2024-09-04 REL PDBe PDBe PDBe 2024-04-14 2024-09-04 2024-09-04 2024-09-04 European Research Council (ERC) 820150 European Union Vibrio cholerae DdmD-DdmE holo complex Loeff L Jinek M Helicase, Nuclease, Complex, Effector, Argonaute, IMMUNE SYSTEM Loeff L Adams DW Chanez C Stutzmann S Righi L Blokesch M Jinek M Molecular mechanism of plasmid elimination by the DdmDE defense system. Science US 385 188 194 2024 38870273 doi:10.1126/science.adq0534 1095-9203 0038 SCIEAS 9ezy FULLOVERLAP DdmD-DdmE Holocomplex DdmD-DdmE Holocomplex 0 1 2 3 4 5 Vibrio cholerae Helicase/UvrB N-terminal domain-containing protein Vibrio cholerae 0.136427594 1 Escherichia coli BL21(DE3) LEVO SNAMNVSIEEFTHFDFQLVPEPSPLDLVITEPLKNHIEVNGVKSGALLPLPFQTGIGKTYTALNFLLQQMLEQVRSELKE ENTGKKSKRLLYYVTDSVDNVVSAKADLLKLIEKQTVKGEPRFTLEQQEYLKAQIVHLPNQSEQLLQCSDAVLNDVLIGF NLNAERDVQAEWSAISGLRRHASNPEVKISLNRQAGYFYRNLIDRLQKKQKGADRVLLSGSLLASVETLLPGEKIRNGSA HVAFLTTSKFLKGFHNTRSRYSPLRDLSGAVLIIDEIDKQNQVILSELCKQQAQDLIWAIRTLRANFRDHQLESSPRYDK IEDLFEPLRERLEEFGTNWNLAFAFNTEGANLNERPVRLFSDRSFTHVSSATHKLSLKSDFLRRKNLIFSDEKVEGSLIE KHGLLTRFVNEADVIYQWFLGTMRKAVFQYWENVRGLEIEVRENRSLEGTFQEAVQSLLTHFNLQEFESAVYESFDTRGL RQSAGGKANKLSSSKSYHHTGLKLVEVAHNQGTRDTVNCKASFLNTSPSGVLADMVDAGAVILGISATARADTVIHNFDF KYLNERLGNKLLSLSREQKQRVNNYYHSRRNYKDNGVVLTVKYLNSRDAFLDALLEEYKPEARSSHFILNHYLGIAESEQ AFVRSWLSKLLASIKAFISSPDNRYMLSLLNRTLDTTRQNINDFIQFCCDKWAKEFNVKTKTFFGVNADWMRLVGYDEIS KHLNTELGKVVVFSTYASMGAGKNPDYAVNLALEGESLISVADVTYSTQLRSDIDSIYLEKPTQLLLSDDYSHTANQLCQ FHQILSLQENGELSPKSAENWCRQQLMGMSRERSLQQYHQTSDYQSAVRKYIEQAVGRAGRTSLKRKQILLFVDSGLKEI LAEESRDPSLFSHEYVALVNKAKSAGKSIVEDRAVRRLFNLAQRNNKDGMLSIKALVHRLHNQPASKSDIQEWQDIRTQL LRYPTVAFQPERFNRLYLQSMTKGYYRYQGNLDGDPNSFEFFDRVPYGDMVSEEDCSLATLVQNQYVRPWFERKGFACSW QKEANVMTPIMFTNIYKGALGEQAVEAVLTAFDFTFEEVPNSIYERFDNRVIFAGIEQPIWLDSKYWKHEGNESSEGYSS KIALVEEEFGPSKFIYVNALGDTSKPIRYLNSCFVETSPQLAKVIEIPALIDDSNADTNRTAVQELIKWLHHS Q9KR72 Vibrio cholerae DdmE Vibrio cholerae 0.079468156 1 Escherichia coli BL21(DE3) LEVO SNAMVTPQLEPSSQGPLSTLIEQISIDTDWVDRSFAIYCVSYKGIDFSERPKRLVTLASETYKSGSVYCLVKGANKEACY WVLLPKDSKLDLKDTSLAIKPSSAAELPTWQLARLLIKAIPKVLSGTMPEIKRFESEGLYYLVKSKKLPKDHSGYELTTV EIDLAPCAALGFKQTLSMGTKTFSPLSWFTLENGEVQKKARFATRYQLDDVGKLVSKSIKGDYIKKPLYSNAKNRIQAID ITKESYSGFQLSKVGILEQFMQDLKQAYGDSVSVKLQRIPGEKHRFVSDTIVKNHYVGLFDALKEHRLVICDLTENQDTD AALTLLHGIEHLDINAEIAEVPIRGALNILIVGNKDTYKSDEEDPYQVYRKKYQDTVFQSCYPERLWNRQGQPNRHVVEV LLKELLIKLEVHTRKHLIEYPSGPERCVYYMPQRPKDESSEVRDEPWPVYASKLVGDEWQYTQATQEELEDIELDLGNDK RHVFHGFERSPVIYWPETGDYAIFIDTGIQMLPEFEAVAERLRELKEGRSQDVPIALLAQFIEENPESKVINKLRAILSE WDDVAPLPFDEFSTIAYKSSDEKQFYDWLREQGFFLKTSIRGQSEGFFNASLGFFYNREQGMYFAGGKGSPQSKIETFSH LYLIKHSFDALPEEVENLFDVYHLRHRLPTVTPYPFKHLREYVEMQRFRS Q9KR73 14 nucleotide DNA guide with terminal 5' phosphate synthetic construct 0.004567997999999999
