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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/s41467-020-17202-8
  • Primary Citation of Related Structures:  
    6X0O

  • 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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integral membrane indolylacetylinositol arabinosyltransferase EmbB1,098Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: embBMSMEI_6221
EC: 2.4.2.34 (PDB Primary Data), 2.4.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0R614 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R614 
Go to UniProtKB:  A0R614
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R614
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2
RECONSTRUCTIONcryoSPARC2
MODEL REFINEMENTPHENIX1.14

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 ITNEuropean UnionNo 731005
Marie Sklodowska-Curie Actions, FragNET ITNEuropean UnionNo 823780
Canadian Glycomics Network (GLYCONET)Canada--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM116799

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-06
    Changes: Author supporting evidence, Data collection, Database references, Refinement description