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- PDB-8q41: Crystal structure of Can2 (E341A) bound to cA4 and TTTAAA ssDNA -

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Basic information

Entry
Database: PDB / ID: 8q41
TitleCrystal structure of Can2 (E341A) bound to cA4 and TTTAAA ssDNA
Components
  • Cyclic tetraadenosine monophosphate (cA4)
  • DNA (5'-D(*TP*TP*AP*AP*A)-3')
  • DUF1887 family protein
KeywordsDNA BINDING PROTEIN / Can2 / cyclic oligoadenylates / cA4 / CARF / CRISPR ancillary nuclease / Protein-DNA complex
Function / homologytRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / metal ion binding / : / : / DNA / RNA / DUF1887 family protein
Function and homology information
Biological speciesThermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsJungfer, K. / Sigg, A. / Jinek, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-820152European Union
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2.
Authors: Jungfer, K. / Sigg, A. / Jinek, M.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 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: DUF1887 family protein
B: DUF1887 family protein
D: DNA (5'-D(*TP*TP*AP*AP*A)-3')
C: DNA (5'-D(*TP*TP*AP*AP*A)-3')
X: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7368
Polymers107,5715
Non-polymers1653
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-42 kcal/mol
Surface area34330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.009, 79.322, 95.430
Angle α, β, γ (deg.)90.000, 94.850, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DUF1887 family protein


Mass: 51342.438 Da / Num. of mol.: 2 / Mutation: E341A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
Gene: Thebr_0943 / Production host: Escherichia coli (E. coli) / References: UniProt: E8URK0
#2: DNA chain DNA (5'-D(*TP*TP*AP*AP*A)-3')


Mass: 1807.242 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Thermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
#3: RNA chain Cyclic tetraadenosine monophosphate (cA4)


