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- PDB-8sm3: Structure of Bacillus cereus VD045 Gabija GajA-GajB Complex -

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Basic information

Entry
Database: PDB / ID: 8sm3
TitleStructure of Bacillus cereus VD045 Gabija GajA-GajB Complex
Components
  • Endonuclease GajA
  • Gabija protein GajB
KeywordsDNA BINDING PROTEIN/Hydrolase / Anti-phage / Nuclease / Helicase / DNA BINDING PROTEIN / DNA BINDING PROTEIN-Hydrolase complex
Function / homology
Function and homology information


recombinational repair / 3'-5' DNA helicase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
AAA domain, group 15 / : / Overcoming lysogenization defect protein-like, TOPRIM domain / OLD protein-like, TOPRIM domain / AAA ATPase domain / AAA domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type ...AAA domain, group 15 / : / Overcoming lysogenization defect protein-like, TOPRIM domain / OLD protein-like, TOPRIM domain / AAA ATPase domain / AAA domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / UvrD-like helicase, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Endonuclease GajA / Gabija protein GajB
Similarity search - Component
Biological speciesBacillus cereus VD045 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAntine, S.P. / Mooney, S.E. / Johnson, A.G. / Kranzusch, P.J.
Funding support United States, 5items
OrganizationGrant numberCountry
The Pew Charitable Trusts United States
Burroughs Wellcome Fund United States
The G. Harold and Leila Y. Mathers Foundation United States
The Mark Foundation United States
Parker Institute for Cancer Immunotherapy United States
CitationJournal: Nature / Year: 2024
Title: Structural basis of Gabija anti-phage defence and viral immune evasion.
Authors: Sadie P Antine / Alex G Johnson / Sarah E Mooney / Azita Leavitt / Megan L Mayer / Erez Yirmiya / Gil Amitai / Rotem Sorek / Philip J Kranzusch /
Abstract: Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage defence systems, occurring in ...Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.
History
DepositionApr 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease GajA
B: Gabija protein GajB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8613
Polymers124,7652
Non-polymers961
Water00
1
A: Endonuclease GajA
B: Gabija protein GajB
hetero molecules

A: Endonuclease GajA
B: Gabija protein GajB
hetero molecules

A: Endonuclease GajA
B: Gabija protein GajB
hetero molecules

A: Endonuclease GajA
B: Gabija protein GajB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,44312
Polymers499,0598
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_545x,x-y-1,-z+1/31
Unit cell
Length a, b, c (Å)215.791, 215.791, 173.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein Endonuclease GajA / Gabija protein GajA / Nicking endonuclease GajA


Mass: 67755.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus VD045 (bacteria) / Gene: gajA, IIE_04982 / Production host: Escherichia coli (E. coli)
References: UniProt: J8H9C1, Hydrolases; Acting on ester bonds
#2: Protein Gabija protein GajB / Putative helicase GajB


