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- EMDB-46976: Arabinosyltransferase AftB in complex with Fab_B3 -

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Basic information

Entry
Database: EMDB / ID: EMD-46976
TitleArabinosyltransferase AftB in complex with Fab_B3
Map data
Sample
  • Complex: Arabinosyltransferase AftB in complex with Fab_B3
    • Protein or peptide: Arabinosyltransferase AftB
    • Protein or peptide: Fab_B3 light chain
    • Protein or peptide: Fab_B3 heavy chain
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
KeywordsArabinosyltransferase / MEMBRANE PROTEIN
Function / homology: / : / membrane / Terminal beta-(1->2)-arabinofuranosyltransferase
Function and homology information
Biological speciesMycolicibacterium chubuense (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsLiu Y / Mancia F
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46976.png

Downloads & links

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Map

FileDownload / File: emd_46976.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.585127 - 3.1761088
Average (Standard dev.)-0.00029580097 (±0.062521316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46976_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_46976_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Arabinosyltransferase AftB in complex with Fab_B3

EntireName: Arabinosyltransferase AftB in complex with Fab_B3
Components
  • Complex: Arabinosyltransferase AftB in complex with Fab_B3
    • Protein or peptide: Arabinosyltransferase AftB
    • Protein or peptide: Fab_B3 light chain
    • Protein or peptide: Fab_B3 heavy chain
  • Ligand: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate

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Supramolecule #1: Arabinosyltransferase AftB in complex with Fab_B3

SupramoleculeName: Arabinosyltransferase AftB in complex with Fab_B3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycolicibacterium chubuense (bacteria)

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Macromolecule #1: Arabinosyltransferase AftB

MacromoleculeName: Arabinosyltransferase AftB / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium chubuense (bacteria)
Molecular weightTheoretical: 72.830609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPQSSSADRL SRPFTEAAAT RLNRWPAFPY HVWVRVSLWV SVVTVAALFG WGAWQRRWIA DDGLIVLRTV RNLLAGNGPV FNAGERVEA NTSTVWSYLV TLGGFVAGSA RLEYVALVLA LTLSVLGVVL VMFGTARLYA PGLTGRRAVF LPAGALVYIA I PPARDFAT ...String:
MPQSSSADRL SRPFTEAAAT RLNRWPAFPY HVWVRVSLWV SVVTVAALFG WGAWQRRWIA DDGLIVLRTV RNLLAGNGPV FNAGERVEA NTSTVWSYLV TLGGFVAGSA RLEYVALVLA LTLSVLGVVL VMFGTARLYA PGLTGRRAVF LPAGALVYIA I PPARDFAT SGLENGLVLA YLGLLWWMMV CWSQGLRRPD GERTSRGFDA TLAVVAGMSV LVRPELALIG GLALVMMLVA AP TWRRRLA LVVVGGLIPV AYQIFRMGYY GLLVPGTALA KDASGAKWDQ GLVYLANFNQ PYLLWAPAVL LIGLGLMVLL LRG RPSWGD RGARKESGWI ARTVQSPPAV VAFMLISGLL QAVYWIRQGG DFMHGRVLLT PLFCLLAPVA VIPLLLPDRS RMAR GAGYL YAGATAVLWL AVAGWALWAA NSPGMGADAT RVTYSGIVDE RRFYSQATGH AHPLTAADYL DYPRMRAVLT AIENT PDGA LLLPSGDYDR WDVVPALPPP PDVRAAAVGG YVGPHTVFFT NLGMLGMNVG LDVRVIDQIG LANPLAAHTA RLTDGR IGH DKNLFPDWAV AEGPFLKEPP WIPQYLDEDW IRQAEAALKC PETDKVLDAI RAPMGFRRFL SNVMHAAEYT RYRIDRV PL YELARCGLPV PEPVDPPYTG LPPTGPA

UniProtKB: Terminal beta-(1->2)-arabinofuranosyltransferase

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Macromolecule #2: Fab_B3 light chain

MacromoleculeName: Fab_B3 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.677979 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSPPYGPIT FGQGTKVELK

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Macromolecule #3: Fab_B3 heavy chain

MacromoleculeName: Fab_B3 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.713124 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCAASGFNVS SSYIHWVRQA PGKGLEWVAS ISSYYGYTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARG YMYSHWVYSY GAIDYWGQGT LVTVSSA

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Macromolecule #4: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...

MacromoleculeName: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate
type: ligand / ID: 4 / Number of copies: 1 / Formula: 6OU
Molecular weightTheoretical: 717.996 Da
Chemical component information

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192312
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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