Sugar | ChemComp-LMT / #4: Chemical | ![]() 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: apo DltB tetramer in DDM. / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 48 kDa/nm / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.5 / Details: 20 mM Hopes-Na, pH7.5, 0.03% DDM |
Buffer component | Conc.: 25 mM / Name: Hepes![]() |
Specimen | Conc.: 9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() Details: The DltB protein was purified in DDM, the tetramer fractions from gel filtration column were concentrated to about 10 mg/ml. |
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: After incubation on the grids at 277K under 100% humidity for 10 s, the grids were bloted for 3.0 s and then plunged frozen into liquid ethane cooled by liquid nitrogen using a Vitrobot. |
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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: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
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EM software | Name: SerialEM / Category: image acquisition | ||||||||||||||||||||||||
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3538544 | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128038 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 152.98 Å2 | ||||||||||||||||||||||||
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