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- PDB-9vcf: Cryo-EM structure of Shewanella putrefaciens ComEC in complex wit... -

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Basic information

Entry
Database: PDB / ID: 9vcf
TitleCryo-EM structure of Shewanella putrefaciens ComEC in complex with dsDNA
Components
  • (DNA (30-MER)) x 2
  • DNA internalization-related competence protein ComEC/Rec2
KeywordsMEMBRANE PROTEIN / Competence / DNA channel / Hydrolase
Function / homology
Function and homology information


establishment of competence for transformation / plasma membrane
Similarity search - Function
ComEC/Rec2-related protein / Competence protein ComEC/Rec2 / Domain of unknown function DUF4131 / Competence protein / Domain of unknown function (DUF4131) / ComA-like, MBL domain / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA internalization-related competence protein ComEC/Rec2
Similarity search - Component
Biological speciesShewanella putrefaciens (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsHirano, H. / Nureki, O.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K15027 Japan
Japan Science and TechnologyJPMJCR20E2 Japan
Japan Agency for Medical Research and Development (AMED)24ama121012j0003 Japan
CitationJournal: Science / Year: 2026
Title: Structural basis for DNA processing and membrane translocation by ComEC in natural transformation.
Authors: Hisato Hirano / Naoko Tsuji / Shinobu Chiba / Osamu Nureki /
Abstract: Natural transformation is one of the major pathways of horizontal gene transfer in bacteria, enabling the acquisition of extracellular DNA and its integration into the host genome. ComEC is a ...Natural transformation is one of the major pathways of horizontal gene transfer in bacteria, enabling the acquisition of extracellular DNA and its integration into the host genome. ComEC is a membrane protein responsible for DNA translocation in this process, yet its precise function and structure have remained elusive. Here, we report cryo-electron microscopy structures of ComEC in DNA-free, single-stranded DNA (ssDNA)-bound, and double-stranded DNA (dsDNA)-bound forms, together with biochemical analyses. These structures reveal that ComEC cleaves one strand of dsDNA at its extracellular domain and guides the remaining strand into a positively charged pore formed within the membrane domain. These findings provide a structural basis for the long-hypothesized roles of ComEC in both DNA processing and translocation across the inner membrane during natural transformation.
History
DepositionJun 5, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA internalization-related competence protein ComEC/Rec2
B: DNA (30-MER)
C: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,5634
Polymers111,4983
Non-polymers651
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 DNA internalization-related competence protein ComEC/Rec2


Mass: 93053.609 Da / Num. of mol.: 1 / Mutation: D577A, D579A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens (bacteria) / Gene: Sputcn32_1556 / Production host: Escherichia coli (E. coli) / References: UniProt: A4Y5P8
#2: DNA chain DNA (30-MER)


Mass: 9177.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (30-MER)


Mass: 9265.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / 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

ComponentName: Shewanella putrefaciens ComEC / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Shewanella putrefaciens (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: 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: 16000 nm / Nominal defocus min: 8000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2Servalcat0.4.88model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42796 / Symmetry type: POINT

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