Mass: 57008.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus VD045 (bacteria) / Gene: gajB, IIE_04983 / Production host: Escherichia coli (E. coli) / References: UniProt: J8HQ06
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 4.68 Å3/Da / Density % sol: 73.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES-NaOH pH 7.5, 2.4% PEG-400, and 2.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→49.24 Å / Num. obs: 48144 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 91.77 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.163 / Net I/σ(I): 15.4
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 3.069 / Num. unique obs: 4353 / CC1/2: 0.624 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.24 Å / SU ML: 0.4515 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 1994 4.16 %
Rwork0.2369 45965 -
obs0.2381 47959 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.19 Å2
Refinement stepCycle: LAST / Resolution: 3→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8501 0 5 0 8506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028646
X-RAY DIFFRACTIONf_angle_d0.44211628
X-RAY DIFFRACTIONf_chiral_restr0.03991301
X-RAY DIFFRACTIONf_plane_restr0.00391483
X-RAY DIFFRACTIONf_dihedral_angle_d12.66223295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.39731390.36933192X-RAY DIFFRACTION98.32
3.08-3.160.36891390.3523200X-RAY DIFFRACTION99.67
3.16-3.250.42241390.34823237X-RAY DIFFRACTION99.76
3.25-3.360.35241410.3083232X-RAY DIFFRACTION99.62
3.36-3.480.32561400.27473228X-RAY DIFFRACTION99.67
3.48-3.620.28811400.25493256X-RAY DIFFRACTION99.79
3.62-3.780.27911430.25773257X-RAY DIFFRACTION99.85
3.78-3.980.30551410.24453253X-RAY DIFFRACTION99.85
3.98-4.230.25031420.21333271X-RAY DIFFRACTION99.97
4.23-4.550.19071430.19273291X-RAY DIFFRACTION99.94
4.56-5.010.25911430.19593298X-RAY DIFFRACTION99.97
5.01-5.740.23551450.21913330X-RAY DIFFRACTION100
5.74-7.220.24181470.27573371X-RAY DIFFRACTION99.97
7.23-49.240.25131520.20913549X-RAY DIFFRACTION99.76
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.369629052960.523934865191.076990524041.098715848031.265134117732.135131691020.18870626768-0.138118883106-0.01380095294650.130526708717-0.116164293484-0.03565942686580.3728132653610.0222691451966-0.01017563884570.584633058687-0.2789061954710.01268835328710.652173962977-0.008451576024880.56978360834780.1234314505-83.762572886313.444642628
20.150730707375-0.983508977043-0.3163414516140.314940842969-0.2175418784850.2813203349170.0064451772829-0.134732243136-0.192310602682-0.03206742003460.06313150798790.0611929207046-0.05725925587740.135639145267-0.000745475948770.545902386411-0.2821106369410.0644622208960.784445439642-0.0912474255030.60218974778749.6458063838-72.220318943424.1789070697
31.251095024750.06493568678830.03617306655170.9483185095250.3536562480312.26492108578-0.1492177285810.336158105628-0.0356964432571-0.2008462267810.12380481102-0.04875455129920.07785257672850.008096069253820.005458242817190.58881004689-0.2931281033910.04266995958970.766306421612-0.03360361735220.51637525669664.3640493797-96.8505006896-22.9151127774
40.784286416718-0.420344645408-0.3453505890092.841769324040.9302804551771.49592399988-0.1832207747570.07067717609430.5423300545580.1114903583910.166472761004-0.133168713972-0.2562080478780.117260773585-0.0005990717426510.864781965468-0.280778889288-0.1116315061480.636001542405-0.1278486357080.96684510859987.4937362488-47.688007196218.2884029677
50.9823339626660.4897000010780.6454055946921.424073268870.8137019716050.8169608520820.0446705614541-0.3152928612780.4189433939370.742435546592-0.07829567058420.3969742056830.1862731917460.0686445272568-6.45437522802E-51.20626691322-0.03323985829830.1379044012961.13562177163-0.2669496536251.1384868971680.37325581-30.395581324542.8650524092
60.529219266412-0.5208823394810.09425491222330.4867991333710.6251773294390.664554631707-0.0335924726756-0.3360862689620.1985830383240.369215225698-0.1195890841630.143968590095-0.2992903217540.197624547563-0.001381122468221.48565807531-0.1953920327320.2673720090171.14552682586-0.4372215976371.7968717538170.3677834977-18.961950089838.1133678678
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 143 )AA0 - 1431 - 144
22chain 'A' and (resid 144 through 295 )AA144 - 295145 - 268
33chain 'A' and (resid 296 through 575 )AA296 - 575269 - 548
44chain 'B' and (resid 2 through 229 )BB2 - 2291 - 228
55chain 'B' and (resid 230 through 405 )BB230 - 405229 - 404
66chain 'B' and (resid 406 through 494 )BB406 - 494405 - 493

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