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- PDB-9mtn: Crystal structure of KwaB -

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Basic information

Entry
Database: PDB / ID: 9mtn
TitleCrystal structure of KwaB
ComponentsKiwa protein KwaB
KeywordsIMMUNE SYSTEM / KwaB dimer / anti-phage defense / Kiwa system
Function / homologyProtein of unknown function DUF4868 / : / Kiwa protein KwaB-like / defense response to virus / Kiwa protein KwaB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.92 Å
AuthorsZhiying, Z. / Dinshaw, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateP30CA008748 United States
CitationJournal: Cell / Year: 2025
Title: Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites.
Authors: Zhiying Zhang / Thomas C Todeschini / Yi Wu / Roman Kogay / Ameena Naji / Joaquin Cardenas Rodriguez / Rupavidhya Mondi / Daniel Kaganovich / David W Taylor / Jack P K Bravo / Marianna ...Authors: Zhiying Zhang / Thomas C Todeschini / Yi Wu / Roman Kogay / Ameena Naji / Joaquin Cardenas Rodriguez / Rupavidhya Mondi / Daniel Kaganovich / David W Taylor / Jack P K Bravo / Marianna Teplova / Triana Amen / Eugene V Koonin / Dinshaw J Patel / Franklin L Nobrega /
Abstract: Bacteria and archaea deploy diverse antiviral defense systems, many of which remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread two-component system composed of the ...Bacteria and archaea deploy diverse antiviral defense systems, many of which remain mechanistically uncharacterized. Here, we characterize Kiwa, a widespread two-component system composed of the transmembrane sensor KwaA and the DNA-binding effector KwaB. Cryogenic electron microscopy (cryo-EM) analysis reveals that KwaA and KwaB assemble into a large, membrane-associated supercomplex. Upon phage binding, KwaA senses infection at the membrane, leading to KwaB binding of ejected phage DNA and inhibition of replication and late transcription, without inducing host cell death. Although KwaB can bind DNA independently, its antiviral activity requires association with KwaA, suggesting spatial or conformational regulation. We show that the phage-encoded DNA-mimic protein Gam directly binds and inhibits KwaB but that co-expression with the Gam-targeted RecBCD system restores protection by Kiwa. Our findings support a model in which Kiwa coordinates membrane-associated detection of phage infection with downstream DNA binding by its effector, forming a spatially coordinated antiviral mechanism.
History
DepositionJan 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1May 20, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kiwa protein KwaB
K: Kiwa protein KwaB
B: Kiwa protein KwaB
C: Kiwa protein KwaB


Theoretical massNumber of molelcules
Total (without water)144,5904
Polymers144,5904
Non-polymers00
Water00
1
A: Kiwa protein KwaB
K: Kiwa protein KwaB


Theoretical massNumber of molelcules
Total (without water)72,2952
Polymers72,2952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-38 kcal/mol
Surface area26530 Å2
MethodPISA
2
B: Kiwa protein KwaB
C: Kiwa protein KwaB


Theoretical massNumber of molelcules
Total (without water)72,2952
Polymers72,2952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-31 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)283.105, 283.105, 76.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein
Kiwa protein KwaB


Mass: 36147.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kwaB, ECO55CA74_24530 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW46
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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 290 K / Method: evaporation / Details: 0.1 M Tris, pH 8.5, 5% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.88→33.28 Å / Num. obs: 20404 / % possible obs: 97.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 129.85 Å2 / CC1/2: 0.972 / Net I/σ(I): 8
Reflection shellResolution: 3.88→4.09 Å / Num. unique obs: 2586 / CC1/2: 0.303

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
AUTOMARdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.92→33.28 Å / SU ML: 0.6714 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.3934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2746 1754 9.95 %
Rwork0.238 15867 -
obs0.2417 17621 86.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.78 Å2
Refinement stepCycle: LAST / Resolution: 3.92→33.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9722 0 0 0 9722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00569865
X-RAY DIFFRACTIONf_angle_d1.007213277
X-RAY DIFFRACTIONf_chiral_restr0.05821547
X-RAY DIFFRACTIONf_plane_restr0.00721676
X-RAY DIFFRACTIONf_dihedral_angle_d6.61831278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.92-4.020.4309350.4256349X-RAY DIFFRACTION24.17
4.02-4.140.3661190.34181074X-RAY DIFFRACTION76.52
4.14-4.270.3608990.3361909X-RAY DIFFRACTION64
4.27-4.430.413900.3812780X-RAY DIFFRACTION56.35
4.43-4.60.31531580.27741420X-RAY DIFFRACTION99
4.6-4.810.3181570.27211419X-RAY DIFFRACTION100
4.81-5.070.31841550.24991426X-RAY DIFFRACTION100
5.07-5.380.30491570.26471393X-RAY DIFFRACTION99.87
5.38-5.80.29931580.26071418X-RAY DIFFRACTION100
5.8-6.370.3031580.27411438X-RAY DIFFRACTION100
6.38-7.290.2961560.26691398X-RAY DIFFRACTION100
7.29-9.150.21981540.1991431X-RAY DIFFRACTION100
9.15-33.280.19741580.1481412X-RAY DIFFRACTION99.62

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