Type: Polycyclic / Class: Antiviral / Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Cyclic oligoadenylates such as c-tetraAMP were found to be novel bacterial second messengers. Antiviral in context of signalling for Type III CRISPR-Cas systems.
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002431
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic ...CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic oligoadenylate signaling was found to be essential for the type III system against the jumbo phage.
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.98 % / Description: plate-shaped crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Tris pH 8, 17.1% (v/v) PEG 550 MME, 4.3% (w/v) PEG 2000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→49.33 Å / Num. obs: 29023 / % possible obs: 88.04 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.02389 / Rrim(I) all: 0.06282 / Net I/σ(I): 21.16
Reflection shellResolution: 2.38→2.465 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.3893 / Mean I/σ(I) obs: 5.01 / Num. unique obs: 3265 / CC1/2: 0.947 / Rpim(I) all: 0.1564 / Rrim(I) all: 0.42 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROC20230726data scaling
XDS20220110data reduction
Coot0.9.8.9model building
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→49.33 Å / SU ML: 0.2483 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.9558
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 1443 4.97 %
Rwork0.1863 27569 -
obs0.1887 29012 88.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.68 Å2
Refinement stepCycle: LAST / Resolution: 2.38→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 200 91 154 7431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00367457
X-RAY DIFFRACTIONf_angle_d0.650610087
X-RAY DIFFRACTIONf_chiral_restr0.04321099
X-RAY DIFFRACTIONf_plane_restr0.00351215
X-RAY DIFFRACTIONf_dihedral_angle_d13.48752786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.470.28211630.21313101X-RAY DIFFRACTION99.97
2.47-2.560.30411530.22223106X-RAY DIFFRACTION99.88
2.56-2.630.3609950.23831943X-RAY DIFFRACTION100
2.71-2.820.28841260.23442475X-RAY DIFFRACTION98.52
2.82-30.27261450.21683132X-RAY DIFFRACTION99.94
3-3.230.26081580.21593146X-RAY DIFFRACTION99.94
3.23-3.550.21021550.19172240X-RAY DIFFRACTION73.24
3.56-4.070.21341170.17182066X-RAY DIFFRACTION66.35
4.07-5.130.19091490.14573171X-RAY DIFFRACTION100
5.13-49.330.22581820.17733189X-RAY DIFFRACTION99.62
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)
10.124834629304-0.1949959840710.1163206346480.456535513473-0.157150591450.289253112311-0.271904736335-0.995585088451-0.2118817925270.2592660831220.120962389287-0.2176184539550.0953655696890.0567393595368-0.1700313491170.3934533791370.0838545496621-0.06656500130470.7550781374010.08479221932460.25131210215226.5751907467-12.36092292349.3512854009
20.0539661953192-0.03733872218710.0264822414220.0108936327249-0.02094522895120.01609879161710.00829077942641-0.6327721234770.400993684180.3408499568220.266583887335-0.128143819104-0.1850928301060.2268510557120.2671999137860.4464891069420.0674141735431-0.1521222717910.901850523804-0.1702047489320.28188307071822.40884144280.39152826752552.7054426114
30.0278994785345-0.03076853564760.02985824109110.0520425126489-0.1138606039990.3015854221220.0661989419711-0.201741807919-0.0848905227979-0.147060297306-0.165100393709-0.02802630879710.1353215387930.453298784158-0.0172157834190.2030101972710.00735992892406-0.02484853934060.282760924174-0.006438619608940.38166563777934.9372056179-5.4283413894826.5707775539
40.9814941761240.3568607496990.6428669231771.432923110710.5661900052411.186191550210.4982774804841.125218962070.542677509598-0.0611337741604-0.0247494259117-0.199900400544-0.426828257055-0.26075253961.207723365820.3013754291830.1466489656330.114412446120.6805360036510.3378248181390.3051019082828.71880775580.176517113547-6.72489018671
50.1243672405810.1517989413690.2563893408690.2452476570580.336120899660.5793114519680.1125756922530.424342670031-0.05806003260380.000155337336335-0.00999467498462-0.2261346695460.2426430877020.3326631773380.04544370036950.3040017314040.1006227318080.07717255823880.6886765166060.1023601145720.36970090599132.6950736565-7.8278676987-10.8408429988
60.7696995792220.0431901855862-0.03052553907810.3627201110680.3042981515780.6655210081240.0313251129775-0.175083162930.2967693621730.0345354583288-0.0758264372835-0.0694919836716-0.050457491082-0.0670309369768-0.06423513726080.175826547516-0.02172090893440.03280633676850.1718230344010.06763610205350.31552450083625.2921652773-0.58456751288118.7185497746
70.2443190675270.00942582497760.2669862030990.1134962656290.03570678803620.5211089586970.0119995990719-0.04095865475650.426421178070.4041789378820.0789864775948-0.100445118752-0.0710311726526-0.145944470442-0.03414447163650.3262440004420.004503212266180.0001124135704590.1989440192940.06059646104870.50332790334320.98666485948.7388448380621.4271270805
80.975309472325-0.2003408420380.4385988203420.288773867384-0.03539773221620.851878805481-0.583001501921-1.310973641490.4706683626240.3617564482820.362621041120.212760152167-0.32873450831-0.365199726649-0.5491529369210.3879225314180.1867968540450.08584560439790.857138070656-0.1261358349590.02121206295052.553663385480.3199909921147.8705708746
90.3964370776430.07725384217820.3545427863130.430059901395-0.07688364361040.3883942783840.0787552302444-0.148586984438-0.105244893983-0.03943359441250.02023841571810.1699705758780.321006634043-0.3415282482070.1888906494120.354936462001-0.0619587822498-0.0380233304350.122877456468-0.030906911280.275425575955-5.55151421105-17.05960116611.6701571637
100.336661423745-0.0141792105262-0.1699207337340.632647624050.3967202183290.3688887909860.2900758042330.5470039796040.00480323563268-0.8797723794780.0578598416930.2738234921650.534566914409-0.2322927975820.4836703242330.8532508004950.0540565839031-0.1348414670470.210032083223-0.1740225474860.349935779445-0.0995165896434-16.5458795113-8.93936092577
110.761957635031-0.00129966625914-0.218566476220.418603592886-0.184904900020.684422177434-0.0487490851214-0.188201786638-0.2243544036740.02612491326210.006919399182293.07735029989E-50.1049417708910.161005181080.0088752776240.2289253295890.01000875383170.0234553373110.1539218076420.02774647785550.2959131898393.89318353348-16.954403358821.6137892835
120.02348324272180.0209134271450.0009748368847740.0150777416120.008554184659660.00753742236669-0.02601321922770.0550267795848-0.2542565206680.2756009450460.007179700526950.3083297654740.520669146081-0.116825183791-1.55236678235E-50.6757429193730.0647811531063-0.06164471230430.7265665186320.08825857349240.60490837260422.55639276-9.770274141985.40515507044
130.00390939464010.001121204426910.01038911640950.005181999524360.003708372830660.00343414488547-0.1047790194190.0916131198591-0.0145543715438-0.0146063944987-0.0281408786244-0.228864651234-0.5501528163840.07588103346-1.82311754042E-51.115535218550.02898263399530.2054812174380.93655029495-0.09264247284831.145975810316.18270748115-8.802173039615.65893109741
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 102 )AA3 - 1021 - 100
22chain 'A' and (resid 103 through 146 )AA103 - 146101 - 140
33chain 'A' and (resid 147 through 175 )AA147 - 175141 - 169
44chain 'A' and (resid 176 through 272 )AA176 - 272170 - 262
55chain 'A' and (resid 273 through 300 )AA273 - 300263 - 290
66chain 'A' and (resid 301 through 405 )AA301 - 405291 - 395
77chain 'A' and (resid 406 through 437 )AA406 - 437396 - 427
88chain 'B' and (resid 3 through 154 )BB3 - 1541 - 141
99chain 'B' and (resid 155 through 209 )BB155 - 209142 - 196
1010chain 'B' and (resid 210 through 300 )BB210 - 300197 - 282
1111chain 'B' and (resid 301 through 437 )BB301 - 437283 - 419
1212chain 'D' and (resid 0 through 4 )DF0 - 4
1313chain 'C' and (resid 0 through 4 )CG0 - 4

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