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- EMDB-72967: Hna Monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-72967
TitleHna Monomer
Map data
Sample
  • Complex: Hna monomer
    • Protein or peptide: Helicase ATP-binding domain-containing protein
  • Ligand: CALCIUM ION
KeywordsPD(D/E)XK nuclease. Superfamily 2 helicase. Anti-bacteriophage protein / IMMUNE SYSTEM
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleobase-containing compound metabolic process / helicase activity / DNA binding / ATP binding
Similarity search - Function
HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Helicase ATP-binding domain-containing protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsHooper M
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Welch FoundationF-1938 United States
CitationJournal: bioRxiv / Year: 2025
Title: Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system.
Authors: Matthew M Hooper / Benjamin T Hoover / Hongshan Zhang / Adam S Franco / Ilya J Finkelstein / David W Taylor
Abstract: Prokaryotic organisms have evolved unique strategies to acquire immunity against the constant threat of bacteriophage (phage) and mobile genetic elements. Hna is a broadly distributed anti-phage ...Prokaryotic organisms have evolved unique strategies to acquire immunity against the constant threat of bacteriophage (phage) and mobile genetic elements. Hna is a broadly distributed anti-phage immune system that confers resistance against diverse phage by eliciting an abortive infection response. Using a combination of biochemistry, cryo-electron microscopy, and single-molecule fluorescence imaging, we reveal that Hna functions as a 3'-5' single-stranded DNA exonuclease that forms an auto-inhibited dimer under physiological ATP concentrations. We observed that Hna autoinhibition can be overcome by incorporation of a phage-encoded single-stranded DNA binding protein (SSB), stimulating unregulated Hna nuclease activity. Furthermore, phage escape mutants encode SSB variants that evade Hna surveillance by adopting higher order stoichiometries with enhanced DNA binding affinity. Our work establishes the molecular basis of Hna-mediated anti-phage activity and provides novel insights into how phage-encoded proteins can directly stimulate a bacterial immune response.
History
DepositionSep 30, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72967.png

Downloads & links

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Map

FileDownload / File: emd_72967.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.95
Minimum - Maximum-50.878337999999999 - 131.128700000000009
Average (Standard dev.)-0.000000000004198 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_72967_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72967_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hna monomer

EntireName: Hna monomer
Components
  • Complex: Hna monomer
    • Protein or peptide: Helicase ATP-binding domain-containing protein
  • Ligand: CALCIUM ION

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Supramolecule #1: Hna monomer

SupramoleculeName: Hna monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sinorhizobium meliloti (bacteria)
Molecular weightTheoretical: 94.7 KDa

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Macromolecule #1: Helicase ATP-binding domain-containing protein

MacromoleculeName: Helicase ATP-binding domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sinorhizobium meliloti (bacteria)
Molecular weightTheoretical: 94.84125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVDFRKRLGS TEAKKVVDPV ALYETLDRAT DKGPLRPAQE AVLGDWFKNY GGDVSGGSKR DVIIKLHTGQ GKTLIGLLIL QSRLNDNRR PCVYLCPDNF LIEQTCEQAS QFGIKVSTVE DDLPDDFLAG KSILVTSVQK LFNGLTKFGL HRQSIEIDTI L MDDAHACS ...String:
MVDFRKRLGS TEAKKVVDPV ALYETLDRAT DKGPLRPAQE AVLGDWFKNY GGDVSGGSKR DVIIKLHTGQ GKTLIGLLIL QSRLNDNRR PCVYLCPDNF LIEQTCEQAS QFGIKVSTVE DDLPDDFLAG KSILVTSVQK LFNGLTKFGL HRQSIEIDTI L MDDAHACS DRIRDACKIK IPKDEPAYHA LFKLFSTELE LQGVGTFADL ENGKRDALLP VPYWAWMAKE GEVAAILSAA AD KKSIKFT WPLLKDRLRL CQCIFSGAAL EIEPHIAPLE DFGSYARAKH RIFMSATVTD DSFLVKGLQL SPDTISNPLT YAK ETWSGE KMVLIPSMMH EDLDRAKIVA WLAPVNPKLK FGIVALVPSF ARNKDWGAYG AKTVDKDSVS EAVSDLKKGQ YGTP LVLAN RYDGIDLPDN TCRVLVFDSR PFSENLTDLY QEHCRPESEA TLMRTIRSIE QGMGRSVRGE KDYSVVVAIG ADLVR TLRD VSSRRYLSSQ MATQIEIGLE IAEMAREEIA AGKEPLAALV GLINQCLKRD DGWKDFYADQ MKKVAPKGAN KEILEL YSR ELAAEQAYAA GDYNRAEQTI QKLLDDGLAH PDDRGWYLQE RARYLHDGNR VEAQKLQVAA HRNNKLLLKP PTGVTVT KL TIVSQGRTER IANWVNKFES YADLDATVSD ILGRLVFGTK AEKFESALNE LAFALGFAGE RPDAEWKEGP DNLWALND I QYLLFECKSE VDTTRSEIHK RETEQMNRSA AWFDKHYLGM KVKRLIVHPA NKIQSAAAFT HEVDGMLDSN LKAFVRSAR AFFKSFENQN LKDLSVLHIQ GLIDAHHLSV DNLINRYCSK LKNVK

UniProtKB: Helicase ATP-binding domain-containing protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 278967
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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