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- EMDB-64953: Cryo-EM structure of Shewanella putrefaciens ComEC in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-64953
TitleCryo-EM structure of Shewanella putrefaciens ComEC in complex with dsDNA
Map data
Sample
  • Complex: Shewanella putrefaciens ComEC
    • Protein or peptide: DNA internalization-related competence protein ComEC/Rec2
    • DNA: DNA (30-MER)
    • DNA: DNA (30-MER)
  • Ligand: ZINC ION
KeywordsCompetence / DNA channel / Membrane protein / 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 internalization-related competence protein ComEC/Rec2
Similarity search - Component
Biological speciesShewanella putrefaciens (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsHirano H / Nureki O
Funding support Japan, 3 items
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, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64953.png

Downloads & links

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Map

FileDownload / File: emd_64953.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 265.608 Å		1.11 Å/pix.
x 240 pix.
= 265.608 Å		1.11 Å/pix.
x 240 pix.
= 265.608 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5887139 - 0.78758913
Average (Standard dev.)-0.00033282855 (±0.015822934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 265.60797 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64953_msk_1.map
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Half map: #2

Fileemd_64953_half_map_1.map
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Half map: #1

Fileemd_64953_half_map_2.map
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Sample components

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Entire : Shewanella putrefaciens ComEC

EntireName: Shewanella putrefaciens ComEC
Components
  • Complex: Shewanella putrefaciens ComEC
    • Protein or peptide: DNA internalization-related competence protein ComEC/Rec2
    • DNA: DNA (30-MER)
    • DNA: DNA (30-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Shewanella putrefaciens ComEC

SupramoleculeName: Shewanella putrefaciens ComEC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Shewanella putrefaciens (bacteria)

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Macromolecule #1: DNA internalization-related competence protein ComEC/Rec2

MacromoleculeName: DNA internalization-related competence protein ComEC/Rec2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shewanella putrefaciens (bacteria)
Molecular weightTheoretical: 93.053609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGLEVLF QGPGGGSGTG SGSGSMNRFI LGFSASLLSA MLWPSLPPVA YLPYLLVGAL ILYQKAPLCS GVLFAMLWL TVFCLGLSRQ DLPVQQQPLQ VRGEIISLVS QNSDWLSLDI AIIKPNLILR PRAKLRLTWK APPDVAVGQV W LFTITPKS ...String:
MGHHHHHHHH HHSSGLEVLF QGPGGGSGTG SGSGSMNRFI LGFSASLLSA MLWPSLPPVA YLPYLLVGAL ILYQKAPLCS GVLFAMLWL TVFCLGLSRQ DLPVQQQPLQ VRGEIISLVS QNSDWLSLDI AIIKPNLILR PRAKLRLTWK APPDVAVGQV W LFTITPKS VSNVLNQGGY NEQKQLISQH IVGKGRVIKA ELIESQPSLR NQLVSALAPQ LAPLQQGDLL LALILGDKQL IS SERWQML RQTATGHLVA ISGLHLSVVT AWIYAVMIFG LTRFVPHPSR RNWVFALLLS GIGAAFYAYL AGFGISTQRA LVM ILLLML LSLLKRFSSP WERLLFALFM VLLIDPLACL SAGFWLSFCA LAIILYTLEA APKVHQLTND ITPLGRVRAG LLQF WSIQW RLSLGLGFVQ AVLFGGISAH SLWINMLAVP WFSFVVIPIA MAGFVCWWIG TALGFSWMGL LELSNWALMP YGQLL AISG QLPIHWQVVS ESVLALALCG VLGGVLWRYI PKQRLYWPWR FIVSLLFVPF LLSFLLKWLP LKSATWSMHL LDVGQG LAV VIEKEGRGLI YDTGAAFGES FSYSQRVIIP FLNAKGIREI DYVFISHSAN AHAGGASALL AAYPKAQWIT DVTEIAG KG CRPQQINWQD LKISIIFPQK PIAGNNGSCV VRIDDTQQRV LLTGDIEKNS EMKLLTQVKM QPTILMSQVL IAPHHGSK S SSTEAFIDAV SPELVLFPAG LGNRYGFPKP VVVDRYQARN IPHLTTGIEG QISVIFRHDS REVKTYRRDL APFWYNRLF RFGDLINPEG SGDYKDDDDK GSPSRLEEEL RRRLTEP

UniProtKB: DNA internalization-related competence protein ComEC/Rec2

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Macromolecule #2: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.177974 KDa
SequenceString:
(DC)(DC)(DC)(DG)(DC)(DA)(DG)(DC)(DA)(DA) (DT)(DG)(DT)(DA)(DC)(DA)(DA)(DA)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DA)(DC)(DA)(DG) (DT)

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Macromolecule #3: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.265956 KDa
SequenceString:
(DA)(DC)(DT)(DG)(DT)(DT)(DA)(DT)(DG)(DT) (DT)(DA)(DT)(DT)(DT)(DG)(DT)(DA)(DC)(DA) (DT)(DT)(DG)(DC)(DT)(DG)(DC)(DG)(DG) (DG)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 16.0 µm / Nominal defocus min: 8.0 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: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 42796
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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