The first adenosine nucleotide was added to obtain three oxygen groups on the 5' phosphate of the DNA guide. This nucleotide was not present on the DNA guide used for structure determination.
1 (DA)(DT)(DA)(DA)(DT)(DT)(DC)(DT)(DG)(DT)(DC)(DC)(DA)(DG)(DA) DNA Target DNA strand synthetic construct 0.020341028999999997 1 (DA)(DT)(DC)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DT)(DC)(DG)(DT)(DT)(DG)(DT)(DC)(DG)(DT) (DC)(DG)(DT)(DC)(DT)(DG)(DG)(DA)(DC)(DA)(DG)(DA)(DA)(DT)(DT)(DA)(DC)(DT)(DG)(DG) (DT)(DA)(DA)(DC)(DT)(DA)(DC)(DG)(DG)(DT)(DG)(DG)(DA)(DC)(DA)(DA)(DT)(DG)(DC)(DT) (DA)(DC)(DC)(DT)(DT)(DA) DNA Non-target DNA strand synthetic construct 0.020305029 1 (DT)(DA)(DA)(DG)(DG)(DT)(DA)(DG)(DC)(DA)(DT)(DT)(DG)(DT)(DC)(DC)(DA)(DC)(DC)(DG) (DT)(DA)(DG)(DT)(DT)(DA)(DC)(DC)(DA)(DG)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DC)(DG)(DA)(DC)(DG)(DA)(DC)(DA)(DA)(DC)(DG)(DA)(DT)(DC)(DA)(DG) (DA)(DT)(DA)(DG)(DA)(DT) DNA MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 2.5 8.0 20.0 Tris-HCl Tris hydrochloride 225.0 NaCl Sodium chloride 2.5 Desthiobiotin Desthiobiotin ETHANE FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 2.4 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 60.99 1 1283702 2.56 FSC 0.143 CUT-OFF cryoSPARC 4.4.1. 229173 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD cryoSPARC 4.4.1. emd_50091.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 572 572 572 0 0 0 572 572 572 371.8 371.8 371.8 90.0 90.0 90.0 X Y Z -0.07145727 0.19073372 -0.000052482726 0.0033284551 0.65 0.65 0.65 0.0257 AUTHOR Unsharpened EM volume AlphaFold in silico model
Initial model was generated with alpha fold
 emd_50091_msk_1.map emd_50091_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 572 572 572 0 0 0 572 572 572 371.8 371.8 371.8 90.0 90.0 90.0 X Y Z -0.31501117 0.60483325 -0.000052482726 0.008204508 0.65 0.65 0.65 AUTHOR Sharpened EM volume emd_50091_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 572 572 572 0 0 0 572 572 572 371.8 371.8 371.8 90.0 90.0 90.0 X Y Z -0.13124909 0.27928877 0.000037686066 0.0146830855 0.65 0.65 0.65 AUTHOR Half map B emd_50091_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 572 572 572 0 0 0 572 572 572 371.8 371.8 371.8 90.0 90.0 90.0 X Y Z -0.14428802 0.24412449 0.000036356792 0.0146158375 0.65 0.65 0.65 AUTHOR Half map A