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- EMDB-45280: HerA-DUF4297 supramolecular anti-phage defense complex with dsDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-45280
TitleHerA-DUF4297 supramolecular anti-phage defense complex with dsDNA
Map datacryosparc refined map
Sample
  • Complex: HerA-DUF4297
    • Protein or peptide: HerA
    • Protein or peptide: DUF4297
KeywordsdsDNA / nuclease / ATPase / 18-mer / ANTIVIRAL PROTEIN
Biological speciesBacillus sp. HMF5848 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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: To Be Published
Title: Structure-guided characterization of a novel bacterial anti-phage defense system
Authors: Rish AD / Fosuah E / Fu TM
History
DepositionJun 10, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45280.png

Downloads & links

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Map

FileDownload / File: emd_45280.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryosparc 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: 0.09
Minimum - Maximum-2.0325115 - 3.1161857
Average (Standard dev.)0.00070970703 (±0.06359632)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: half map A

Fileemd_45280_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_45280_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HerA-DUF4297

EntireName: HerA-DUF4297
Components
  • Complex: HerA-DUF4297
    • Protein or peptide: HerA
    • Protein or peptide: DUF4297

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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

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Macromolecule #1: HerA

MacromoleculeName: HerA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIGSVIESS PHSILVKIDT LKIFEKAKSA LQIGKYLKIQ EGNHNFVLCV IQNIKISTDK DEDIFILTVQ PVGIFKGEEF FQGNSMLPSP TEPVFLVEDD ILNKIFSNEK TKIFHLGNLA QNEEVSFTLD GDKFFSKHVA VVGSTGSGKS CAVAKILQNV VGINDARNIN ...String:
MKIGSVIESS PHSILVKIDT LKIFEKAKSA LQIGKYLKIQ EGNHNFVLCV IQNIKISTDK DEDIFILTVQ PVGIFKGEEF FQGNSMLPSP TEPVFLVEDD ILNKIFSNEK TKIFHLGNLA QNEEVSFTLD GDKFFSKHVA VVGSTGSGKS CAVAKILQNV VGINDARNIN KSDKKNSHII IFDIHSEYKS AFEIDKNEDF NLNYLDVEKL KLPYWLMNSE ELETLFIESN EQNSHNQVSQ FKRAVVLNKE KYNPEFKKIT YDSPVYFNIN EVFNYIYNLN EEVINKIEGE PSLPKLSNGE LVENRQIYFN EKLEFTSSNT SKATKASNGP FNGEFNRFLS RFETKLTDKR LEFLLLNQDV EENSKYRTEH FEDILKQFMG YLDRSNVSII DLSGIPFEVL SITISLISRL IFDFAFHYSK LQHQKDELND IPFMIVCEEA HNYIPRTGGI EFKAAKKSIE RIAKEGRKYG LSLMVVSQRP SEVSDTILSQ CNNFINLRLT NINDQNYIKN LLPDNSRSIS EILPTLGAGE CLVVGDSTPI PSIVKLELPN PEPRSQSIKF HKKWSESWRT PSFEEVIMRW RKENG

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Macromolecule #2: DUF4297

MacromoleculeName: DUF4297 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMSREADHTI KGFLYQFNKT LNSILSSTDQ DEIQIEGIIE DIDIKNSNIT NAIQCKYHES KVRHNLSDIY KPILQMLLHF LENDSLNIKY ALYAYFPNEQ VGVKEVTKSQ IEEILSSSNF DYISKYISKI KPPKEQIIKE LLGKTSKTTE DKTRIKKYYE TSKLETIVDI ...String:
MMSREADHTI KGFLYQFNKT LNSILSSTDQ DEIQIEGIIE DIDIKNSNIT NAIQCKYHES KVRHNLSDIY KPILQMLLHF LENDSLNIKY ALYAYFPNEQ VGVKEVTKSQ IEEILSSSNF DYISKYISKI KPPKEQIIKE LLGKTSKTTE DKTRIKKYYE TSKLETIVDI DKFLRDHFVF EIGLSYEELM NETKNLLMKE GFSLEDVKDL FYPNSIQYIA ELSILPEAEK RISSKNKLID YLKGNKKTAM SRWTSEVLTR KQLLKVRKNQ LVPSLNINSR SRYFIIDPDT IDNFDDEFIL FVKDYLDKYN SKIKLHTETP CFILKTDVNN LSEYHKRFVS RNIQIITGYI GDTFYFKEFN KEPKRIIKDN WVEFKARISC NSDEVIKCIN YKKCDDLYIV GGVDVSLLDT ADVNIENLEI NNFRELKYLL SMLKEI

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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

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

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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

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 434093
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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