Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode

2017-08-30 REL PDBe PDBe PDBe 2016-10-12 2016-10-26 2017-01-18 2017-08-30 Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode Fernandez-Leiro R Conrad J Scheres SHW Lamers MH Fernandez-Leiro R Conrad J Yang JC Freund SM Scheres SH Lamers MH Self-correcting mismatches during high-fidelity DNA replication. Nat. Struct. Mol. Biol. US 24 140 143 2017 28067916 doi:10.1038/nsmb.3348 1545-9985 EMD-4142 associated EM volume

DNA polyerase III alpha, beta, epsilon, theta complex with mismatched DNA duplex DNA polyerase III alpha, beta, epsilon, theta complex with mismatched DNA duplex 0 1 2 3 4 5 6 Escherichia coli K12 Escherichia coli BL21 (DE3) pET28a 0.250 DNA polyerase III alpha, epsilon, theta complex with mismatched DNA duplex 1 1 3 4 5 6

Map obtained after signal subtraction of the beta subunit and alignment of the remaining parts. Final reconstruction obtained with non-subtracted images and angles from local alignment

Escherichia coli K12 Escherichia coli BL21 (DE3) pET28a singleParticle particle 0.25 7.5 20.0 Hepes 50.0 Potassium glutamate 5.0 Magnesium Acetate 2.0 Dithiothreitol Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE AIR ETHANE 100 277 FEI VITROBOT MARK IV

Prior to sample preparation 0.1 volumes of 0.05% Tween 20 were added to the sample 3 microliters were pipetted onto the grid and blotted for 4 seconds.

Sample was run over a gel filtration column prior to vitrification

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.8 3.5 64000. 79545. FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 80.0 GIF Quantum 0 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3710 3 1157 25.0 2.0 1 150000 Gctf EMD-3198

low pass filtered to 60 angtrom

FOURIER SPACE 6.7 FSC 0.143 CUT-OFF RELION 2 15616 PROJECTION MATCHING RELION 2 PROJECTION MATCHING RELION 2 RELION 2 emd_4142.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 140 140 140 0 0 0 140 140 140 246.4 246.4 246.4 90.0 90.0 90.0 X Y Z -0.14866291 0.33609918 0.00007027035 0.016236395 1.76 1.76 1.76 0.08 AUTHOR ::::EMDATABANK.org::::EMD-4142:::: Related to EMD-4142 Local alignment after signal subtraction of the beta subunit OTHER

The cryo-EM structure of the PolIIIalpha-clamp-exonuclease complex in the polymerase mode (PDB code: 5FKW)1 was used as a starting model, and the NMR structure of theta bound to the ? catalytic domain (PDB code: 2XY8)13 was used to place ? into the cryo-EM map. The model was manually adjusted in Coot35 and geometry of the protein optimized in Refmac536 using DNA-specific restraints generated in LibG36

emd_4142_msk_1.map emd_4142_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 140 140 140 0 0 0 140 140 140 246.4 246.4 246.4 90.0 90.0 90.0 X Y Z -0.04999094 0.11845305 0.000038404993 0.009204214 1.76 1.76 1.76 0.04 AUTHOR ::::EMDATABANK.org::::EMD-4142:::: emd_4142_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 140 140 140 0 0 0 140 140 140 246.4 246.4 246.4 90.0 90.0 90.0 X Y Z -0.048364304 0.1208156 0.000031865355 0.009192827 1.76 1.76 1.76 0.04 AUTHOR ::::EMDATABANK.org::::EMD-4142::::