HEADER TRANSCRIPTION, TRANSFERASE/DNA 31-DEC-69 6XL9 TITLE Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex TITLE 2 with 3-nt RNA transcript (EcmrR-RPitc-3nt) COMPND MOL_ID: 4; COMPND 2 MOLECULE: RNA polymerase sigma factor RpoD; COMPND 3 CHAIN: F; COMPND 4 ENGINEERED: YES; EXPDTA ELECTRON MICROSCOPY DBREF 6XL9 F 1 613 UNP P00579 RPOD_ECOLI 1 613 SEQRES 1 F 32 ARG THR ILE ARG ILE PRO VAL HIS MET ILE GLU THR ILE SEQRES 2 F 32 ASN LYS LEU ASN ARG ILE SER ARG GLN MET LEU GLN GLU SEQRES 3 F 32 MET GLY ARG GLU PRO THR ATOM 1 N ARG F 448 146.881 156.290 150.172 1.00 75.35 ATOM 2 CA ARG F 448 147.821 155.425 150.869 1.00 75.35 ATOM 3 C ARG F 448 149.112 155.423 150.075 1.00 75.35 ATOM 4 O ARG F 448 149.076 155.349 148.847 1.00 75.35 ATOM 5 CB ARG F 448 147.281 154.006 151.017 1.00 75.35 ATOM 6 CG ARG F 448 146.781 153.683 152.403 1.00 75.35 ATOM 7 CD ARG F 448 146.356 152.242 152.494 1.00 75.35 ATOM 8 NE ARG F 448 145.843 151.895 153.812 1.00 75.35 ATOM 9 CZ ARG F 448 146.546 151.269 154.748 1.00 75.35 ATOM 10 NH1 ARG F 448 147.803 150.926 154.516 1.00 75.35 ATOM 11 NH2 ARG F 448 145.995 150.990 155.917 1.00 75.35 ATOM 12 N THR F 449 150.244 155.520 150.773 1.00 72.62 ATOM 13 CA THR F 449 151.534 155.526 150.093 1.00 72.62 ATOM 14 C THR F 449 151.782 154.201 149.391 1.00 72.62 ATOM 15 O THR F 449 152.149 154.168 148.213 1.00 72.62 ATOM 16 CB THR F 449 152.653 155.818 151.085 1.00 72.62 ATOM 17 OG1 THR F 449 152.333 156.994 151.829 1.00 72.62 ATOM 18 CG2 THR F 449 153.952 156.046 150.356 1.00 72.62 ATOM 19 N ILE F 450 151.590 153.095 150.101 1.00 70.95 ATOM 20 CA ILE F 450 151.618 151.761 149.515 1.00 70.95 ATOM 21 C ILE F 450 150.177 151.302 149.357 1.00 70.95 ATOM 22 O ILE F 450 149.449 151.183 150.346 1.00 70.95 ATOM 23 CB ILE F 450 152.430 150.783 150.377 1.00 70.95 ATOM 24 CG1 ILE F 450 153.854 151.300 150.567 1.00 70.95 ATOM 25 CG2 ILE F 450 152.485 149.437 149.722 1.00 70.95 ATOM 26 CD1 ILE F 450 154.478 150.907 151.868 1.00 70.95 ATOM 27 N ARG F 451 149.764 151.062 148.116 1.00 71.98 ATOM 28 CA ARG F 451 148.361 150.849 147.790 1.00 71.98 ATOM 29 C ARG F 451 147.922 149.416 148.057 1.00 71.98 ATOM 30 O ARG F 451 148.605 148.462 147.683 1.00 71.98 ATOM 31 CB ARG F 451 148.111 151.199 146.326 1.00 71.98 ATOM 32 CG ARG F 451 146.678 151.051 145.895 1.00 71.98 ATOM 33 CD ARG F 451 146.516 151.241 144.408 1.00 71.98 ATOM 34 NE ARG F 451 147.049 150.125 143.639 1.00 71.98 ATOM 35 CZ ARG F 451 146.355 149.045 143.299 1.00 71.98 ATOM 36 NH1 ARG F 451 146.926 148.086 142.597 1.00 71.98 ATOM 37 