[English] 日本語
Yorodumi
- EMDB-64944: Cryo-EM structure of Bacillus halodurans ComEC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64944
TitleCryo-EM structure of Bacillus halodurans ComEC
Map data
Sample
  • Complex: Bacillus halodurans ComEC
    • Protein or peptide: Competence protein ComEC
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: ZINC ION
KeywordsCompetence / DNA channel / Membrane protein / Hydrolase
Biological speciesHalalkalibacterium halodurans C-125 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 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

-
Structure visualization

Supplemental images

emd_64944.png

Downloads & links

-
Map

FileDownload / File: emd_64944.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 240 pix.
= 265.6 Å		1.11 Å/pix.
x 240 pix.
= 265.6 Å		1.11 Å/pix.
x 240 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.10667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.7102336 - 1.1753982
Average (Standard dev.)-0.00032352348 (±0.022017112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_64944_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_64944_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64944_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bacillus halodurans ComEC

EntireName: Bacillus halodurans ComEC
Components
  • Complex: Bacillus halodurans ComEC
    • Protein or peptide: Competence protein ComEC
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: ZINC ION

-
Supramolecule #1: Bacillus halodurans ComEC

SupramoleculeName: Bacillus halodurans ComEC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Halalkalibacterium halodurans C-125 (bacteria)

-
Macromolecule #1: Competence protein ComEC

MacromoleculeName: Competence protein ComEC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Halalkalibacterium halodurans C-125 (bacteria)
Molecular weightTheoretical: 92.433984 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHHH HHSSGLEVLF QGPGGGSGTG SGSGSMASRI IFLFSLLIML GLATGLRGFS ASFGFLTFLL LLIILCQQYR RFQLLFLAI LLFLCAWLYG VVQERQNETQ LNPLDQNVGG TLISDPELDG DQFSVTVKTT DGEKVLIRGR VQVEAEKDKL E MMQIGMFC ...String:
MGHHHHHHHH HHSSGLEVLF QGPGGGSGTG SGSGSMASRI IFLFSLLIML GLATGLRGFS ASFGFLTFLL LLIILCQQYR RFQLLFLAI LLFLCAWLYG VVQERQNETQ LNPLDQNVGG TLISDPELDG DQFSVTVKTT DGEKVLIRGR VQVEAEKDKL E MMQIGMFC SFVGQLEIPN EPTNPYQFNY RQFLYNNRIH WIFRTDLSQW QCSDQPTTLF IKVKRWRSER LQDIYDLASD ET AGLIAAF VYGDRSELDD ELLSAYQSLG VIHLLAVSGL HVGLVVAAVF YLLIRLGVTR ERAYELLLLF LPFYAIVAGA APS VVREVG MTITVLLALR FQKRLAPVIV LSIVAVLYII IEPYAIFTLG FQLSFLTTCA LLLSSSTLLQ AINRPLLSLL KVTF LAQLI SMPVILYHFF ELPVLSVPLN LLFVPIVSFV LLPLSFFVAS SLLIHPAVAE LPLFILEIIV PIVHQLLLVL NEQSF ATVV IGKPSLNSVF LMMISLIIGW AWLERKEPFK AWGAFSVVLF LIGWQIYSPY WSNEAVVTMI DVGQGDSFLI ELPRRE AIY MIDTGGWVTY GEMEPWQERR NTRDIGEQVL TPILKGKGIQ GIDKLILTHG AEAHFGGAEG LVRSIKVDEI VYGYKHG EY TEREREVLSA LKKAGASIRF VKSGDQWVIG SSSFRVLSPF GDEEELNDQS VVVYAVIEGV RFLFTGDLEE VGEKRLLE F HGNLKADVLK VGHHGSATST TDPFLEAVHP VVALISAGRN NLYGHPNQDV LAALEQYEAF VLRTDLHGAV KLTIRDGAI YARVMTTDGS GSPSRLEEEL RRRLTEP

-
Macromolecule #2: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 3 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 251581
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more