2024-07-24 REL PDBe PDBe PDBe 2022-09-12 2022-12-28 2022-12-28 2024-07-24 Wellcome Trust 100401/Z/12/Z United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BB/S007261/1 United Kingdom Medical Research Council (MRC, United Kingdom) United Kingdom RecBCD-DNA in complex with the phage protein Abc2 and host PpiB Wilkinson M Wilkinson OJ Feyerherm C Fletcher EE Wigley DB Dillingham MS Homologous recombination, DNA repair, phage, Helicase, Nuclease, Inhibitor, Protein complex, Enzyme, DNA mimic, DNA BINDING PROTEIN Wilkinson M Wilkinson OJ Feyerherm C Fletcher EE Wigley DB Dillingham MS Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub. Elife US 11 2022 36533901 doi:10.7554/eLife.83409 2050-084X EMD-15804 other EM volume
CryoEM map of the RecBCD-Abc2-DNA complex from the same particle dataset
 8b1u FULLOVERLAP RecBCD-Abc2-PpiB-DNA complex RecBCD-Abc2-PpiB-DNA complex 0 1 2 3 4 5
All proteins co-expressed and purified as one complex. DNA added prior to making grids in a 1.5x molar excess. Host PpiB interacts with complex and was pulled through purification.
 RecBCD enzyme subunits RecB, RecC and RecD 1 1 2 3 Escherichia coli DNA (70-MER) 1 4 synthetic construct Anti-RecBCD protein 2 1 5 Salmonella phage P22 RecBCD enzyme subunit RecB Escherichia coli 0.134066625
Nuclease-dead mutant D1080A
1 Escherichia coli BL21 LEVO MSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNI HELRIACLRETTDNPLYERLLEEIDDKAQAAQWLLLAERQMDEAAVFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLLR YQACADFWRRHCYPLPREIAQVVFETWKGPQALLRDINRYLQGEAPVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAV GELDALIESSGIDRRKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFSQRFLEDRTKAGGETPRHPLFEAIDQLLAEP LSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSESGEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRI WHHQPETALLLIGDPKQAIYAFRGADIFTYMKARSEVHAHYTLDTNWRSAPGMVNSVNKLFSQTDDAFMFREIPFIPVKS AGKNQALRFVFKGETQPAMKMWLMEGESCGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPVRASDISVLVRS RQEAAQVRDALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPERENTLRSALATSMMGLNALDIETLNNDEHAWDV VVEEFDGYRQIWRKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEPDS NASSQQMRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFYHDRHSFEAVLDLNAAPESVDLAEAERLAEDLR LLYVALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLRTCIEALCDDDIAWQTAQTGDNQPWQV NDVSTAELNAKTLQRLPGDNWRVTSYSGLQQRGHGIAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLFE DLDFTQPVDPNWVREKLELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEFYLPISEPLIASQLDTLI RQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLAYKSNWLGEDSSAYTQQAMAAAMQAHRYDLQYQLYTLALHR YLRHRIADYDYEHHFGGVIYLFLRGVDKEHPQQGIYTTRPNAGLIALMDEMFAGMTLEEA A0A024LB08 3.1.11.5 RecBCD enzyme subunit RecC Escherichia coli 0.12897410199999998 1 Escherichia coli BL21 LEVO MLRVYHSNRLDVLEALMEFIVERERLDDPFEPEMILVQSTGMAQWLQMTLSQKFGIAANIDFPLPASFIWDMFVRVLPEI PKESAFNKQSMSWKLMTLLPQLLEREDFTLLRHYLTDDSDKRKLFQLSSKAADLFDQYLVYRPDWLAQWETGHLVEGLGE AQAWQAPLWKALVEYTHQLGQPRWHRANLYQRFIETLESATTCPPGLPSRVFICGISALPPVYLQALQALGKHIEIHLLF TNPCRYYWGDIKDPAYLAKLLTRQRRHSFEDRELPLFRDSENAGQLFNSDGEQDVGNPLLASWGKLGRDYIYLLSDLESS QELDAFVDVTPDNLLHNIQSDILELENRAVAGVNIEEFSRSDNKRPLDPLDSSITFHVCHSPQREVEVLHDRLLAMLEED PTLTPRDIIVMVADIDSYSPFIQAVFGSAPADRYLPYAISDRRARQSHPVLEAFISLLSLPDSRFVSEDVLALLDVPVLA ARFDITEEGLRYLRQWVNESGIRWGIDDDNVRELELPATGQHTWRFGLTRMLLGYAMESAQGEWQSVLPYDESSGLIAEL VGHLASLLMQLNIWRRGLAQERPLEEWLPVCRDMLNAFFLPDAETEAAMTLIEQQWQAIIAEGLGAQYGDAVPLSLLRDE