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- PDB-6x0o: Single-Particle Cryo-EM Structure of Arabinosyltransferase EmbB f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6x0o | |||||||||||||||||||||||||||||||||||||||
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Title | Single-Particle Cryo-EM Structure of Arabinosyltransferase EmbB from Mycobacterium smegmatis | |||||||||||||||||||||||||||||||||||||||
![]() | Integral membrane indolylacetylinositol arabinosyltransferase EmbB | |||||||||||||||||||||||||||||||||||||||
![]() | MEMBRANE PROTEIN / Glycosyltransferase / nanodisc | |||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() indolylacetylinositol arabinosyltransferase / indolylacetylinositol arabinosyltransferase activity / arabinosyltransferase activity / Actinobacterium-type cell wall biogenesis / Transferases; Glycosyltransferases; Pentosyltransferases / cell wall organization / plasma membrane Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||||||||||||||||||||
![]() | Tan, Y.Z. / Rodrigues, J. / Keener, J.E. / Zheng, R.B. / Brunton, R. / Kloss, B. / Giacometti, S.I. / Rosario, A.L. / Zhang, L. / Niederweis, M. ...Tan, Y.Z. / Rodrigues, J. / Keener, J.E. / Zheng, R.B. / Brunton, R. / Kloss, B. / Giacometti, S.I. / Rosario, A.L. / Zhang, L. / Niederweis, M. / Clarke, O.B. / Lowary, T.L. / Marty, M.T. / Archer, M. / Potter, C.S. / Carragher, B. / Mancia, F. | |||||||||||||||||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
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![]() | ![]() Title: Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. Authors: Yong Zi Tan / José Rodrigues / James E Keener / Ruixiang Blake Zheng / Richard Brunton / Brian Kloss / Sabrina I Giacometti / Ana L Rosário / Lei Zhang / Michael Niederweis / Oliver B ...Authors: Yong Zi Tan / José Rodrigues / James E Keener / Ruixiang Blake Zheng / Richard Brunton / Brian Kloss / Sabrina I Giacometti / Ana L Rosário / Lei Zhang / Michael Niederweis / Oliver B Clarke / Todd L Lowary / Michael T Marty / Margarida Archer / Clinton S Potter / Bridget Carragher / Filippo Mancia / ![]() ![]() ![]() ![]() Abstract: Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti- ...Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti-tuberculosis drug ethambutol. We present the 3.3 Å resolution single-particle cryo-electron microscopy structure of Mycobacterium smegmatis EmbB, providing insights on substrate binding and reaction mechanism. Mutations that confer ethambutol resistance map mostly around the putative active site, suggesting this to be the location of drug binding. | |||||||||||||||||||||||||||||||||||||||
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 | ![]() | 345.1 KB | Display | ![]() |
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PDB format | ![]() | 280.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 41.8 KB | Display | |
Data in CIF | ![]() | 62.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 21983MC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 4.5 TB Data #1: Unaligned and compressed multiframe movies from Falcon III Detector [micrographs - multiframe] Data #2: Unaligned and compressed multiframe movies from K2 Summit Detector [micrographs - multiframe] Data #3: Aligned and dose-weighted micrographs from Falcon III Detector [micrographs - single frame] Data #4: Aligned and dose-weighted micrographs from K2 Summit Detector [micrographs - single frame] Data #5: Final Particle Stack with Refined Euler Angles and Shifts [picked particles - single frame - processed]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 118835.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: embB, MSMEI_6221 / Production host: ![]() ![]() References: UniProt: I7GAQ2, UniProt: A0R614*PLUS, indolylacetylinositol arabinosyltransferase | ||||
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#2: Chemical | #3: Chemical | Has ligand of interest | Y | |
-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
Component | Name: Integral membrane indolylacetylinositol arabinosyltransferase EmbB Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.119 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 278 K |
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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 / Alignment procedure: ZEMLIN TABLEAU | |||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | |||||||||||||||
Image recording | Imaging-ID: 1 / Detector mode: COUNTING / Num. of grids imaged: 1
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Image scans | Sampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 80 |
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Processing
EM software |
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Image processing |
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CTF correction |
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Particle selection |
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Symmetry |
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3D reconstruction | Entry-ID: 6X0O / Num. of particles: 57970 / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT
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Atomic model building | Protocol: AB INITIO MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3PTY Accession code: 3PTY / Source name: PDB / Type: experimental model |