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- PDB-9wop: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme T... -

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Basic information

Entry
Database: PDB / ID: 9wop
TitleCryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC with chain A bounded to substrate TherA and ATPrS.
Components
  • Lantibiotic
  • Protein kinase domain-containing protein
KeywordsPEPTIDE BINDING PROTEIN / Lanthipeptide modification enzyme
Function / homologyPHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / :
Function and homology information
Biological speciesThermoactinomyces sp. DSM 45892 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsZhang, H. / Luo, M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Structural Basis for the lanthipeptide biosynthesis mechanism of a dimeric Class III lanthipeptide synthetase
Authors: Zhang, H. / Luo, M.
History
DepositionSep 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 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
B: Lantibiotic
A: Protein kinase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5633
Polymers104,0402
Non-polymers5231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide Lantibiotic / TherA


Mass: 4678.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces sp. DSM 45892 (bacteria)
Gene: SAMN05444416_10475
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1H3JBM1
#2: Protein Protein kinase domain-containing protein / Lanthipeptide modification enzyme TherKC


Mass: 99361.719 Da / Num. of mol.: 1 / Mutation: R685A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces sp. DSM 45892 (bacteria)
Gene: SAMN05444416_10474
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1H3JBN8
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY
Has protein modificationN

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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: Cryo-EM structure of ClassIII Lanthipeptide modification enzyme TherKC mutant R685A.
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Thermoactinomyces sp. DSM 45892 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174223 / Symmetry type: POINT
RefinementHighest resolution: 4.25 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046563
ELECTRON MICROSCOPYf_angle_d0.9728930
ELECTRON MICROSCOPYf_dihedral_angle_d7.612943
ELECTRON MICROSCOPYf_chiral_restr0.0541019
ELECTRON MICROSCOPYf_plane_restr0.0061140

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