NH2 ARG F 451 145.093 148.922 143.662 1.00 71.98 ATOM 38 N ILE F 452 146.760 149.277 148.686 1.00 71.81 ATOM 39 CA ILE F 452 146.137 148.000 149.027 1.00 71.81 ATOM 40 C ILE F 452 144.962 147.756 148.085 1.00 71.81 ATOM 41 O ILE F 452 144.218 148.698 147.788 1.00 71.81 ATOM 42 CB ILE F 452 145.667 148.003 150.487 1.00 71.81 ATOM 43 CG1 ILE F 452 146.743 148.571 151.393 1.00 71.81 ATOM 44 CG2 ILE F 452 145.353 146.637 150.945 1.00 71.81 ATOM 45 CD1 ILE F 452 147.921 147.697 151.537 1.00 71.81 ATOM 46 N PRO F 453 144.746 146.538 147.592 1.00 74.26 ATOM 47 CA PRO F 453 143.581 146.281 146.737 1.00 74.26 ATOM 48 C PRO F 453 142.275 146.376 147.512 1.00 74.26 ATOM 49 O PRO F 453 142.247 146.416 148.739 1.00 74.26 ATOM 50 CB PRO F 453 143.833 144.863 146.230 1.00 74.26 ATOM 51 CG PRO F 453 145.271 144.682 146.347 1.00 74.26 ATOM 52 CD PRO F 453 145.670 145.399 147.578 1.00 74.26 ATOM 53 N VAL F 454 141.168 146.391 146.766 1.00 76.60 ATOM 54 CA VAL F 454 139.869 146.704 147.358 1.00 76.60 ATOM 55 C VAL F 454 139.383 145.572 148.257 1.00 76.60 ATOM 56 O VAL F 454 138.783 145.814 149.315 1.00 76.60 ATOM 57 CB VAL F 454 138.847 147.021 146.253 1.00 76.60 ATOM 58 CG1 VAL F 454 137.502 147.322 146.852 1.00 76.60 ATOM 59 CG2 VAL F 454 139.314 148.178 145.422 1.00 76.60 ATOM 60 N HIS F 455 139.625 144.322 147.859 1.00 81.86 ATOM 61 CA HIS F 455 139.183 143.202 148.679 1.00 81.86 ATOM 62 C HIS F 455 139.917 143.168 150.013 1.00 81.86 ATOM 63 O HIS F 455 139.325 142.847 151.052 1.00 81.86 ATOM 64 CB HIS F 455 139.346 141.892 147.909 1.00 81.86 ATOM 65 CG HIS F 455 140.763 141.438 147.734 1.00 81.86 ATOM 66 ND1 HIS F 455 141.400 140.620 148.641 1.00 81.86 ATOM 67 CD2 HIS F 455 141.646 141.641 146.729 1.00 81.86 ATOM 68 CE1 HIS F 455 142.624 140.368 148.218 1.00 81.86 ATOM 69 NE2 HIS F 455 142.797 140.972 147.059 1.00 81.86 ATOM 70 N MET F 456 141.187 143.550 150.023 1.00 80.97 ATOM 71 CA MET F 456 141.894 143.626 151.289 1.00 80.97 ATOM 72 C MET F 456 141.398 144.785 152.133 1.00 80.97 ATOM 73 O MET F 456 141.382 144.688 153.363 1.00 80.97 ATOM 74 CB MET F 456 143.386 143.741 151.042 1.00 80.97 ATOM 75 CG MET F 456 144.206 143.142 152.131 1.00 80.97 ATOM 76 SD MET F 456 144.106 141.363 152.052 1.00 80.97 ATOM 77 CE MET F 456 144.843 140.958 153.613 1.00 80.97 ATOM 78 N ILE F 457 140.971 145.876 151.496 1.00 80.32 ATOM 79 CA ILE F 457 140.377 146.986 152.232 1.00 80.32 ATOM 80 C ILE F 457 139.116 146.533 152.949 1.00 80.32 ATOM 81 O ILE F 457 138.909 146.844 154.130 1.00 80.32 ATOM 82 CB ILE F 457 140.087 148.165 