2024-03-20 REL PDBe PDBe PDBe 2023-08-15 2024-01-31 2024-01-31 2024-03-20 European Research Council (ERC) 724482 European Union E. coli plasmid-borne JetABCD(E248A) core in a cleavage-competent state Roisne-Hamelin F Li Y Gruber S SMC complexes, DNA loop extrusion, nuclease, bacterial immunity, defense system, topoisomerase, plamid restriction, MksBEFG, Wadjet, EptABCD, horizontal gene transfer, DNA binding protein, DNA kinking Roisne-Hamelin F Liu HW Taschner M Li Y Gruber S Structural basis for plasmid restriction by SMC JET nuclease. Mol.Cell US 84 883 2024 38309275 doi:10.1016/j.molcel.2024.01.009 1097-2765 2168 MOCEFL EMD-18211 other EM volume
E. coli plasmid-borne JetABC in a cleavage-competent state
 EMD-18208 other EM volume
E. coli plasmid-borne JetABCD(E248A) in a cleavage-competent state
 EMD-18209 other EM volume
E. coli plasmid-borne JetD(E248A) in a cleavage-competent state
 8q72 FULLOVERLAP JetABCD(E248A) loaded onto plasmid DNA JetABCD(E248A) loaded onto plasmid DNA 0 1 2 3 4 5
E. coli JetABC, JetD(E248A) and plasmid DNA were mixed and incubated with ATP prior freezing.
Escherichia coli GF4-3 JetC Escherichia coli GF4-3 0.12456293799999998
The last "G" in the theorical sequence is the result of a DNA cloning scar.
4 Escherichia coli LEVO MNQVSGLAGKESFILTRIELFNWGGFHGLHQAAIHQDGTAVIGPTGSGKTTLVDALMTLLCANPRYNLASTGGHESDRDL ISYVRGVSGPGDGGEGQSHIARPGKTVTGIAATLEREGKQVRLGALLWFDSTSSSVTDMKRLWLFSDNPGQTLEHWLNVY HEGGTRLLRQMEKEAIGLWTYPNKKQYLARLRDFFEVGENAFTLLNRAAGLKQLNSIDEIFRELVLDDHSAFDRAAEVAN SFDGLTEIHQELETARKQQQSLQPVALSWEKYQKQERQLADWLTLESLLPLWFAQQASHLWREKINLLNARLAEAQTSEE QLQSQLDLQKKVVSDCMQRYLQVGGANIDELNERIKDWQKTLGSREALARQYQQLTRNLGLPSDLSQPQLEANQHEAEAR CEQIAVDIKLKQEEAYQKGALSHHITEELRERENERAEIARRPDSNLPAHYQAFRSELAKALNVDESELPFVAELIQVKP EEAQWRGAIERAVGSNRLRILVAPESAQEALRWVNQRNNRLHVRLLEVKLPHSPARFFDDGFTRKLLWKDHPWREAVKAL LAESDRHCVDSPEQLHDTPHAMTVQGLMSGKQRFYDKHDQKRLDEDWLTGFDNRDRLNFLAKEIATLQEQVKTANAAFEF AKGEVGLLQNQAASFQKIEQIDFDSIDVPGAKSQLDALRERLENLTRPDSDASVAKAKLDEAQTIESELDKQLRAANKVT NVLDTELTLARAAERKAQQTAQQGMKEEERELCASHFPVVTLEQLPDIRDLERQHERGIQHEIERVKAELHRLNIELTKR MSEAKRVDTGALVEAGADLDDIPVYLQRLQELTEEALPEKLNRFLDYLNRSSDDGVTQLLSHIEHEVLVIEERLNELNET MFRVDFQPDRYLRLDTKKVVHESLRTLEKAQRQLNAARFVDDNGESHYKALQVLVAQLRDACERNRTLGAKALLDPRFRL EFAVSVMDRQSGNVIESRTGSQGGSGGEKEIIASYVLTASLSYALCPAGSRYPLFGTIILDEAFSRSSHAVAGRIIAALR EFGLHAVFITPNKEMRLLRDHTRSAIVVHRRGQNSNMASLSWEELERHYQRRGNAG A0A6D0I2P0 JetB Escherichia coli GF4-3 0.028020416
The last "G" in the theorical sequence is the result of a DNA cloning scar.
