2024-01-10 REL PDBe PDBe PDBe 2022-07-07 2023-11-08 2023-11-08 2024-01-10 European Commission 725685 European Union European Molecular Biology Organization (EMBO) 556-2018 European Union Structure of dimeric yeast RNA polymerase II bound to a transcription bubble (consensus map) Carminati M Manav MC Bellini D Passmore LA transcription regulation, RNA 3' end processing, transcription termination, GENE REGULATION Carminati M Rodriguez-Molina JB Manav MC Bellini D Passmore LA A direct interaction between CPF and RNA Pol II links RNA 3' end processing to transcription. Mol.Cell US 83 4461 4478.e13 2023 38029752 doi:10.1016/j.molcel.2023.11.004 1097-2765 2168 MOCEFL EMD-15359 other EM volume
focused refinement monomer 1
 EMD-15360 other EM volume
focused refinement monomer 2
 S. cerevisiae RNA polymerase II S. cerevisiae RNA polymerase II 0
RNA polymerase 'stalk-to-stalk' homodimer loaded with a DNA-RNA scaffold mimicking a transcription bubble
Saccharomyces cerevisiae .552 singleParticle particle 1.1 8.0 10.0 K-HEPES 100.0 KCl 0.5 TCEP
0.005 % v/v Tween-20 was added to the sample just before vitrification to prevent preferred orientation problems.
 UltrAuFoil R1.2/1.3 GOLD 300 PLASMA CLEANING ETHANE 100 277.15 FEI VITROBOT MARK IV
blot for 4 seconds (force -12) before plunging.
The vitrified sample contained Pol II (with transcription bubble) bound to Ref2:Glc7:Swd2. We observed a dimeric Pol II population (~10 % of particles) which is reported in the present deposition.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.5 2.7 105000.0 NITROGEN 20
The movies were collected without tilt or with a tilt angle over a 33-45 degrees range.
GATAN K3 BIOQUANTUM (6k x 4k) 6 25411 40.0 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.5 2.7 75000.0 NITROGEN
The movies were collected without tilt or with a tilt angle over a 30-40 degrees range.
FEI FALCON III (4k x 4k) COUNTING 2 2035 40.0 1
Consensus (refined) map of the intact Pol II dimer before focused refinement on monomer 1 (EMD-15359) and monomer 2 (EMD-15360).
5000000
800000 particles from the Falcon II datasets were used for the final reconstruction (please refer to the methods in the paper)
 EMD-8736 1 C1 4.6 FSC 0.143 CUT-OFF RELION 3.1
Consensus refined map of homodimeric RNA Pol II before focused refinement on monomer 1 (EMD-15359) or monomer 2 (EMD-15360).
151000 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 6 RELION 3.1 emd_15358.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 415.0 415.0 415.0 90.0 90.0 90.0 X Y Z -0.007801991 0.02486588 0.0002527381 0.0013749115 0.83 0.83 0.83 0.008 AUTHOR RNA Polymerase II dimer loaded with a DNA-RNA scaffold 5C4X PDB experimental model RIGID BODY FIT
Two copies of the monomeric Pol II structure (PDB: 5C4X) were rigid fit into the dimeric Pol II EM density
 emd_15358_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 415.0 415.0 415.0 90.0 90.0 90.0 X Y Z -0.009756114 0.022948926 0.00025152112 0.0014917133 0.83 0.83 0.83 AUTHOR emd_15358_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 500 500 500 0 0 0 500 500 500 415.0 415.0 415.0 90.0 90.0 90.0 X Y Z -0.0104628 0.024941294 0.00025395508 0.0015127619 0.83 0.83 0.83 AUTHOR