151.289 1.00 80.32 ATOM 83 CG1 ILE F 457 141.380 148.769 150.760 1.00 80.32 ATOM 84 CG2 ILE F 457 139.304 149.224 152.010 1.00 80.32 ATOM 85 CD1 ILE F 457 142.166 149.481 151.799 1.00 80.32 ATOM 86 N GLU F 458 138.260 145.777 152.260 1.00 85.49 ATOM 87 CA GLU F 458 137.035 145.322 152.910 1.00 85.49 ATOM 88 C GLU F 458 137.316 144.292 154.003 1.00 85.49 ATOM 89 O GLU F 458 136.626 144.287 155.029 1.00 85.49 ATOM 90 CB GLU F 458 136.054 144.782 151.870 1.00 85.49 ATOM 91 CG GLU F 458 136.282 143.355 151.438 1.00 85.49 ATOM 92 CD GLU F 458 135.481 142.971 150.217 1.00 85.49 ATOM 93 OE1 GLU F 458 134.806 143.853 149.648 1.00 85.49 ATOM 94 OE2 GLU F 458 135.537 141.787 149.821 1.00 85.49 ATOM 95 N THR F 459 138.341 143.449 153.836 1.00 87.93 ATOM 96 CA THR F 459 138.709 142.524 154.908 1.00 87.93 ATOM 97 C THR F 459 139.193 143.268 156.150 1.00 87.93 ATOM 98 O THR F 459 138.791 142.946 157.278 1.00 87.93 ATOM 99 CB THR F 459 139.783 141.559 154.417 1.00 87.93 ATOM 100 OG1 THR F 459 139.292 140.824 153.295 1.00 87.93 ATOM 101 CG2 THR F 459 140.160 140.593 155.501 1.00 87.93 ATOM 102 N ILE F 460 140.059 144.266 155.962 1.00 89.32 ATOM 103 CA ILE F 460 140.533 145.086 157.074 1.00 89.32 ATOM 104 C ILE F 460 139.367 145.758 157.786 1.00 89.32 ATOM 105 O ILE F 460 139.296 145.763 159.023 1.00 89.32 ATOM 106 CB ILE F 460 141.545 146.127 156.566 1.00 89.32 ATOM 107 CG1 ILE F 460 142.841 145.462 156.130 1.00 89.32 ATOM 108 CG2 ILE F 460 141.835 147.145 157.630 1.00 89.32 ATOM 109 CD1 ILE F 460 143.730 146.362 155.320 1.00 89.32 ATOM 110 N ASN F 461 138.442 146.347 157.021 1.00 93.67 ATOM 111 CA ASN F 461 137.313 147.046 157.629 1.00 93.67 ATOM 112 C ASN F 461 136.432 146.096 158.426 1.00 93.67 ATOM 113 O ASN F 461 135.971 146.436 159.523 1.00 93.67 ATOM 114 CB ASN F 461 136.495 147.756 156.557 1.00 93.67 ATOM 115 CG ASN F 461 137.199 148.972 155.995 1.00 93.67 ATOM 116 OD1 ASN F 461 136.863 149.455 154.916 1.00 93.67 ATOM 117 ND2 ASN F 461 138.183 149.475 156.724 1.00 93.67 ATOM 118 N LYS F 462 136.199 144.892 157.902 1.00 98.49 ATOM 119 CA LYS F 462 135.378 143.927 158.623 1.00 98.49 ATOM 120 C LYS F 462 136.038 143.490 159.924 1.00 98.49 ATOM 121 O LYS F 462 135.366 143.355 160.955 1.00 98.49 ATOM 122 CB LYS F 462 135.100 142.727 157.729 1.00 98.49 ATOM 123 CG LYS F 462 134.275 141.645 158.366 1.00 98.49 ATOM 124 CD LYS F 462 134.538 140.317 157.692 1.00 98.49 ATOM 125 CE LYS F 462 134.462 140.443 156.183 1.00 98.49 ATOM 126 NZ LYS F 462 135.271 139.399 155.497 1.00 98.49 ATOM 127 N LEU F 463 137.352 