E. coli JetABC monomer in a DNA boarding conformation

2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation DERIVED_CALCULATIONS em_admin pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order _em_admin.last_update PDBe PDBe 2025-04-16 2025-10-01 2025-10-01 2026-09-02 European Research Council (ERC) 724482 European Union Swiss National Science Foundation 10001017 Switzerland E. coli JetABC monomer in a DNA boarding conformation Roisne-Hamelin F Gruber S Gruber S SMC complexes, Wadjet, JetABCD, DNA loop extrusion, DNA BINDING PROTEIN Roisne-Hamelin F Liu HW Marechal N Uchikawa E Durand A Gruber S Mechanism of DNA entrapment by a loop-extruding Wadjet SMC motor. Mol.Cell US 85 3898 2025 41072419 doi:10.1016/j.molcel.2025.09.015 1097-2765 2168 MOCEFL 9qxr FULLOVERLAP EMDB EMD-53442 associated EM volume

JetABC DNA boarding state, a step of the loading reaction on DNA JetABC DNA boarding state, a step of the loading reaction on DNA 0 1 2 3 4

E. coli JetABC was incubated with biotinylated plasmid DNA in presence of ATP. The reaction was poisoned with beryllium fluoride prior grid freezing.

Escherichia coli GF4-3 JetB Escherichia coli GF4-3 0.028020416

The last "G" in the theorical sequence is the result of a DNA cloning scar.

2 Escherichia coli BL21 LEVO MAGFFDKLINRSVTANAGCEPEPSDEEVTDESVEDSLASSETRTLQKIREATQELLKYGLLEEASKPNLYRIVLSHPEEV TRILEPLDLDIGIDEIRGLLYVKVRLDETPAQDEWAHPLVRRQRLNLEQSLLVAILRQHFVAWEQESGTGASQAQIAIDD LLPQLQIYLGDPGSESKERTRLLTLLDQLKGHGLVTSPDAHERIVIRPIIAHLADPINLQALLAWLREQIAQQTSPNDAP EKDSSEEDVG JetA Escherichia coli GF4-3 0.05781891

The last "G" in the theorical sequence is the result of a DNA cloning scar. "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 BL21 LEVO GPAAMEENTRQRTENYISAKNQHPAWILLATRRAPLVLSCLKTLFEKSHDGIPLEEAIQSLSSILIEHVSQEQYDINQDN PFLQASRELREWIKRRLIVERDGRIFATDALEVAITFVESLDNRFMTSTASRLSTVQREIENLETRLNPNPANRVATLRR RISELERELQEAEAGHIEVLETHQAVEHIRDVYNLASSLRADFRRVEDSWREADRALRQSIIGEQYHRGDIVERLLNDQD ALLNTPEGRVFDSFQQQLRQSSELKAMSERLRVILSHPSASDALNRLQRHDLRWLVKRLVDESQTVLQARARSERDVRGF MKTGLAAEHHRVGHLLNEFLNLALKLDWQRQMIRKQEVPLPAVGVAVTGIPAIERLRFKEVDDEAEQTLDLSNHAADLTQ IGDDFWDAFNGLDREVLIQQTLQLLAKENRPVGLAELAELLPPAHDLETFAVWIGMAREAGIEVIDSQREFAELSDGEGR RWRFNLPTTGLESQALMDIDWEG JetC Escherichia coli GF4-3 0.12456293799999998

The last "G" in the theorical sequence is the result of a DNA cloning scar.

