6X0O

Single-Particle Cryo-EM Structure of Arabinosyltransferase EmbB from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis.

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.

(2020) Nat Commun 11: 3396-3396

  • DOI: 10.1038/s41467-020-17202-8
  • Structures With Same Primary Citation

  • PubMed 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-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 ...

    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.


    Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA. fm123@cumc.columbia.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integral membrane indolylacetylinositol arabinosyltransferase EmbBA1098Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: embBMSMEI_6221
EC: 2.4.2.34
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Glycosyltransfereases
Protein: 
EmbB Arabinosyltransferase
Find proteins for I7GAQ2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore I7GAQ2 
Go to UniProtKB:  I7GAQ2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LHG
Query on LHG

Download CCD File 
A
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM128624
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM111980
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM132120
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR21 AI119672
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103310
Fundacao para a Ciencia e a TecnologiaPortugalPD/BD/128261/2016
Fundacao para a Ciencia e a TecnologiaPortugalPTDC/BIA-BQM/30421/2017
Fundacao para a Ciencia e a TecnologiaPortugalIF/00656/2014
Marie Sklodowska-Curie Actions, FragNET ITNPortugalNo 731005
Marie Sklodowska-Curie Actions, FragNET ITNPortugalNo 823780
Canadian Glycomics Network (GLYCONET)Canada--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM116799

Revision History 

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references, Structure summary
  • Version 1.2: 2020-07-22
    Changes: Database references