LAQRLDQERISQRFLAGPVNICTLMPMRSIPFKVVCLLGMNDGVYPRQLAPLGFDLMSQKPKRGDRSRRDDDRYLFLEAL ISAQQKLYISYIGRSIQDNSERFPSVLVQELIDYIGQSHYLPGDEALNCDESEARVKAHLTCLHTRMPFDPQNYQPGERQ SYAREWLPAASQAGKAHSEFVQPLPFTLPETVPLETLQRFWAHPVRAFFQMRLQVNFRTEDSEIPDTEPFILEGLSRYQI NQQLLNALVEQDDAERLFRRFRAAGDLPYGAFGEIFWETQCQEMQQLADRVIACRQPGQSMEIDLACNGVQITGWLPQVQ PDGLLRWRPSLLSVAQGMQLWLEHLVYCASGGNGESRLFLRKDGEWRFPPLAAEQALHYLSQLIEGYREGMSAPLLVLPE SGGAWLKTCYDAQNDAMLDDDSTLQKARTKFLQAYEGNMMVRGEGDDIWYQRLWRQLTPETMEAIVEQSQRFLLPLFRFN QS P07648 3.1.11.5 RecBCD enzyme subunit RecD Escherichia coli 0.066990367 1 Escherichia coli BL21 LEVO MKLQKQLLEAVEHKQLRPLDVQFALTVAGDEHPAVTLAAALLSHDAGEGHVCLPLSRLENNEASHPLLATCVSEIGELQN WEECLLASQAVSRGDEPTPMILCGDRLYLNRMWCNERTVARFFNEVNHAIEVDEALLAQTLDKLFPVSDEINWQKVAAAV ALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEDASTL HRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDALPDHARVIFLGDRDQLASVEAGAVLGDICAYANAG FTAERARQLSRLTGTHVPAGTGTEAASLRDSLCLLQKSYRFGSDSGIGQLAAAINRGDKTAVKTVFQQDFTDIEKRLLQS GEDYIAMLEEALAGYGRYLDLLQARAEPDLIIQAFNEYQLLCALREGPFGVAGLNERIEQFMQQKRKIHRHPHSRWYEGR PVMIARNDSALGLFNGDIGIALDRGQGTRVWFAMPDGNIKSVQPSRLPEHETTWAMTVHKSQGSEFDHAALILPSQRTPV VTRELVYTAVTRARRRLSLYADERILSAAIATRTERRSGLAALFSSRE P04993 3.1.11.5 DNA (70-MER) synthetic construct 0.021440706999999996
Synthesised hairpin substrate with unpaired ssDNA tails
1 (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DG)(DC) (DG)(DA)(DG)(DC)(DA)(DC)(DT)(DG)(DC)(DT)(DA)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DT)(DC) (DC)(DC)(DA)(DT)(DG)(DC)(DT)(DG)(DT)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DC)(DT)(DC)(DG) (DC)(DA)(DT)(DT)(DA)(DG)(DA)(DT)(DT)(DT) DNA Anti-RecBCD protein 2 Salmonella phage P22 0.011640209999999998 1 Escherichia coli BL21 LEVO MPAPLYGADDPRRCSGNSVSEVLDKFRKNYDLIMSLPQETKEEKEFRHCIWLAEKEERERIYQTAIRPFRKATYTKFIEI DPRLRDYRSRYAGISNN P11191 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER 0.000506196 1 ANP MAGNESIUM ION 2.4305e-05 1 MG singleParticle particle 0.1 7.5 25.0 Tris-HCl 100.0 NaCl Sodium chloride 0.5 TCEP 5.0 MgCl2 Magnesium chloride 2.0 ADPNP C-flat-2/1 COPPER 400 GRAPHENE OXIDE
Mixture of graphene oxide with 0.3 mM DDM detergent applied directly to grids twice before application of sample
 ETHANE 90 FEI VITROBOT MARK IV
1.5s blot time.
RecBCD-Abc2 mixed with 1.5x molar excess of synthesised DNA substrate, 2 mM ADPNP and 5 mM MgCl2 prior to making grids
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.2 2.4 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 2500 12.0 56.0 1 467613 EMD-4038
30 Angstrom lowpass-filtered template
 C1 3.8 FSC 0.143 CUT-OFF RELION 3 37072 MAXIMUM LIKELIHOOD RELION 3 MAXIMUM LIKELIHOOD RELION 3 emd_15805.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 245.91998 245.91998 245.91998 90.0 90.0 90.0 X Y Z -0.040271144 0.07460165 0.000058282527 0.0039121397 1.06 1.06 1.06 0.015 AUTHOR Final CryoEM map of the RecBCD-Abc2-DNA complex bound to the host PpiB protein 8B1T PDB experimental model FLEXIBLE FIT Correlation coefficient REAL 68.0 emd_15805_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 245.91998 245.91998 245.91998 90.0 90.0 90.0 X Y Z -0.06635635 0.09355625 0.00005708705 0.0069261845 1.06 1.06 1.06 AUTHOR halfmap1 emd_15805_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 232 232 0 0 0 232 232 232 245.91998 245.91998 245.91998 90.0 90.0 90.0 X Y Z -0.06932088 0.09374919 0.000059478 0.006961539 1.06 1.06 1.06 AUTHOR halfmap2