2 Escherichia coli BL21 LEVO MNQVSGLAGKESFILTRIELFNWGGFHGLHQAAIHQDGTAVIGPTGSGKTTLVDALMTLLCANPRYNLASTGGHESDRDL ISYVRGVSGPGDGGEGQSHIARPGKTVTGIAATLEREGKQVRLGALLWFDSTSSSVTDMKRLWLFSDNPGQTLEHWLNVY HEGGTRLLRQMEKEAIGLWTYPNKKQYLARLRDFFEVGENAFTLLNRAAGLKQLNSIDEIFRELVLDDHSAFDRAAEVAN SFDGLTEIHQELETARKQQQSLQPVALSWEKYQKQERQLADWLTLESLLPLWFAQQASHLWREKINLLNARLAEAQTSEE QLQSQLDLQKKVVSDCMQRYLQVGGANIDELNERIKDWQKTLGSREALARQYQQLTRNLGLPSDLSQPQLEANQHEAEAR CEQIAVDIKLKQEEAYQKGALSHHITEELRERENERAEIARRPDSNLPAHYQAFRSELAKALNVDESELPFVAELIQVKP EEAQWRGAIERAVGSNRLRILVAPESAQEALRWVNQRNNRLHVRLLEVKLPHSPARFFDDGFTRKLLWKDHPWREAVKAL LAESDRHCVDSPEQLHDTPHAMTVQGLMSGKQRFYDKHDQKRLDEDWLTGFDNRDRLNFLAKEIATLQEQVKTANAAFEF AKGEVGLLQNQAASFQKIEQIDFDSIDVPGAKSQLDALRERLENLTRPDSDASVAKAKLDEAQTIESELDKQLRAANKVT NVLDTELTLARAAERKAQQTAQQGMKEEERELCASHFPVVTLEQLPDIRDLERQHERGIQHEIERVKAELHRLNIELTKR MSEAKRVDTGALVEAGADLDDIPVYLQRLQELTEEALPEKLNRFLDYLNRSSDDGVTQLLSHIEHEVLVIEERLNELNET MFRVDFQPDRYLRLDTKKVVHESLRTLEKAQRQLNAARFVDDNGESHYKALQVLVAQLRDACERNRTLGAKALLDPRFRL EFAVSVMDRQSGNVIESRTGSQGGSGGEKEIIASYVLTASLSYALCPAGSRYPLFGTIILDEAFSRSSHAVAGRIIAALR EFGLHAVFITPNKEMRLLRDHTRSAIVVHRRGQNSNMASLSWEELERHYQRRGNAG Biotinylated circular plasmid DNA (1894-MER) Escherichia coli 0.018477025

Only a portion of the biotinylated plasmid (pSG7427, 1894bp) has been modelled as polyAT track, because the complex is expected to load at random positions and the local resolution of the DNA does not allow any sequence assignment.

2 (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) (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 2 ADP MAGNESIUM ION 2.4305e-05 2 MG BERYLLIUM TRIFLUORIDE ION 6.600700000000001e-05 2 BEF singleParticle particle 7.5 ETHANE 100 279 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.4 FEI FALCON IV (4k x 4k) 1 31601 39.48 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.25 FSC 0.143 CUT-OFF cryoSPARC 78524 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_53442.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 466.56 466.56 466.56 90.0 90.0 90.0 X Y Z -1.5919358 3.150732 0.000121863406 0.06942904 1.1664 1.1664 1.1664 0.47 AUTHOR ::::EMDATABANK.org::::EMD-53442:::: Full EM map 8as8 PDB experimental model 8bfn PDB experimental model 8q72 PDB experimental model Other in silico model

Idealized B-form DNA was flexibly fitted

FLEXIBLE FIT emd_53442_msk_1.map emd_53442_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 466.56 466.56 466.56 90.0 90.0 90.0 X Y Z -0.59467804 1.8683802 0.00012186332 0.045195892 1.1664 1.1664 1.1664 AUTHOR ::::EMDATABANK.org::::EMD-53442:::: Full EM map emd_53442_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 466.56 466.56 466.56 90.0 90.0 90.0 X Y Z -1.2486016 2.6612086 0.0010236118 0.16839752 1.1664 1.1664 1.1664 AUTHOR ::::EMDATABANK.org::::EMD-53442:::: Full EM map emd_53442_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 466.56 466.56 466.56 90.0 90.0 90.0 X Y Z -1.4318523 2.581521 0.0010223371 0.16687344 1.1664 1.1664 1.1664 AUTHOR ::::EMDATABANK.org::::EMD-53442:::: Full EM map