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- EMDB-38207: Cryo-EM structure of an anti-phage defense complex bound to ATPrS... -

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Basic information

Entry
Database: EMDB / ID: EMD-38207
TitleCryo-EM structure of an anti-phage defense complex bound to ATPrS and DNA
Map data
Sample
  • Complex: DUF4297-HerA
    • Protein or peptide: ATP-binding protein
    • Protein or peptide: DUF4297
    • Other: S20DNA3
    • DNA: S20DNA4
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHerA / Helicase DUF4297 / Endonuclease / DNA BINDING PROTEIN
Function / homology: / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsAn Q / Deng Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Res / Year: 2024
Title: Molecular and structural basis of an ATPase-nuclease dual-enzyme anti-phage defense complex.
Authors: Qiyin An / Yong Wang / Zhenhua Tian / Jie Han / Jinyue Li / Fumeng Liao / Feiyang Yu / Haiyan Zhao / Yancheng Wen / Heng Zhang / Zengqin Deng /
Abstract: Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in ...Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in the type III CRISPR-Cas system. However, concerted enzymatic activities in other bacterial defense systems are poorly understood. Here, we biochemically and structurally characterize a two-component defense system DUF4297-HerA, demonstrating that DUF4297-HerA confers resistance against phage infection by cooperatively cleaving dsDNA and hydrolyzing ATP. DUF4297 alone forms a dimer, and HerA alone exists as a nonplanar split spiral hexamer, both of which exhibit extremely low enzymatic activity. Interestingly, DUF4297 and HerA assemble into an approximately 1 MDa supramolecular complex, where two layers of DUF4297 (6 DUF4297 molecules per layer) linked via inter-layer dimerization of neighboring DUF4297 molecules are stacked on top of the HerA hexamer. Importantly, the complex assembly promotes dimerization of DUF4297 molecules in the upper layer and enables a transition of HerA from a nonplanar hexamer to a planar hexamer, thus activating their respective enzymatic activities to abrogate phage infection. Together, our findings not only characterize a novel dual-enzyme anti-phage defense system, but also reveal a unique activation mechanism by cooperative complex assembly in bacterial immunity.
History
DepositionDec 5, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38207.png

Downloads & links

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Map

FileDownload / File: emd_38207.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.)
0.95 Å/pix.
x 320 pix.
= 304. Å		0.95 Å/pix.
x 320 pix.
= 304. Å		0.95 Å/pix.
x 320 pix.
= 304. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-1.0948356 - 2.263044
Average (Standard dev.)0.002804284 (±0.06774541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 304.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38207_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38207_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : DUF4297-HerA

EntireName: DUF4297-HerA
Components
  • Complex: DUF4297-HerA
    • Protein or peptide: ATP-binding protein
    • Protein or peptide: DUF4297
    • Other: S20DNA3
    • DNA: S20DNA4
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: DUF4297-HerA

SupramoleculeName: DUF4297-HerA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: ATP-binding protein

MacromoleculeName: ATP-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 64.870047 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSRNNDINAE VVSVSPNKLK ISVDDLEEFK IAEEKLGVGS YLRVSDNQDV ALLAIIDNFS IEVKESQKQK YMIEASPIGL VKNGKFYRG GDSLALPPKK VEPAKLDEII SIYSDSIDIN DRFTFSSLSL NTKVSVPVNG NRFFNKHIAI VGSTGSGKSH T VAKILQKA ...String:
MSRNNDINAE VVSVSPNKLK ISVDDLEEFK IAEEKLGVGS YLRVSDNQDV ALLAIIDNFS IEVKESQKQK YMIEASPIGL VKNGKFYRG GDSLALPPKK VEPAKLDEII SIYSDSIDIN DRFTFSSLSL NTKVSVPVNG NRFFNKHIAI VGSTGSGKSH T VAKILQKA VDEKQEGYKG LNNSHIIIFD IHSEYENAFP NSNVLNVDTL TLPYWLLNGD ELEELFLDTE ANDHNQRNVF RQ AITLNKK IHFQGDPATK EIISFHSPYY FDINEVINYI NNRNNERKNK DNEHIWSDEE GNFKFDNENA HRLFKENVTP DGS SAGALN GKLLNFVDRL QSKIFDKRLD FILGEGSKSV TFKETLETLI SYGKDKSNIT ILDVSGVPFE VLSICVSLIS RLIF EFGYH SKKIKRKSNE NQDIPILIVY EEAHKYAPKS DLSKYRTSKE AIERIAKEGR KYGVTLLLAS QRPSEISETI FSQCN TFIS MRLTNPDDQN YVKRLLPDTV GDITNLLPSL KEGEALIMGD SISIPSIVKI EKCTIPPSSI DIKYLDEWRK EWVDSE FDK IIEQWSKS

