2024-03-13 REL RCSB RCSB RCSB 2018-10-29 2018-11-21 2019-06-19 2024-03-13 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM124847 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM100008 United States EM structure of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha subunit and NrdF beta subunit with dATP Thomas WC Bacik JP Kaelber JT Ando N ribonucleotide reductase, allostery, nucleotide metabolism, filament, dATP, ATP, OXIDOREDUCTASE Thomas WC Brooks 3rd FP Burnim AA Bacik JP Stubbe J Kaelber JT Chen JZ Ando N Convergent allostery in ribonucleotide reductase. Nat Commun UK 10 2653 2653 2019 31201319 doi:10.1038/s41467-019-10568-4 2041-1723 EMD-9293 other EM volume 6mw3 FULLOVERLAP Inhibited filament of ribonucleoside-diphosphate reductase composed of NrdE alpha subunits and NrdF beta subunit tails Inhibited filament of ribonucleoside-diphosphate reductase composed of NrdE alpha subunits and NrdF beta subunit tails 0 1 2
Beta subunit core density only visible at low threshold. Beta subunit tail is bound with strong density to alpha subunit and modeled as a poly-A peptide in the model.
Bacillus subtilis Ribonucleoside-diphosphate reductase Bacillus subtilis 0.08079146899999999 2 Escherichia coli LEVO MSQNQVPKWIQLNNEIMIQKDGKFQFDKDKEAVHSYFVDYINQNTVFFHNLKEKLDYLVENQYYEEEFLSLYSFEDIKEV FKTAYAKKFRFPSFMSAFKFYNDYALKTNDKKKILERYEDRISIVALFFANGDTEKAKEYVNLMINQEYQPSTPTFLNAG RKRRGELVSCFLLEVNDSLNDISRAIDISMQLSKLGGGVSLNLSKLRAKGEAIKDVENATKGVVGVMKLLDNAFRYADQM GQRQGSGAAYLNIFHRDINDFLDTKKISADEDVRVKTLSIGVVIPDKFVELAREDKAAYVFYPHTIYKEYGQHMDEMDMN EMYDKFVDNPRVKKEKINPRKLLEKLAMLRSESGYPYIMFQDNVNKVHANNHISKVKFSNLCSEVLQASQVSSYTDYDEE DEIGLDISCNLGSLNILNVMEHKSIEKTVKLATDSLTHVSETTDIRNAPAVRRANKAMKSIGLGAMNLHGYLAQNGIAYE SPEARDFANTFFMMVNFYSIQRSAEIAKEKGETFDQYEGSTYATGEYFDKYVSTDFSPKYEKIANLFEGMHIPTTEDWKK LKAFVAEHGMYHSYRLCIAPTGSISYVQSSTASVMPIMERIEERTYGNSKTYYPMPGLASNNWFFYKEAYDMDMFKVVDM IATIQQHIDQGISFTLFLKDTMTTRDLNRIDLYAHHRGIKTIYYARTKDTGQDSCLSCVV A0A162Q3J9 1.17.4.1 Ribonucleoside-diphosphate reductase NrdF beta subunit Bacillus subtilis 0.0006988540000000001
C-terminus modeled as a polyalanine chain
2 Escherichia coli LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE 0.000491182 4 DTP helical filament 0.40 7.6 50.0 C8H18N2O4S HEPES 150.0 NaCl sodium chloride 15.0 MgCl2 magnesium chloride 1.0 C9H15O6P TCEP
Glycerol in original storage buffer was diluted to < 0.25% w/v.
unspecified
 ETHANE 95 LEICA EM GP
Cryo-EM samples of the NrdEF filament were prepared by mixing 20 uM C382S holo-NrdE with 20 or 40 uM Mn-reconstituted NrdF in assay buffer with 100 uM dATP and 1 mM CDP, prior to dilution with nucleotide-containing buffer to a concentration of 5 uM protein. A subset of the grids were pre-coated with a support film of continuous, amorphous carbon by flotation of cleaved mica. For these grids, the sample was diluted to a final protein concentration of 2 uM.
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 2843 8.0 1 73.8 88.6 C1 FOURIER SPACE 4.65 FSC 0.143 CUT-OFF cryoSPARC 2.0.27 126224 281591
ab initio model
 NOT APPLICABLE cryoSPARC 2.0.27 emd_9272.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 251.99998 251.99998 251.99998 90.0 90.0 90.0 X Y Z -2.6790166 4.963113 0.068803266 0.25537685 1.05 1.05 1.05 1.14 AUTHOR ASU of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha and NrdF beta subunits with dATP. Handedness already corrected by reference to NrdE crystal structures. 6CGN PDB experimental model OTHER Correlation coefficient REAL emd_9272_msk_1.map emd_9272_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 -120 -120 -120 480 480 480 503.99997 503.99997 503.99997 90.0 90.0 90.0 X Y Z -0.9484331 1.1481826 0.0018945284 0.11869314 1.05 1.05 1.05 AUTHOR Unfiltered, unmasked, half-map from refinement of NrdEF emd_9272_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 -120 -120 -120 480 480 480 503.99997 503.99997 503.99997 90.0 90.0 90.0 X Y Z -0.997486 1.1562638 0.0018479157 0.11867748 1.05 1.05 1.05 AUTHOR Unfiltered, unmasked half-map from refinement of NrdEF