2017-08-02 REL PDBe PDBe PDBe 2016-11-03 2016-12-07 2017-05-17 2017-08-02 negative-stain volume of Sso DNA PolB1 Abrescia NGA Bell SD Yan J Beattie TR Rojas AL Schermerhorn K Gristwood T Trinidad JC Albers SV Roversi P Gardner AF Abrescia NGA Bell SD Identification and characterization of a heterotrimeric archaeal DNA polymerase holoenzyme. Nat Commun UK 8 15075 15075 2017 28462924 doi:10.1038/ncomms15075 2041-1723 EMD-3458 associated EM volume
Gadolinium phased PBP2 (Sso6202) at 2.2 Ang
 archaeal DNA polymerase B1 archaeal DNA polymerase B1 0 1
This is the apo enzyme.
Archaea Escherichia coli pET33b 0.101 DNA polymerase B1 Archaea Escherichia coli LEVO MAKQLTLFDIPSSKPAKSEQNTQQSQQSAPVEEKKVVRREWLEEAQENKIYFLLQVDYDGKKGKAVCKLFDKETQKIYALYDNTGHKPYFLVDLEPDKVGKIPKIVRDPSFDHIETVSKIDPYTWNKFKLTKIVVRDPLAVRRLRNDVPKAYEAHIKYFNNYMYDIGLIPGMPYVVKNGKLESVYLSLDEKDVEEIKKAFADSDEMTRQMAVDWLPIFETEIPKIKRVAIDIEVYTPVKGRIPDSQKAEFPIISIALAGSDGLKKVLVLNRNDVNEGSVKLDGISVERFNTEYELLGRFFDILLEYPIVLTFNGDDFDLPYIYFRALKLGYFPEEIPIDVAGKDEAKYLAGLHIDLYKFFFNKAVRNYAFEGKYNEYNLDAVAKALLGTSKVKVDTLISFLDVEKLIEYNFRDAEITLQLTTFNNDLTMKLIVLFSRISRLGIEELTRTEISTWVKNLYYWEHRKRNWLIPLKEEILAKSSNIRTSALIKGKGYKGAVVIDPPAGIFFNITVLDFASLYPSIIRTWNLSYETVDIQQCKKPYEVKDETGEVLHIVCMDRPGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFGAETFPLYAPAVAESVTALGRYVITSTVKKAREEGLTVLYGDTDSLFLLNPPKNSLENIIKWVKTTFNLDLEVDKTYKFVAFSGLKKNYFGVYQDGKVDIKGMLVKKRNTPEFVKKVFNEVKELMISINSPNDVKEIKRKIVDVVKGSYEKLKNKGYNLDELAFKVMLSKPLDAYKKNTPQHVKAALQLRPFGVNVLPRDIIYYVKVRSKDGVKPVQLAKVTEIDAEKYLEALRSTFEQILRAFGVSWDEIAATMSIDSFFSYPSKGNS singleParticle particle 0.01 7.5 10.0 Hepes Hepes 100.0 NaCl sodium chloride 1.0 DTT Dithiothreitol NEGATIVE uranyl formate
Negatively stained EM specimens were prepared using carbon-coated grids and stained with 2% of uranyl formate solution.
 EMS COPPER 300 CARBON CONTINUOUS GLOW DISCHARGE AIR 0.02 JEOL 2200FSC FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.0 1.3 1.7 60000. 90201. JEOL In-column Omega Filter 0 20 GATAN ULTRASCAN 4000 (4k x 4k) 108 0.5 30.0 1 20000 CTFFIND 3
phase flipping was performed using XMIPP software
 1S5J
The initial reference map was generated using the atomic model.
 1 C1 22.8 FSC 0.5 CUT-OFF RELION RELION through SCIPION
Calculated for the converged iteration 10 in Relion using Scipion
14582 PROJECTION MATCHING RELION 1.4 PROJECTION MATCHING 3.75 RELION RELION through SCIPION emd_3458.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 212.48 212.48 212.48 90.0 90.0 90.0 X Y Z -0.04231351 0.08533787 0.0006148041 0.006312904 1.66 1.66 1.66 0.025 AUTHOR Final map from iteration 10 onto which FSC has been calculated and displayed (Figure S4C, right). Contour level in Chimera RIGID BODY FIT Cross-correlation coefficient REAL emd_3458_msk_1.map emd_3458_additional.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 212.48 212.48 212.48 90.0 90.0 90.0 X Y Z -0.07120246 0.16377145 0.001263435 0.010744331 1.66 1.66 1.66 0.036 AUTHOR This is the masked map used in Figure 4A and in submitted figure. Contour level in Chimera. emd_3458_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 212.48 212.48 212.48 90.0 90.0 90.0 X Y Z -0.046752308 0.089033954 0.00056355563 0.006532639 1.66 1.66 1.66 0.022 AUTHOR half2 map from iteration 10. Contour level in Chimera emd_3458_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 0 0 0 128 128 128 212.48 212.48 212.48 90.0 90.0 90.0 X Y Z -0.045601033 0.084069684 0.0005635458 0.006523366 1.66 1.66 1.66 0.022 AUTHOR half1 map from iteration 10. Contour level in Chimera