[English] 日本語
Yorodumi
- EMDB-67286: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-67286
TitleCryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
Map data
Sample
  • Complex: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
    • Protein or peptide: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
    • Protein or peptide: KomC(H146N), a SIR2-domain NADase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsKomBC / NAD hydrolysis protein / IMMUNE SYSTEM
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXie W / Feng H / Luo M
Funding support Singapore, 1 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: Mol Cell / Year: 2026
Title: Filament-mediated repurposing of toxic dITP for immunity in the Kongming system.
Authors: Hao Feng / Kai Shao / Zhifeng Zeng / Eddie Yong Jun Tan / Zeyu Hu / Ruiliang Zhao / Jikai Rao / Jian Shi / Zhuojian Chen / Rafael Pinilla Redondo / Bin Wu / Wenyuan Han / Min Luo /
Abstract: Abortive infection systems protect bacteria by triggering self-destruction in response to phage attack. Most known systems rely on stable cyclic nucleotides that accumulate to stoichiometric levels ...Abortive infection systems protect bacteria by triggering self-destruction in response to phage attack. Most known systems rely on stable cyclic nucleotides that accumulate to stoichiometric levels to activate effectors; the Kongming (Kom) system employs the toxic metabolite deoxyinosine triphosphate (dITP) as its signaling molecule. Here, we show that the Escherichia coli KomB-KomC (KomBC) complex forms a preassembled filament that remains inactive until dITP binding induces cooperative allosteric activation. KomB, a homolog of the nucleotide-hydrolyzing enzyme HAM1, has lost catalytic activity but evolved a high-affinity, hydrolysis-resistant binding pocket for dITP. Interestingly, substoichiometric dITP binding is sufficient to activate adjacent KomC NADase domains, which propagate activation cooperatively along the filament. This filament-based architecture enables ultrasensitive, long-range allosteric signaling in response to a low-abundance and short-lived metabolite. Our findings reveal an ultrasensitive immune strategy that transforms a toxic byproduct into a robust antiviral trigger, expanding the known repertoire of bacterial defense strategies.
History
DepositionNov 26, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_67286.png

Downloads & links

-
Map

FileDownload / File: emd_67286.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.234
Minimum - Maximum-0.56117296 - 1.2342453
Average (Standard dev.)0.00066803524 (±0.04159246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_67286_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_67286_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with N...

EntireName: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
Components
  • Complex: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
    • Protein or peptide: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
    • Protein or peptide: KomC(H146N), a SIR2-domain NADase
  • Ligand: 2'-deoxyinosine 5'-triphosphate
  • Ligand: ADENOSINE MONOPHOSPHATE

-
Supramolecule #1: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with N...

SupramoleculeName: Cryo-EM Helical Structure of the dITP-KomBC(H146N) Complex with NAD Fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase

MacromoleculeName: KomB, HAM-like protein, Non-canonical purine NTP pyrophosphatase
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 20.929131 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNIRFITRNR HKIKEINKIL SGTGVVVLAS EHSIDEIQTE NVHALIKDKL LKAFKLVGRP VFVEHTGLYI ESLNGFPGGL TQIFWDKLQ ADKFSQLLGT SENPRLVAKT IIGYCDSMKI YIFEGETQGT ISPVPKGPRD FQWDCIFIPD GESETFAEMG D RKNEISMR KKAFDKFKEY LLEGGK

-
Macromolecule #2: KomC(H146N), a SIR2-domain NADase

MacromoleculeName: KomC(H146N), a SIR2-domain NADase / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 30.631842 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEQLLADYKK GNVILFVGAG VSMNLGLPSW SQLVDHIATE LGYDPDIYRT FGSALELAEY YKLKKGKIGP LRSWMDRMWH SSDIDINKS KVHEYIAKAN FPIIYTTNYD RWIETALSNY GKEYIKISSV SDIAKIDNNK TQIIKFNGDF DDDSSIVLDE T SYFQRLEF ...String:
MEQLLADYKK GNVILFVGAG VSMNLGLPSW SQLVDHIATE LGYDPDIYRT FGSALELAEY YKLKKGKIGP LRSWMDRMWH SSDIDINKS KVHEYIAKAN FPIIYTTNYD RWIETALSNY GKEYIKISSV SDIAKIDNNK TQIIKFNGDF DDDSSIVLDE T SYFQRLEF ETPLDIKFRS DVLGKSVLFI GYSLSDINIR LLFYKLSKLW KEQKLEEAQP KSYIFLPRPN PIQEEILEQW RI GMISSEN DNPGESLEEF LKNFVLV

-
Macromolecule #3: 2'-deoxyinosine 5'-triphosphate

MacromoleculeName: 2'-deoxyinosine 5'-triphosphate / type: ligand / ID: 3 / Number of copies: 8 / Formula: Y43
Molecular weightTheoretical: 492.166 Da
Chemical component information

ChemComp-Y43:
2'-deoxyinosine 5'-triphosphate

-
Macromolecule #4: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 47.06 Å
Applied symmetry - Helical parameters - Δ&Phi: -79.93 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 208086
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
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