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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: To Be Published
Title: Iterative acylation on mature lasso peptides by widespread GNATs for lipolasso production
Authors: Xiong J / Wu S / Liang Z / Gong X / Fang S / Tao F / Wu Q / Cui J / Gao K / Luo S / Lei D / Dong S
History
DepositionApr 2, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64004_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_64004_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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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