2017-09-20 REL PDBe PDBe PDBe 2017-01-12 2017-02-15 2017-03-01 2017-09-20 3D reconstruction for the thin CcdA-CcdB-DNA filaments based on the negative stain electron microscopy dataset. Vandervelde A Efremov R Loris R Vandervelde A Drobnak I Hadzi S Sterckx YG Welte T De Greve H Charlier D Efremov R Loris R Lah J Molecular mechanism governing ratio-dependent transcription regulation in the ccdAB operon. Nucleic Acids Res. UK 45 2937 2950 2017 28334797 doi:10.1093/nar/gkx108 1362-4962 0389 NARHAD EMD-3569 other EM volume
3D reconstruction for the thick CcdA-CcdB-DNA filaments based on the cryo-electron microscopy dataset.
 EMD-3568 associated EM volume Thin filaments formed as the complex between DNA, antitoxin CcdA and toxin CcdB. Thin filaments formed as the complex between DNA, antitoxin CcdA and toxin CcdB. 0 1 2 3 antitoxin CcdA and toxin CcdB 1 1 2 Escherichia coli K-12 DNA 1 3 Escherichia coli Antitoxin CcdA Escherichia coli K-12 Escherichia coli LEVO MKQRITVTVDSDSYQLLKAYDVNISGLVSTTMQNEARRLRAERWKAENQEGMAEVARFIEMNGSFADENRDW Toxin CcdB Escherichia coli K-12 Escherichia coli LEVO MQFKVYTYKRESRYRLFVDVQSDIIDTPGRRMVIPLASARLLSDKVSRELYPVVHIGDESWRMMTTDMASVPVSVIGEEV ADLSHRENDIKNAINLMFWGI DNA Escherichia coli AATTGT GATGCTTCTAAAATTACTAAAATTGAGGATTTTAATGCTACAACAATGCC TGCCTCTTCTTATTTCTCCGGAGATCCGAAAACCCCAAGTTACGGATCTT CCTCTCCCTCCGCACAGCGTTACATCCCGTCAGCACAGCATGTAGTGCCT CATACAGTTGCCCATGGCACTATATGTTGTGTTGTATCTCTGGACTGTGA TGCGCCGCGCAGGGGCGGAAAACAGCGATATGATGATTTTCTCAGCGTTG TACACTTCCGGAAAGTCGTTTATTCAAATAAAGTCGGATCCATACGAAAC GGGAATGCGGTAATTACGCTTTGTTTTTATAAGTCAGATTTTAATTTTTA TTGGTTAACATAACGAAAGGTAAAATACATAAGGCTTACTAAAAGCCAGA TAACAGTATGCGTATTTGCGCGCTGATTTTTGCGGTATAAGAATATATAC TGATATGTATACCCGAAGTATGTCAAAAAGAGGTGTGCTATGAAGCAGCG TATTACAGTGACAGTTGACAGCGACAGCTATCAGTTGCTCAAGGCATATG ATGTCAATATCTCCGGTCTGGTAAGCACAACCATGCAGAATGAAGCCCGT CGTCTGCGTGCCGAACGCTGGAAAGCGGAAAATCAGGAAGGGATGGCTGA GGTCGCCCGGTTTATTGAAATGAACGGCTCTTTTGCTGACGAGAACAGGG ACTGGTGAAATGCAGTTTAAGGTTTACACCTATAAAAGAGAGAGCCGTTA TCGTCTGTTTGTGGATGTACAGAGTGATATTATTGACACGCCCGGGCGAC GGATGGTGATCCCCCTGGCCAGTGCACGTCTGCTGTCAGATAAAGTCTCC CGTGAACTTTACCCGGTGGTGCATATCGGGGATGAAAGCTGGCGCATGAT GACCACCGATATGGCCAGTGTGCCGGTCTCCGTTATCGGGGAAGAAGTGG CTGATCTCAGCCACCGCGAAAATGACATCAAAAACGCCATTAACC DNA helical filament 7.5 30.0 Tris 200.0 NaCl 0.5 EDTA
Just before staining, the sample was supplemented with 5 mM MgAc2 (final concentration).
 NEGATIVE Uranyl formate
The sample was applied to a freshly glow-discharged grid for five minutes after which the grid was washed with 5 mM MgAc2 and adsorbed protein stained with 1% uranyl formate.
 Electron Microscopy Sciences, continuous carbon/formvar COPPER 400 CARBON HOLEY GLOW DISCHARGE AIR 0.045
ELMO glow discharger
The binding reactions occurred at 20degC. DNA: 15 nM CcdA: 2.5 uM (dimer concentration) CcdB: 2.5 uM (dimer concentration) DNA was first incubated with CcdA for 15 minutes. After adding CcdB, the resulting mixture was incubated for another 15 minutes before preparing the EM sample.
 JEOL 1400 FLOOD BEAM BRIGHT FIELD LAB6 120 3.4 1.8 1.2 2.5 3.0 50000. JEOL TVIPS TEMCAM-F416 (4k x 4k) 1 358 50.0 1 38.4 64.3 C1 23.0 FSC 0.5 CUT-OFF SPARX 2600 SPARX find_ctf home written software 8260 e2helixboxer
Before sorting according to pitch
Cylinder
 NOT APPLICABLE SPARX emd_3568.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 90 90 90 -45 -45 -45 90 90 90 412.19998 412.19998 412.19998 90.0 90.0 90.0 X Y Z -0.02525345 0.15503567 -0.00061731157 0.009161664 4.58 4.58 4.58 0.0421 AUTHOR 3D reconstruction for the thin CcdA-CcdB-DNA filaments based on the negative stain electron microscopy dataset.