6W98 | pdb_00006w98

Single-Particle Cryo-EM Structure of Arabinofuranosyltransferase AftD from Mycobacteria


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6W98

This is version 1.3 of the entry. See complete history

Literature

Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria.

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.

(2020) Mol Cell 78: 683

  • DOI: https://doi.org/10.1016/j.molcel.2020.04.014
  • Primary Citation Related Structures: 
    6W98, 6WBX, 6WBY

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.

Macromolecule Content 

  • Total Structure Weight: 159.39 kDa 
  • Atom Count: 10,317 
  • Modeled Residue Count: 1,389 
  • Deposited Residue Count: 1,491 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
F5/8 type C domain-containing protein1,413Mycobacteroides abscessus subsp. abscessusMutation(s): 0 
Gene Names: SAMEA2161603_00457
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Acyl carrier protein78Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A6A8 (Escherichia coli (strain K12))
Explore P0A6A8 
Go to UniProtKB:  P0A6A8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6A8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103310
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 GM116799
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103310

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2020-06-03
    Changes: Database references
  • Version 1.3: 2025-04-02
    Changes: Data collection, Database references, Structure summary