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- EMDB-46998: Product-Bound mannosyltransferase PimE -

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Basic information

Entry
Database: EMDB / ID: EMD-46998
TitleProduct-Bound mannosyltransferase PimE
Map data
Sample
  • Complex: Mannosyltransferase PimE
    • Protein or peptide: Mannosyltransferase
  • Ligand: (2S)-1-{[(S)-{[(1S,2R,3R,4S,5S,6R)-2-[(6-O-hexadecanoyl-beta-L-gulopyranosyl)oxy]-3,4,5-trihydroxy-6-{[beta-D-mannopyranosyl-(1->2)-alpha-D-mannopyranosyl-(1->6)-beta-D-mannopyranosyl-(1->6)-alpha-D-mannopyranosyl]oxy}cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}-3-(hexadecanoyloxy)propan-2-yl 10-methyloctadecanoate
  • Ligand: MONO-TRANS, OCTA-CIS DECAPRENYL-PHOSPHATE
Keywordsmannosyltransferase / MEMBRANE PROTEIN
Function / homology: / :
Function and homology information
Biological speciesMycobacteroides abscessus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsLiu Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS) 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 12, 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_46998.png

Downloads & links

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Map

FileDownload / File: emd_46998.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 412 pix.
= 339.9 Å		0.83 Å/pix.
x 412 pix.
= 339.9 Å		0.83 Å/pix.
x 412 pix.
= 339.9 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.0353217 - 2.3735793
Average (Standard dev.)-0.0006486831 (±0.018305019)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions412412412
Spacing412412412
CellA=B=C: 339.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_46998_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_46998_half_map_2.map
Projections & Slices
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Sample components

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Entire : Mannosyltransferase PimE

EntireName: Mannosyltransferase PimE
Components
  • Complex: Mannosyltransferase PimE
    • Protein or peptide: Mannosyltransferase
  • Ligand: (2S)-1-{[(S)-{[(1S,2R,3R,4S,5S,6R)-2-[(6-O-hexadecanoyl-beta-L-gulopyranosyl)oxy]-3,4,5-trihydroxy-6-{[beta-D-mannopyranosyl-(1->2)-alpha-D-mannopyranosyl-(1->6)-beta-D-mannopyranosyl-(1->6)-alpha-D-mannopyranosyl]oxy}cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}-3-(hexadecanoyloxy)propan-2-yl 10-methyloctadecanoate
  • Ligand: MONO-TRANS, OCTA-CIS DECAPRENYL-PHOSPHATE

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Supramolecule #1: Mannosyltransferase PimE

SupramoleculeName: Mannosyltransferase PimE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacteroides abscessus (bacteria)

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Macromolecule #1: Mannosyltransferase

MacromoleculeName: Mannosyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacteroides abscessus (bacteria)
Molecular weightTheoretical: 46.06809 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATEKTEPTR ANVEPPMPTR GASAWRRVRA WGPWLLGLSV AVRLAWAYLT PHGADLVDLH VYVSGPATLG HGNLYEFTYP DKTPDFPLP FTYPPFAAVV FWPLHLIPFT LLGLCWILGT IAALYAVVRL SQRLLGFDDA RAAAVWTAVT MWTEPVRSTL D YGQINVLL ...String:
MATEKTEPTR ANVEPPMPTR GASAWRRVRA WGPWLLGLSV AVRLAWAYLT PHGADLVDLH VYVSGPATLG HGNLYEFTYP DKTPDFPLP FTYPPFAAVV FWPLHLIPFT LLGLCWILGT IAALYAVVRL SQRLLGFDDA RAAAVWTAVT MWTEPVRSTL D YGQINVLL MLLILLAVAS SRWWISGTLI GLAGGVKLTP LVSGLYFLGA RRWTTAIWAG VVFLLTVVVG IAVVGEQGRY YF TDLLGKP DRIGPIATVF NQSWRGGISR ILGHDAGSGV LVLFAYAVTA ILAFLAWRAV NDRLGQICVV EMFGLLISPI SWT HHWVWM VPFMVWLLHG PWRDKVGAKV FGCGWLVLLL IGVPWLLSFA QPDIWRIDRP WPLAWAGLVD IVAAIATLTW MAVV GRRSG HLGRLPWRHV

UniProtKB: UNIPROTKB: A0A418LCK8

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Macromolecule #2: (2S)-1-{[(S)-{[(1S,2R,3R,4S,5S,6R)-2-[(6-O-hexadecanoyl-beta-L-gu...

MacromoleculeName: (2S)-1-{[(S)-{[(1S,2R,3R,4S,5S,6R)-2-[(6-O-hexadecanoyl-beta-L-gulopyranosyl)oxy]-3,4,5-trihydroxy-6-{[beta-D-mannopyranosyl-(1->2)-alpha-D-mannopyranosyl-(1->6)-beta-D-mannopyranosyl-(1->6)- ...Name: (2S)-1-{[(S)-{[(1S,2R,3R,4S,5S,6R)-2-[(6-O-hexadecanoyl-beta-L-gulopyranosyl)oxy]-3,4,5-trihydroxy-6-{[beta-D-mannopyranosyl-(1->2)-alpha-D-mannopyranosyl-(1->6)-beta-D-mannopyranosyl-(1->6)-alpha-D-mannopyranosyl]oxy}cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}-3-(hexadecanoyloxy)propan-2-yl 10-methyloctadecanoate
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1A8B
Molecular weightTheoretical: 1.841747 KDa

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Macromolecule #3: MONO-TRANS, OCTA-CIS DECAPRENYL-PHOSPHATE

MacromoleculeName: MONO-TRANS, OCTA-CIS DECAPRENYL-PHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: DSL
Molecular weightTheoretical: 779.165 Da
Chemical component information

ChemComp-DSL:
MONO-TRANS, OCTA-CIS DECAPRENYL-PHOSPHATE

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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: 2.5 µm / Nominal defocus min: 0.8 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: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56510
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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