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Yorodumi- PDB-6wbx: Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wbx | |||||||||||||||||||||
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Title | Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria, Mutant R1389S Class 1 | |||||||||||||||||||||
Components | DUF3367 domain-containing protein | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Glycosyltransferase / nanodisc / acyl carrier protein | |||||||||||||||||||||
Function / homology | Alpha-(1->3)-arabinofuranosyltransferase / Alpha-(1->3)-arabinofuranosyltransferase / Coagulation factors 5/8 type C domain (FA58C) profile. / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / transferase activity / membrane => GO:0016020 / DUF3367 domain-containing protein Function and homology information | |||||||||||||||||||||
Biological species | Mycobacteroides abscessus (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Tan, Y.Z. / Zhang, L. / Rodrigues, J. / Zheng, R.B. / Giacometti, S.I. / Rosario, A.L. / Kloss, B. / Dandey, V.P. / Wei, H. / Brunton, R. ...Tan, Y.Z. / Zhang, L. / Rodrigues, J. / Zheng, R.B. / Giacometti, S.I. / Rosario, A.L. / Kloss, B. / Dandey, V.P. / Wei, H. / Brunton, R. / Raczkowski, A.M. / Athayde, D. / Catalao, M.J. / Pimentel, M. / Clarke, O.B. / Lowary, T.L. / Archer, M. / Niederweis, M. / Potter, C.S. / Carragher, B. / Mancia, F. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: Mol Cell / Year: 2020 Title: Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Authors: Yong Zi Tan / Lei Zhang / José Rodrigues / Ruixiang Blake Zheng / Sabrina I Giacometti / Ana L Rosário / Brian Kloss / Venkata P Dandey / Hui Wei / Richard Brunton / Ashleigh M Raczkowski ...Authors: Yong Zi Tan / Lei Zhang / José Rodrigues / Ruixiang Blake Zheng / Sabrina I Giacometti / Ana L Rosário / Brian Kloss / Venkata P Dandey / Hui Wei / Richard Brunton / Ashleigh M Raczkowski / Diogo Athayde / Maria João Catalão / Madalena Pimentel / Oliver B Clarke / Todd L Lowary / Margarida Archer / Michael Niederweis / Clinton S Potter / Bridget Carragher / Filippo Mancia / Abstract: Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two ...Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two lipidated polysaccharides-arabinogalactan and lipoarabinomannan. Arabinofuranosyltransferase D (AftD) is an essential enzyme involved in assembling these glycolipids. We present the 2.9-Å resolution structure of M. abscessus AftD, determined by single-particle cryo-electron microscopy. AftD has a conserved GT-C glycosyltransferase fold and three carbohydrate-binding modules. Glycan array analysis shows that AftD binds complex arabinose glycans. Additionally, AftD is non-covalently complexed with an acyl carrier protein (ACP). 3.4- and 3.5-Å structures of a mutant with impaired ACP binding reveal a conformational change, suggesting that ACP may regulate AftD function. Mutagenesis experiments using a conditional knockout constructed in M. smegmatis confirm the essentiality of the putative active site and the ACP binding for AftD function. | |||||||||||||||||||||
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 | 6wbx.cif.gz | 218.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wbx.ent.gz | 171.5 KB | Display | PDB format |
PDBx/mmJSON format | 6wbx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/6wbx ftp://data.pdbj.org/pub/pdb/validation_reports/wb/6wbx | HTTPS FTP |
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-Related structure data
Related structure data | 21600MC 6w98C 6wbyC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10391 (Title: Single-Particle Cryo-EM of Arabinofuranosyltransferase AftD from Mycobacteria, Mutant R1389S Data size: 2.3 TB Data #1: Unaligned and compressed multi-frame movies [micrographs - multiframe] Data #2: Aligned and dose-weighted micrographs [micrographs - single frame] Data #3: Final Particle Stacks with Refined Euler Angles and Shifts (Overall and Focused Refined on CBM3) [picked particles - single frame - processed]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 152818.641 Da / Num. of mol.: 1 / Mutation: R1389S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: D2E76_26050 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A418KZ72 | ||
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#2: Chemical | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mutant R1389S Class 1 Mycobacterial Arabinofuranosyltransferase AftD Complexed with Acyl Carrier Protein Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight |
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Source (natural) | Organism: Mycobacteroides abscessus (bacteria) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||
Buffer solution | pH: 7.5 / Details: Solution was filtered and degassed. | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Protein was incorporated into lipid nanodiscs. | ||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil | ||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Chamber temperature: 298 K |
-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 FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 13.05 sec. / Electron dose: 96.78 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4886 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV |
Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 90 / Used frames/image: 1-90 |
-Processing
EM software |
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Image processing | Details: Energy filter slit width of 15 eV was used during the collection and was aligned automatically every hour using Leginon. | ||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: CTF was estimated using GCTF and refined throughout the pipeline using cisTEM. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 226478 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37814 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6W98 Pdb chain-ID: A |