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- PDB-9dlf: Arabinosyltransferase AftB in complex with Fab_B3 -

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Basic information

Entry
Database: PDB / ID: 9dlf
TitleArabinosyltransferase AftB in complex with Fab_B3
Components
  • Arabinosyltransferase AftB
  • Fab_B3 heavy chain
  • Fab_B3 light chain
KeywordsMEMBRANE PROTEIN / Arabinosyltransferase
Function / homology: / : / membrane / Chem-6OU / Terminal beta-(1->2)-arabinofuranosyltransferase
Function and homology information
Biological speciesMycolicibacterium chubuense (bacteria)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsLiu, Y. / Mancia, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2025
Title: Mechanistic studies of mycobacterial glycolipid biosynthesis by the mannosyltransferase PimE.
Authors: Yaqi Liu / Chelsea M Brown / Nuno Borges / Rodrigo N Nobre / Satchal Erramilli / Meagan Belcher Dufrisne / Brian Kloss / Sabrina Giacometti / Ana M Esteves / Cristina G Timóteo / Piotr ...Authors: Yaqi Liu / Chelsea M Brown / Nuno Borges / Rodrigo N Nobre / Satchal Erramilli / Meagan Belcher Dufrisne / Brian Kloss / Sabrina Giacometti / Ana M Esteves / Cristina G Timóteo / Piotr Tokarz / Rosemary J Cater / Todd L Lowary / Yasu S Morita / Anthony A Kossiakoff / Helena Santos / Phillip J Stansfeld / Rie Nygaard / Filippo Mancia /
Abstract: Tuberculosis (TB), a leading cause of death among infectious diseases globally, is caused by Mycobacterium tuberculosis (Mtb). The pathogenicity of Mtb is largely attributed to its complex cell ...Tuberculosis (TB), a leading cause of death among infectious diseases globally, is caused by Mycobacterium tuberculosis (Mtb). The pathogenicity of Mtb is largely attributed to its complex cell envelope, which includes a class of glycolipids called phosphatidyl-myo-inositol mannosides (PIMs). These glycolipids maintain the integrity of the cell envelope, regulate permeability, and mediate host-pathogen interactions. PIMs comprise a phosphatidyl-myo-inositol core decorated with one to six mannose residues and up to four acyl chains. The mannosyltransferase PimE catalyzes the transfer of the fifth PIM mannose residue from a polyprenyl phosphate-mannose (PPM) donor. This step contributes to the proper assembly and function of the mycobacterial cell envelope; however, the structural basis for substrate recognition and the catalytic mechanism of PimE remain poorly understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of PimE from Mycobacterium abscessus in its apo and product-bound form. The structures reveal a distinctive binding cavity that accommodates both donor and acceptor substrates/products. Key residues involved in substrate coordination and catalysis were identified and validated via in vitro assays and in vivo complementation, while molecular dynamics simulations delineated access pathways and binding dynamics. Our integrated approach provides comprehensive insights into PimE function and informs potential strategies for anti-TB therapeutics.
History
DepositionSep 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Arabinosyltransferase AftB
A: Fab_B3 light chain
B: Fab_B3 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9404
Polymers98,2223
Non-polymers7181
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Arabinosyltransferase AftB / Terminal beta-(1->2)-arabinofuranosyltransferase


Mass: 72830.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium chubuense (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J6VB96
#2: Antibody Fab_B3 light chain


Mass: 11677.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab_B3 heavy chain


Mass: 13713.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Arabinosyltransferase AftB in complex with Fab_B3 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Mycolicibacterium chubuense (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192312 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036707
ELECTRON MICROSCOPYf_angle_d0.5699169
ELECTRON MICROSCOPYf_dihedral_angle_d4.089946
ELECTRON MICROSCOPYf_chiral_restr0.0411027
ELECTRON MICROSCOPYf_plane_restr0.0071161

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