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- EMDB-64004: Sub-particle structure of the iterative acetyltransferase from Ac... -

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Basic information

Entry
Database: EMDB / ID: EMD-64004
TitleSub-particle structure of the iterative acetyltransferase from Actinomycetes in complex with AcCoA and monoacetylated lasso peptides
Map data
Sample
  • Complex: Complex of iterative acetyltransferase, AcCoA and monoacetylated lasso peptides
    • Complex: Iterative acetyltransferase
      • Protein or peptide: GCN5-related N-acetyltransferase
    • Complex: monoacetylated lasso peptides
      • Protein or peptide: Albusnodin family lasso peptide
  • Ligand: ACETYL COENZYME *A
KeywordsGCN5-related N-acetyltransferases / Actinomycetes / AcCoA / Lasso peptides / TRANSFERASE
Function / homologyAcetyltransferase (GNAT) domain / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Albusnodin family lasso peptide / GCN5-related N-acetyltransferase
Function and homology information
Biological speciesActinosynnema mirum DSM 43827 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsWu S / Xiong J / Lei D / Dong S
Funding support China, 7 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077056 China
National Natural Science Foundation of China (NSFC)22377046 China
National Natural Science Foundation of China (NSFC)32171300 China
National Natural Science Foundation of China (NSFC)2210070084 China
National Natural Science Foundation of China (NSFC)21907046 China
Other government22ZD6FA006
Other government23ZDFA015
CitationJournal: Nat Chem Biol / Year: 2026
Title: Iterative acylation on mature lasso peptides by widespread acetyltransferases.
Authors: Jiang Xiong / Shanquan Wu / Zi-Qi Liang / Shuo Fang / Fen-Yu Tao / Xiao-Tong Gong / Xing Wu / Qingfeng Wu / Jiao-Jiao Cui / Kun Gao / Kin Kuan Hoi / Yong Peng / Shangwen Luo / Dongsheng Lei / Shi-Hui Dong /
Abstract: The biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs) leverages iterative catalysis to enhance structural and biological diversity. Traditionally, iterative ...The biosynthesis of ribosomally synthesized and posttranslationally modified peptides (RiPPs) leverages iterative catalysis to enhance structural and biological diversity. Traditionally, iterative enzymes install posttranslational modifications on linear peptides, rather than mature RiPPs with intricate three-dimensional structures, which require complex changes in substrate binding. Here we present a prolific class of GCN5-related N-acetyltransferases (GNATs) that iteratively and consecutively acylate two Lys residues within the loop and ring motifs of lasso peptides, diverging from the typical iterative modification of linear peptides. Utilizing high-resolution cryogenic-electron microscopy and enzymatic reconstitution, we define the lasso peptide-binding pocket of IatT and pinpoint key residues that distinguish its two distinct acetylation steps. Structure-based engineering of IatT's acetyl-recognition site expands the cavity to accommodate longer-chain acyl groups, enabling the creation of lipolasso peptides, a class of ribosomal lipopeptide. This engineering strategy can be applied to any RiPP biosynthetic gene cluster encoding GNAT, facilitating the efficient diversification of ribosomal lipopeptides.
History
DepositionApr 2, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64004.png

Downloads & links

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Map

FileDownload / File: emd_64004.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 128 pix.
= 106.368 Å		0.83 Å/pix.
x 128 pix.
= 106.368 Å		0.83 Å/pix.
x 128 pix.
= 106.368 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-0.34032515 - 15.41868
Average (Standard dev.)0.20299736 (±1.0853145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 106.368 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64004_msk_1.map
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Additional map: Sharpened density map of the whole particle reconstructed...

Fileemd_64004_additional_1.map
AnnotationSharpened density map of the whole particle reconstructed with D7 symmetry averaging.
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Additional map: Unsharpened density map of the whole particle reconstructed...

Fileemd_64004_additional_2.map
AnnotationUnsharpened density map of the whole particle reconstructed with D7 symmetry averaging.
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AxesZYX

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Half map: #2

Fileemd_64004_half_map_1.map
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Half map: #1

Fileemd_64004_half_map_2.map
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Sample components

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Entire : Complex of iterative acetyltransferase, AcCoA and monoacetylated ...

EntireName: Complex of iterative acetyltransferase, AcCoA and monoacetylated lasso peptides
Components
  • Complex: Complex of iterative acetyltransferase, AcCoA and monoacetylated lasso peptides
    • Complex: Iterative acetyltransferase
      • Protein or peptide: GCN5-related N-acetyltransferase
    • Complex: monoacetylated lasso peptides
      • Protein or peptide: Albusnodin family lasso peptide
  • Ligand: ACETYL COENZYME *A

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Supramolecule #1: Complex of iterative acetyltransferase, AcCoA and monoacetylated ...

SupramoleculeName: Complex of iterative acetyltransferase, AcCoA and monoacetylated lasso peptides
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Actinosynnema mirum DSM 43827 (bacteria)

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Supramolecule #2: Iterative acetyltransferase

SupramoleculeName: Iterative acetyltransferase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: monoacetylated lasso peptides

SupramoleculeName: monoacetylated lasso peptides / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

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Macromolecule #1: GCN5-related N-acetyltransferase

MacromoleculeName: GCN5-related N-acetyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Actinosynnema mirum DSM 43827 (bacteria)
Molecular weightTheoretical: 21.676164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPQDDLIVW LRGDRAGLGP FSADLVDQYW RWEQDPSVLI GYGRQTPDSL ENRREGYGHQ ARGTDDQLRF TVYDLTGQDP VPVGTTAVL IDHHVRTGEF VIQLGAGHRG RGLGTEATRL TLDYAFHVSA LACVHLAVLT PNTGAIAAYE RAGFRRIGER R DSGFWLGR ...String:
MSPQDDLIVW LRGDRAGLGP FSADLVDQYW RWEQDPSVLI GYGRQTPDSL ENRREGYGHQ ARGTDDQLRF TVYDLTGQDP VPVGTTAVL IDHHVRTGEF VIQLGAGHRG RGLGTEATRL TLDYAFHVSA LACVHLAVLT PNTGAIAAYE RAGFRRIGER R DSGFWLGR RVSETLMDAV PEDFPGPSVV RGFVEGGR

UniProtKB: GCN5-related N-acetyltransferase

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Macromolecule #2: Albusnodin family lasso peptide

MacromoleculeName: Albusnodin family lasso peptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Actinosynnema mirum DSM 43827 (bacteria)
Molecular weightTheoretical: 1.681787 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GQGKGSAED(ALY) RRAYN

UniProtKB: Albusnodin family lasso peptide

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Macromolecule #3: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 3 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78368
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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