UniProtKB: UNIPROTKB: A0A9X9SUP5

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Macromolecule #2: DUF4297

MacromoleculeName: DUF4297 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 46.971949 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDRSAVDTIR GYCYQVDKTI IEIFSLPQMD DSIDIECIED VDVYNDGHLT AIQCKYYEST DYNHSVISKP IRLMLSHFKD NKEKGANYY LYGHYKSGQE KLTLPLKVDF FKSNFLTYTE KKIKHEYHIE NGLTEEDLQA FLDRLVININ AKSFDDQKKE T IQIIKNHF ...String:
MDRSAVDTIR GYCYQVDKTI IEIFSLPQMD DSIDIECIED VDVYNDGHLT AIQCKYYEST DYNHSVISKP IRLMLSHFKD NKEKGANYY LYGHYKSGQE KLTLPLKVDF FKSNFLTYTE KKIKHEYHIE NGLTEEDLQA FLDRLVININ AKSFDDQKKE T IQIIKNHF QCEDYEAEHY LYSNAFRKTY DISCNKKDRR IKKSDFVESI NKSKVLFNIW FYQYEGRKEY LRKLKESFIR RS VNTSPYA RFFILEFQDK TDIKTVKDCI YKIQSNWSNL SKRTDRPYSP FLLFHGTSDA NLYELKNQLF NEDLIFTDGY PFK GSVFTP KMLIEGFSNK EIHFQFINDI DDFNETLNSI NIRKEVYQFY TENCLDIPSQ LPQVNIQVKD FADIKEIV

UniProtKB: UNIPROTKB: A0A9X9SUN3

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Macromolecule #3: S20DNA3

MacromoleculeName: S20DNA3 / type: other / ID: 3 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.229709 KDa
SequenceString: (DG)(DC)(DT)(DT)(DT)(DA)(DT)(DC)(DA)(DG) (DA)(DA)(DG)(DC)(DC)(DA)(DG)(DA)(DC)(DA) (DT)(DT)(DA)(DA)(DC)(DG)(DC)(DT)(DT) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DA)(DC) (DT) (DC)(DA)(DA)(DC)(DG)(DA) ...String:
(DG)(DC)(DT)(DT)(DT)(DA)(DT)(DC)(DA)(DG) (DA)(DA)(DG)(DC)(DC)(DA)(DG)(DA)(DC)(DA) (DT)(DT)(DA)(DA)(DC)(DG)(DC)(DT)(DT) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DA)(DC) (DT) (DC)(DA)(DA)(DC)(DG)(DA)(DG)(DC) (DT)(DG)(DG)(DA)(DC)(DG)(DC)(DG)(DG)(DA) (DT)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #4: S20DNA4

MacromoleculeName: S20DNA4 / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.135602 KDa
SequenceString: (DA)(DT)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DC) (DA)(DG)(DC)(DT)(DC)(DG)(DT)(DT)(DG)(DA) (DG)(DT)(DT)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DA)(DA)(DG)(DC)(DG)(DT)(DT)(DA)(DA) (DT) (DG)(DT)(DC)(DT)(DG)(DG) ...String:
(DA)(DT)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DC) (DA)(DG)(DC)(DT)(DC)(DG)(DT)(DT)(DG)(DA) (DG)(DT)(DT)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DA)(DA)(DG)(DC)(DG)(DT)(DT)(DA)(DA) (DT) (DG)(DT)(DC)(DT)(DG)(DG)(DC)(DT) (DT)(DC)(DT)(DG)(DA)(DT)(DA)(DA)(DA)(DG) (DC)

GENBANK: GENBANK: CP029239.1

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Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 4 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 175703
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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