2024-05-15 REL PDBe PDBe PDBe 2016-11-08 2016-11-16 2017-01-11 2024-05-15 Cryo-EM structure of Lambda Phage protein GamS bound to RecBCD Wilkinson M Chaban Y Inhibitor, Complex, DNA repair, Helicase/Nuclease, DNA binding protein Wilkinson M Troman L Wan Nur Ismah WA Chaban Y Avison MB Dillingham MS Wigley DB Structural basis for the inhibition of RecBCD by Gam and its synergistic antibacterial effect with quinolones. Elife US 5 2016 28009252 doi:10.7554/eLife.22963 2050-084X 5mbv FULLOVERLAP RecBCD complex bound to inhibitory protein lambda GamS RecBCD complex bound to inhibitory protein lambda GamS 0 1 2 3 4 5
RecBCD and GamS were expressed and purified separately. They were mixed with an excess of GamS then passed through a size exclusion column to separate out free GamS.
0.35 RecBCD helicase/nuclease complex 1 1 2 3 Escherichia coli 0.33 Lambda GamS 1 4 5 Enterobacteria phage lambda 0.02 RecBCD enzyme subunit RecB Escherichia coli 0.134167703 1 Escherichia coli BL21(DE3) LEVO GMSDVAETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSN IHELRIACLRETTDNPLYERLLEEIDDKAQAAQWLLLAERQMDEAAVFTIHGFCQRMLNLNAFESGMLFEQQLIEDESLL RYQACADFWRRHCYPLPREIAQVVFETWKGPQALLRDINRYLQGEAPVIKAPPPDDETLASRHAQIVARIDTVKQQWRDA VGELDALIESSGIDRRKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFSQRFLEDRTKAGGETPRHPLFEAIDQLLAE PLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSESGEVLAAAIRTRFPVAMIDEFQDTDPQQYRIFRR IWHHQPETALLLIGDPKQAIYAFRGADIFTYMKARSEVHAHYTLDTNWRSAPGMVNSVNKLFSQTDDAFMFREIPFIPVK SAGKNQALRFVFKGETQPAMKMWLMEGESCGVGDYQSTMAQVCAAQIRDWLQAGQRGEALLMNGDDARPVRASDISVLVR SRQEAAQVRDALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPERENTLRSALATSMMGLNALDIETLNNDEHAWD VVVEEFDGYRQIWRKRGVMPMLRALMSARNIAENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEPD SNASSQQMRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFYHDRHSFEAVLDLNAAPESVDLAEAERLAEDL RLLYVALTRSVWHCSLGVAPLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLRTCIEALCDDDIAWQTAQTGDNQPWQ VNDVSTAELNAKTLQRLPGDNWRVTSYSGLQQRGHGIAQDLMPRLDVDAAGVASVVEEPTLTPHQFPRGASPGTFLHSLF EDLDFTQPVDPNWVREKLELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEFYLPISEPLIASQLDTL IRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHEGRYYLLDYKSNWLGEDSSAYTQQAMAAAMQAHRYDLQYQLYTLALH RYLRHRIADYDYEHHFGGVIYLFLRGVDKEHPQQGIYTTRPNAGLIALMDEMFAGMTLEEA P08394 3.1.11.5 RecBCD enzyme subunit RecC Escherichia coli 0.12897410199999998 1 Escherichia coli BL21(DE3) 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 0.06704742200000001 1 Escherichia coli BL21(DE3) LEVO MGKLQKQLLEAVEHKQLRPLDVQFALTVAGDEHPAVTLAAALLSHDAGEGHVCLPLSRLENNEASHPLLATCVSEIGELQ NWEECLLASQAVSRGDEPTPMILCGDRLYLNRMWCNERTVARFFNEVNHAIEVDEALLAQTLDKLFPVSDEINWQKVAAA VALTRRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESLGKALRQLPLTDEQKKRIPEDAST LHRLLGAQPGSQRLRHHAGNPLHLDVLVVDEASMIDLPMMSRLIDALPDHARVIFLGDRDQLASVEAGAVLGDICAYANA GFTAERARQLSRLTGTHVPAGTGTEAASLRDSLCLLQKSYRFGSDSGIGQLAAAINRGDKTAVKTVFQQDFTDIEKRLLQ SGEDYIAMLEEALAGYGRYLDLLQARAEPDLIIQAFNEYQLLCALREGPFGVAGLNERIEQFMQQKRKIHRHPHSRWYEG RPVMIARNDSALGLFNGDIGIALDRGQGTRVWFAMPDGNIKSVQPSRLPEHETTWAMTVHKSQGSEFDHAALILPSQRTP VVTRELVYTAVTRARRRLSLYADERILSAAIATRTERRSGLAALFSSRE P04993 3.1.11.5 Host-nuclease inhibitor protein gam Enterobacteria phage lambda 0.011661924
GamL is cleaved at position Y44 when expressed in E.coli into GamS (see paper - pubmed id 17544443). We had the GamS gene synthesised to start at M41 for this project. It purifies as a dimer.
2 Escherichia coli BL21(DE3) LEVO MNAYYIQDRLEAQSWARHYQQLAREEKEAELADDMEKGIPQHLFESLCIDHLQRHGASKKSITRAFDDDVEFQERMAEHI RYMVETIAHHQVDIDSEV P03702 singleParticle particle 1.4 7.5 20.0 Tris-HCl 50.0 Sodium chloride 0.5 TCEP-HCl C-flat-1/1 400 CARBON HOLEY GLOW DISCHARGE
Grids were thinned by glow discharge in 30s steps with 1 minute wait in between treatments. Then left for 1-2 weeks prior to overnight treatment with 1 mM Ampiphol A8-35 to render surface hydrophilic. Grids were washed with 5 drops of water prior to use. EMS
 ETHANE 90 277 FEI VITROBOT MARK IV
3 ul sample applied Blot force of -4 for 1 s.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.2 0.6 2.4 2.9 105000.0 37313.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1-25 1 334 0.4 1.4 1
Frames were aligned using motioncorr prior to processing.
134124 3K70
The DNA was removed from the model so there was nothing to bias density where the inhibitor protein Gam was thought to bind.
 C1 3.8 FSC 0.143 CUT-OFF RELION 1.4 122796 ANGULAR RECONSTITUTION RELION 1.4 ANGULAR RECONSTITUTION RELION 1.4 10 RELION 1.4
3D classification without alignment (after running 3D refinement)
 emd_3460.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 241.20001 241.20001 241.20001 90.0 90.0 90.0 X Y Z -0.042780045 0.16285071 -0.0006984152 0.009656814 1.34 1.34 1.34 0.035 AUTHOR 5LD2 PDB experimental model RIGID BODY FIT Cross-correlation coefficient 2UUZ PDB experimental model RIGID BODY FIT Cross-correlation coefficient