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- EMDB-64949: Cryo-EM structure of Shewanella decolorationis ComEC -

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Basic information

Entry
Database: EMDB / ID: EMD-64949
TitleCryo-EM structure of Shewanella decolorationis ComEC
Map data
Sample
  • Complex: Shewanella decolorationis ComEC
    • Protein or peptide: Dna internalization-related competence protein rec2
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: ZINC ION
KeywordsCompetence / DNA channel / Membrane protein / Hydrolase
Function / homology
Function and homology information


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 rec2
Similarity search - Component
Biological speciesShewanella decolorationis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 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_64949.png

Downloads & links

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Map

FileDownload / File: emd_64949.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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: 1.3
Minimum - Maximum-5.5991955 - 8.543499000000001
Average (Standard dev.)0.0031681254 (±0.14592528)
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_64949_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_64949_half_map_1.map
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Half map: #1

Fileemd_64949_half_map_2.map
Projections & Slices
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Sample components

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Entire : Shewanella decolorationis ComEC

EntireName: Shewanella decolorationis ComEC
Components
  • Complex: Shewanella decolorationis ComEC
    • Protein or peptide: Dna internalization-related competence protein rec2
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: ZINC ION

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Supramolecule #1: Shewanella decolorationis ComEC

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

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Macromolecule #1: Dna internalization-related competence protein rec2

MacromoleculeName: Dna internalization-related competence protein rec2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Shewanella decolorationis (bacteria)
Molecular weightTheoretical: 89.670219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGLEVLF QGPGGGSGTG SGSGSMNGFI FGFSATLLSA MLWPSLLPIS YLPYLCLGAL VLFKKASTLS GALFAVFWL TGFCFILSRQ DLPLSLQPVQ VRGEIISLVS QNSDWVSFDI IVDKPNLIFW PRAKLRLTWQ SPEAVQVGQV W SFTLMPKS ...String:
MGHHHHHHHH HHSSGLEVLF QGPGGGSGTG SGSGSMNGFI FGFSATLLSA MLWPSLLPIS YLPYLCLGAL VLFKKASTLS GALFAVFWL TGFCFILSRQ DLPLSLQPVQ VRGEIISLVS QNSDWVSFDI IVDKPNLIFW PRAKLRLTWQ SPEAVQVGQV W SFTLMPKS ISSVLNQGGY NEQKQLISQH IVGKGRVIHA QLLTTHFSLR NHLISQLSPK LSTFAQGDIL LALILGDKQL IP ASKWQAL RQTGTGHLVA ISGLHLSVIT AWVYICTLFL LSRFAAHPSR RNLVIALLLA GGSALFYSYL AGFAVSTQRA LVM ILLIML LSLLRRYSSA WDRLLFALFI VLLFDPLACL SAGFWLSFCA LAIILYTLES APRIQPAEGK ATFRAKARGR LAQF WSIQW RLSLVLGLVQ AVFFGGLSVH SLWMNMLVVP WFSLVVIPLS MLAFILWWLG TFFGQAWFGL FHLADFTVLP YGKLL ELSG NLPVHWHSVS DTLLGASLCV LLALILWRYL PHHSRYGLWH LPITLLFIPA TLVFFPRMTE PSSPQWTLHL LDVGQG LAV VIEQDRRALI YDTGAAFGED FSYSERVIIP FLSSKGLALV DYIVVSHGAN AHAGGAEVLS KAYPRANWIT DVAHLEG MP CLPQQIQWQQ LRLSFISPQT AKGGNNASCV LRIDDGVHSL LLSGDIEKET EAVLIEQALK GAELKSQVLI APHHGSRT S STPAFIDAVA PELVLFPAGL NNRYGFPKPD VVARYQARNI DYFTTGREGQ ISVSFAAGRL EVKTYRRDLA PFWYNRLFR FGDLINPE

UniProtKB: Dna internalization-related competence protein rec2

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Macromolecule #2: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 1 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / 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: 65.0 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: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 226637
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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