[English] 日本語
Yorodumi
- EMDB-45124: HerA-DUF assembly 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45124
TitleHerA-DUF assembly 1
Map dataDeepEmhancer refined map
Sample
  • Complex: HerA-DUF4297
    • Protein or peptide: DUF4297 domain-containing protein
    • Protein or peptide: ATP-binding protein
Keywordsanti-phage / nuclease / ATPase / 18-mer / ANTIVIRAL PROTEIN
Function / homologyHelicase HerA-like / Helicase HerA, central domain / Helicase HerA, central domain / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ATP-binding protein / DUF4297 domain-containing protein
Function and homology information
Biological speciesBacillus sp. HMF5848 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsRish AD / Fosuah E / Fu TM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GR128399 United States
CitationJournal: Mol Cell / Year: 2025
Title: Architecture remodeling activates the HerA-DUF anti-phage defense system.
Authors: Anthony D Rish / Elizabeth Fosuah / Zhangfei Shen / Ila A Marathe / Vicki H Wysocki / Tian-Min Fu /
Abstract: Leveraging AlphaFold models and integrated experiments, we characterized the HerA-DUF4297 (DUF) anti-phage defense system, focusing on DUF's undefined biochemical functions. Guided by structure-based ...Leveraging AlphaFold models and integrated experiments, we characterized the HerA-DUF4297 (DUF) anti-phage defense system, focusing on DUF's undefined biochemical functions. Guided by structure-based genomic analyses, we found DUF homologs to be universally distributed across diverse bacterial immune systems. Notably, one such homolog, Cap4, is a nuclease. Inspired by this evolutionary clue, we tested DUF's nuclease activity and observed that DUF cleaves DNA substrates only when bound to its partner protein HerA. To dissect the mechanism of DUF activation, we determined the structures of DUF and HerA-DUF. Although DUF forms large oligomeric assemblies both alone and with HerA, oligomerization alone was insufficient to elicit nuclease activity. Instead, HerA binding induces a profound architecture remodeling that propagates throughout the complex. This remodeling reconfigures DUF into an active nuclease capable of robust DNA cleavage. Together, we highlight an architecture remodeling-driven mechanism that may inform the activation of other immune systems.
History
DepositionMay 29, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45124.png

Downloads & links

-
Map

FileDownload / File: emd_45124.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEmhancer refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 336 pix.
= 366.24 Å		1.09 Å/pix.
x 336 pix.
= 366.24 Å		1.09 Å/pix.
x 336 pix.
= 366.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.019402351 - 1.7190456
Average (Standard dev.)0.002070009 (±0.027880449)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 366.24002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: cryoSparc refined map

Fileemd_45124_additional_1.map
AnnotationcryoSparc refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: cryosparc refine before C6 symmetry expansion

Fileemd_45124_additional_2.map
Annotationcryosparc refine before C6 symmetry expansion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_45124_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map A

Fileemd_45124_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HerA-DUF4297

EntireName: HerA-DUF4297
Components
  • Complex: HerA-DUF4297
    • Protein or peptide: DUF4297 domain-containing protein
    • Protein or peptide: ATP-binding protein

-
Supramolecule #1: HerA-DUF4297

SupramoleculeName: HerA-DUF4297 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Anti-phage defense supramolecular complex
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Molecular weightTheoretical: 1.02 MDa

-
Macromolecule #1: DUF4297 domain-containing protein

MacromoleculeName: DUF4297 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Molecular weightTheoretical: 51.330734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMSREADHTI KGFLYQFNKT LNSILSSTDQ DEIQIEGIIE DIDIKNSNIT NAIQCKYHES KVRHNLSDIY KPILQMLLHF LENDSLNIK YALYAYFPNE QVGVKEVTKS QIEEILSSSN FDYISKYISK IKPPKEQIIK ELLGKTSKTT EDKTRIKKYY E TSKLETIV ...String:
MMSREADHTI KGFLYQFNKT LNSILSSTDQ DEIQIEGIIE DIDIKNSNIT NAIQCKYHES KVRHNLSDIY KPILQMLLHF LENDSLNIK YALYAYFPNE QVGVKEVTKS QIEEILSSSN FDYISKYISK IKPPKEQIIK ELLGKTSKTT EDKTRIKKYY E TSKLETIV DIDKFLRDHF VFEIGLSYEE LMNETKNLLM KEGFSLEDVK DLFYPNSIQY IAELSILPEA EKRISSKNKL ID YLKGNKK TAMSRWTSEV LTRKQLLKVR KNQLVPSLNI NSRSRYFIID PDTIDNFDDE FILFVKDYLD KYNSKIKLHT ETP CFILKT DVNNLSEYHK RFVSRNIQII TGYIGDTFYF KEFNKEPKRI IKDNWVEFKA RISCNSDEVI KCINYKKCDD LYIV GGVDV SLLDTADVNI ENLEINNFRE LKYLLSMLKE I

UniProtKB: DUF4297 domain-containing protein

-
Macromolecule #2: ATP-binding protein

MacromoleculeName: ATP-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Molecular weightTheoretical: 67.182125 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIGSVIESS PHSILVKIDT LKIFEKAKSA LQIGKYLKIQ EGNHNFVLCV IQNIKISTDK DEDIFILTVQ PVGIFKGEEF FQGNSMLPS PTEPVFLVED DILNKIFSNE KTKIFHLGNL AQNEEVSFTL DGDKFFSKHV AVVGSTGSGK SCAVAKILQN V VGINDARN ...String:
MKIGSVIESS PHSILVKIDT LKIFEKAKSA LQIGKYLKIQ EGNHNFVLCV IQNIKISTDK DEDIFILTVQ PVGIFKGEEF FQGNSMLPS PTEPVFLVED DILNKIFSNE KTKIFHLGNL AQNEEVSFTL DGDKFFSKHV AVVGSTGSGK SCAVAKILQN V VGINDARN INKSDKKNSH IIIFDIHSEY KSAFEIDKNE DFNLNYLDVE KLKLPYWLMN SEELETLFIE SNEQNSHNQV SQ FKRAVVL NKEKYNPEFK KITYDSPVYF NINEVFNYIY NLNEEVINKI EGEPSLPKLS NGELVENRQI YFNEKLEFTS SNT SKATKA SNGPFNGEFN RFLSRFETKL TDKRLEFLLL NQDVEENSKY RTEHFEDILK QFMGYLDRSN VSIIDLSGIP FEVL SITIS LISRLIFDFA FHYSKLQHQK DELNDIPFMI VCEEAHNYIP RTGGIEFKAA KKSIERIAKE GRKYGLSLMV VSQRP SEVS DTILSQCNNF INLRLTNIND QNYIKNLLPD NSRSISEILP TLGAGECLVV GDSTPIPSIV KLELPNPEPR SQSIKF HKK WSESWRTPSF EEVIMRWRKE NG

UniProtKB: ATP-binding protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.75 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 530769
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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