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- PDB-9up2: PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module) -

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Basic information

Entry
Database: PDB / ID: 9up2
TitlePvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)
Components
  • MbtH-like domain-containing protein
  • PvdL
KeywordsBIOSYNTHETIC PROTEIN / Nonribosomal peptide synthetase / LIGASE
Function / homology
Function and homology information


pyoverdine biosynthetic process / monocarboxylic acid biosynthetic process / Actinobacterium-type cell wall biogenesis / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / lipid biosynthetic process / ligase activity / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process ...pyoverdine biosynthetic process / monocarboxylic acid biosynthetic process / Actinobacterium-type cell wall biogenesis / siderophore biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / lipid biosynthetic process / ligase activity / catalytic activity / phosphopantetheine binding / antibiotic biosynthetic process / fatty acid metabolic process / transferase activity / cytosol
Similarity search - Function
MbtH-like protein / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain ...MbtH-like protein / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 2,4-DIAMINOBUTYRIC ACID / PvdL / MbtH-like domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsCao, W. / Wang, J. / Wang, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2021YFA0910500 China
CitationJournal: Nat Synth / Year: 2026
Title: Analysis of heterocycle formation and stereochemical control by a non-ribosomal peptide synthetase condensation domain
Authors: Cao, W. / Wang, J. / Chen, S.L. / Li, D. / Wang, X. / Deng, Z. / Liang, J. / Wang, Z.
History
DepositionApr 27, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: PvdL
B: MbtH-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,5605
Polymers179,8172
Non-polymers7433
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 PvdL


Mass: 172528.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pvdL, PA2424 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I157
#2: Protein MbtH-like domain-containing protein


Mass: 7288.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA2412 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I169
#3: Chemical ChemComp-DAB / 2,4-DIAMINOBUTYRIC ACID


Type: L-peptide linking / Mass: 118.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10N2O2 / Comment: inhibitor*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
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

ComponentName: PvdL-E2-C3-A3-PCP3 in complex with MLP (NRPS cross-module)
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 186 kDa/nm / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: OTHER

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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: OTHER
Electron lensMode: OTHER / Nominal magnification: 64000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165245 / Symmetry type: POINT

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