2026-01-28 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2024-08-05 2025-11-05 2025-11-05 2026-01-28 Agence Nationale de la Recherche (ANR) ANR-21-CE11-0040-01 France Agence Nationale de la Recherche (ANR) ANR-10-INBS-05 France RNAP-TopoI complex on duplex scaffold - consensus map Vidmar V Weixlbaumer A Lamour V RNA polymerase, topoisomerase, DNA topology, TRANSCRIPTION Vidmar V Borde C Bruno L Miropolskaya N Takacs M Batisse C Saint-Andre C Zhu C Espeli O Lamour V Weixlbaumer A DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation. Nat.Struct.Mol.Biol. US 33 134 144 2026 41326756 doi:10.1038/s41594-025-01703-5 1545-9985 EMDB EMD-51252 associated EM volume RNAP-TopoI complex on duplex scaffold RNAP-TopoI complex on duplex scaffold 0 1 2 3 4 5 6 7 8 9 0.1 DNA-directed RNA polymerase elongation complex 1 1 2 3 4 5 7 8 9 Escherichia coli DNA topoisomerase 1 1 6 Escherichia coli singleParticle particle 10 7.5 10.0 HEPES/KOH 150.0 potassium acetate 5.0 magnesium acetate 0.01 zinc chloride 2.0 DTT UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY 50.0 PLASMA CLEANING OTHER ETHANE 100 283 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.5 NITROGEN GATAN K3 (6k x 4k) 56.6 1 cryoSPARC PHASE FLIPPING AND AMPLITUDE CORRECTION 2.7 FSC 0.143 CUT-OFF cryoSPARC 113760 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_51252.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 302.04 302.04 302.04 90.0 90.0 90.0 X Y Z -0.04276322 2.0312064 0.0021497263 0.031392872 0.83900005 0.83900005 0.83900005 0.0177 AUTHOR RNAP-TopoI complex on duplex scaffold - consensus deepemhanced map 6alh PDB experimental model 4rul PDB experimental model
Initial rigid body fit was done in UCSF Chimera, followed by flexible fitting in Isolde. The entire model was further refined in Phenix and Coot.
REAL emd_51252_msk_2.map emd_51252_msk_1.map emd_51252_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 302.04 302.04 302.04 90.0 90.0 90.0 X Y Z -0.33099464 1.0231669 0.0024957228 0.03998191 0.83900005 0.83900005 0.83900005 AUTHOR RNAP-TopoI complex on duplex scaffold - consensus unsharpened map emd_51252_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 302.04 302.04 302.04 90.0 90.0 90.0 X Y Z -0.45856714 1.205244 0.002235548 0.06040261 0.83900005 0.83900005 0.83900005 AUTHOR RNAP-TopoI complex on duplex scaffold consensus map - halfmap B emd_51252_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 302.04 302.04 302.04 90.0 90.0 90.0 X Y Z -0.44999236 1.1394238 0.0021893778 0.06032905 0.83900005 0.83900005 0.83900005 AUTHOR RNAP-TopoI complex on duplex scaffold consensus map - halfmap A