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- PDB-9ubc: Sub-particle structure of the iterative acetyltransferase from Ac... -

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Basic information

Entry
Database: PDB / ID: 9ubc
TitleSub-particle structure of the iterative acetyltransferase from Actinomycetes in complex with AcCoA and monoacetylated lasso peptides
Components
  • Albusnodin family lasso peptide
  • GCN5-related N-acetyltransferase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferases / Actinomycetes / AcCoA / Lasso peptides
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 / ACETYL COENZYME *A / Albusnodin family lasso peptide / GCN5-related N-acetyltransferase
Function and homology information
Biological speciesActinosynnema mirum DSM 43827 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsWu, S. / Xiong, J. / Lei, D. / Dong, S.
Funding support China, 7items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase
C: Albusnodin family lasso peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1683
Polymers23,3582
Non-polymers8101
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein GCN5-related N-acetyltransferase


Mass: 21676.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinosynnema mirum DSM 43827 (bacteria)
Gene: Amir_6318 / Production host: Escherichia coli (E. coli) / References: UniProt: C6WJ45
#2: Protein/peptide Albusnodin family lasso peptide


Mass: 1681.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinosynnema mirum DSM 43827 (bacteria)
Gene: FHR32_000276 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7W7W6P0
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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

Component
IDNameTypeEntity IDParent-IDSource
1Complex of iterative acetyltransferase, AcCoA and monoacetylated lasso peptidesCOMPLEX#1-#20MULTIPLE SOURCES
2Iterative acetyltransferaseCOMPLEX#11RECOMBINANT
3monoacetylated lasso peptidesCOMPLEX#21RECOMBINANT
Source (natural)Organism: Actinosynnema mirum DSM 43827 (bacteria)
Buffer solutionpH: 7.5
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78368 / Symmetry type: POINT
RefinementHighest resolution: 3.43 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0021688
ELECTRON MICROSCOPYf_angle_d0.4472296
ELECTRON MICROSCOPYf_dihedral_angle_d11.245605
ELECTRON MICROSCOPYf_chiral_restr0.038237
ELECTRON MICROSCOPYf_plane_restr0.003303

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