4 Escherichia coli LEVO MAGFFDKLINRSVTANAGCEPEPSDEEVTDESVEDSLASSETRTLQKIREATQELLKYGLLEEASKPNLYRIVLSHPEEV TRILEPLDLDIGIDEIRGLLYVKVRLDETPAQDEWAHPLVRRQRLNLEQSLLVAILRQHFVAWEQESGTGASQAQIAIDD LLPQLQIYLGDPGSESKERTRLLTLLDQLKGHGLVTSPDAHERIVIRPIIAHLADPINLQALLAWLREQIAQQTSPNDAP EKDSSEEDVG JetA Escherichia coli GF4-3 0.05781891
"GPAA" at the begining of the theorical sequence is the remaining of the purification tag after tag cleavage. The last "G" in the theorical sequence is the result of a DNA cloning scar.
2 Escherichia coli LEVO GPAAMEENTRQRTENYISAKNQHPAWILLATRRAPLVLSCLKTLFEKSHDGIPLEEAIQSLSSILIEHVSQEQYDINQDN PFLQASRELREWIKRRLIVERDGRIFATDALEVAITFVESLDNRFMTSTASRLSTVQREIENLETRLNPNPANRVATLRR RISELERELQEAEAGHIEVLETHQAVEHIRDVYNLASSLRADFRRVEDSWREADRALRQSIIGEQYHRGDIVERLLNDQD ALLNTPEGRVFDSFQQQLRQSSELKAMSERLRVILSHPSASDALNRLQRHDLRWLVKRLVDESQTVLQARARSERDVRGF MKTGLAAEHHRVGHLLNEFLNLALKLDWQRQMIRKQEVPLPAVGVAVTGIPAIERLRFKEVDDEAEQTLDLSNHAADLTQ IGDDFWDAFNGLDREVLIQQTLQLLAKENRPVGLAELAELLPPAHDLETFAVWIGMAREAGIEVIDSQREFAELSDGEGR RWRFNLPTTGLESQALMDIDWEG A0A4V3QHV5 JetD(E248A) Escherichia coli 0.043938491999999996
"GSLEVLFQ" at the C-terminus in the theorical sequence is the remaining of the tag after tag cleavage. The sequence carries the "E248A" mutation (nuclease dead).
2 Escherichia coli LEVO MYSPDELREKLARQWDSAKLRAERLLSPGNWPLCLPIGKPSTKIFAEQTQRVLQHVQRWRQVAVGHVEWEAVSFRASDTP VLMPLRWILNSPSEWINAAADPVVSREFRLLEGIIEQVNPIFHPLLVKHRSLWRHKDPQGVISAATLACRLEPGCAKGLP LRLLSGQGVDTKFIENNISLLTRLLDVRFSGEASEQGLTTFLDAFDESSHWVLVVPLSPGLLPFKKCRVTTAELAETTLP ASQVLVVANEQCLHHLPALSDTIAILGCGLDVQWLSSSVLDEKRVAYWGDMDSWGLLMLARARRCRPTLDALLMNRELFE QYASHSAVPEPVIAKEAVPDGLLNEEADFYRYLTRLPRGRLEQEFLPVGIAEEALLRWGKESGSLEVLFQ A0A3T6B0Z0 Circular plasmid DNA (1840-MER) Escherichia coli 0.012303033
Only a portion of the plasmid (pSG6085, 1840 bp) has been modelled as polyAT track, because the complex is expected to bind in random position to the DNA and the resolution of DNA do not allow any sequence assignement.
4 (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) DNA ADENOSINE-5'-DIPHOSPHATE 0.000427201 4 ADP singleParticle particle 7.5 Au-flat 1.2/1.3 GOLD GLOW DISCHARGE ETHANE 100 283 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.6 FEI FALCON IV (4k x 4k) 1 37902 40.0 1 C2 4.17 FSC 0.143 CUT-OFF cryoSPARC 3.3 235956 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_18201.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 531.2 531.2 531.2 90.0 90.0 90.0 X Y Z -0.66107005 1.1526163 0.000082643266 0.019152261 1.6600001 1.6600001 1.6600001 0.102 AUTHOR 8AS8 PDB experimental model AlphaFold in silico model Other in silico model
Idealized B-form DNA was flexibly fitted
 FLEXIBLE FIT emd_18201_msk_1.map emd_18201_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 531.2 531.2 531.2 90.0 90.0 90.0 X Y Z -0.1698389 0.5653158 0.000082643266 0.015501639 1.6600001 1.6600001 1.6600001 AUTHOR This is the unsharpened map. emd_18201_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 531.2 531.2 531.2 90.0 90.0 90.0 X Y Z -0.25854352 0.6801217 0.00042498377 0.019046156 1.6600001 1.6600001 1.6600001 AUTHOR emd_18201_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 531.2 531.2 531.2 90.0 90.0 90.0 X Y Z -0.30488858 0.71896553 0.00042394717 0.019108703 1.6600001 1.6600001 1.6600001 AUTHOR