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- PDB-8zgi: Crystal structure of DUF4297 from E.Coli -

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Basic information

Entry
Database: PDB / ID: 8zgi
TitleCrystal structure of DUF4297 from E.Coli
ComponentsRestriction endonuclease
KeywordsHYDROLASE / Nuclease
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsChen, Q. / Yu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2025
Title: DUF4297 and HerA form abortosome to mediate bacterial immunity against phage infection.
Authors: Dongmei Tang / Ting Liu / Yijun Chen / Zixuan Zhu / Hao Chen / Qiang Chen / Yamei Yu /
Abstract: Immune receptors form higher-order complexes known as inflammasomes in animals and resistosomes in plants to mediate immune signaling. Here, we report a similar bacterial protein complex, DUF4297- ...Immune receptors form higher-order complexes known as inflammasomes in animals and resistosomes in plants to mediate immune signaling. Here, we report a similar bacterial protein complex, DUF4297-HerA, which induces abortive infection to mediate anti-phage immunity by coupling nuclease and ATPase activities. Therefore, we name this defense system "Hailibu" after a hunter in a popular folk tale who sacrifices himself to save his village. Cryoelectron microscopy (cryo-EM) results reveal that DUF4297 and HerA assemble into a higher-order complex, reminiscent of apoptosome, inflammasome, or resistosome, which we refer to as an abortosome. By capturing cryo-EM structures of the pre-loading, DNA-loading, and DNA-transporting states during Hailibu abortosome processing of DNA, we propose that DNA substrates are loaded through the HerA hexamer, with adenosine triphosphate (ATP) hydrolysis providing the energy to transport DNA substrates to the clustered DUF4297 Cap4 nuclease domains for degradation. This study demonstrates the existence of analogous multiprotein complexes in innate immunity across the kingdoms of life.
History
DepositionMay 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Restriction endonuclease
B: Restriction endonuclease


Theoretical massNumber of molelcules
Total (without water)93,9442
Polymers93,9442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-11 kcal/mol
Surface area40620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.296, 144.296, 262.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Restriction endonuclease


Mass: 46971.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CG692_10945 / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 800 mM Sodium phosphate monobasic 1200 mM Potassium phosphate dibasic 100 mM Sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 27392 / % possible obs: 99.9 % / Redundancy: 38.5 % / Biso Wilson estimate: 108.33 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.5
Reflection shellResolution: 3.2→3.39 Å / Num. unique obs: 4282 / CC1/2: 0.546

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→22.311 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3219 997 3.66 %
Rwork0.2826 --
obs0.2839 27274 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→22.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6575 0 0 0 6575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026729
X-RAY DIFFRACTIONf_angle_d0.4559072
X-RAY DIFFRACTIONf_dihedral_angle_d4.6854051
X-RAY DIFFRACTIONf_chiral_restr0.039962
X-RAY DIFFRACTIONf_plane_restr0.0021167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2004-3.36860.34961390.33863666X-RAY DIFFRACTION100
3.3686-3.57890.37781390.32163663X-RAY DIFFRACTION100
3.5789-3.85390.32791390.31083693X-RAY DIFFRACTION100
3.8539-4.23930.37371420.28743727X-RAY DIFFRACTION100
4.2393-4.84730.32051410.2663739X-RAY DIFFRACTION100
4.8473-6.08650.32691440.28643797X-RAY DIFFRACTION100
6.0865-22.3110.28351530.26443992X-RAY DIFFRACTION100

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