143.271 159.904 1.00101.09 ATOM 128 CA LEU F 463 138.034 142.874 161.133 1.00101.09 ATOM 129 C LEU F 463 138.012 143.995 162.166 1.00101.09 ATOM 130 O LEU F 463 137.867 143.737 163.368 1.00101.09 ATOM 131 CB LEU F 463 139.461 142.435 160.811 1.00101.09 ATOM 132 CG LEU F 463 140.339 141.799 161.884 1.00101.09 ATOM 133 CD1 LEU F 463 141.212 140.753 161.247 1.00101.09 ATOM 134 CD2 LEU F 463 141.215 142.844 162.529 1.00101.09 ATOM 135 N ASN F 464 138.139 145.246 161.720 1.00101.89 ATOM 136 CA ASN F 464 138.006 146.369 162.643 1.00101.89 ATOM 137 C ASN F 464 136.624 146.401 163.274 1.00101.89 ATOM 138 O ASN F 464 136.486 146.607 164.488 1.00101.89 ATOM 139 CB ASN F 464 138.277 147.680 161.916 1.00101.89 ATOM 140 CG ASN F 464 139.740 147.903 161.650 1.00101.89 ATOM 141 OD1 ASN F 464 140.589 147.510 162.440 1.00101.89 ATOM 142 ND2 ASN F 464 140.046 148.542 160.533 1.00101.89 ATOM 143 N ARG F 465 135.586 146.191 162.463 1.00105.45 ATOM 144 CA ARG F 465 134.225 146.220 162.981 1.00105.45 ATOM 145 C ARG F 465 133.970 145.099 163.976 1.00105.45 ATOM 146 O ARG F 465 133.211 145.284 164.930 1.00105.45 ATOM 147 CB ARG F 465 133.228 146.134 161.834 1.00105.45 ATOM 148 CG ARG F 465 131.903 146.794 162.127 1.00105.45 ATOM 149 CD ARG F 465 130.997 146.734 160.918 1.00105.45 ATOM 150 NE ARG F 465 130.794 145.361 160.473 1.00105.45 ATOM 151 CZ ARG F 465 130.865 144.973 159.207 1.00105.45 ATOM 152 NH1 ARG F 465 130.670 143.702 158.890 1.00105.45 ATOM 153 NH2 ARG F 465 131.135 145.857 158.260 1.00105.45 ATOM 154 N ILE F 466 134.584 143.934 163.777 1.00107.83 ATOM 155 CA ILE F 466 134.388 142.848 164.737 1.00107.83 ATOM 156 C ILE F 466 135.128 143.134 166.037 1.00107.83 ATOM 157 O ILE F 466 134.589 142.927 167.135 1.00107.83 ATOM 158 CB ILE F 466 134.818 141.502 164.133 1.00107.83 ATOM 159 CG1 ILE F 466 133.768 140.999 163.150 1.00107.83 ATOM 160 CG2 ILE F 466 135.031 140.478 165.221 1.00107.83 ATOM 161 CD1 ILE F 466 134.024 139.598 162.668 1.00107.83 ATOM 162 N SER F 467 136.375 143.601 165.944 1.00108.94 ATOM 163 CA SER F 467 137.146 143.827 167.160 1.00108.94 ATOM 164 C SER F 467 136.567 144.959 167.997 1.00108.94 ATOM 165 O SER F 467 136.677 144.925 169.225 1.00108.94 ATOM 166 CB SER F 467 138.607 144.094 166.815 1.00108.94 ATOM 167 OG SER F 467 138.744 145.276 166.056 1.00108.94 ATOM 168 N ARG F 468 135.916 145.942 167.365 1.00111.58 ATOM 169 CA ARG F 468 135.226 146.981 168.128 1.00111.58 ATOM 170 C ARG F 468 134.179 146.389 169.062 1.00111.58 ATOM 171 O ARG F 468 134.150 146.695 170.260 1.00111.58 ATOM 172 CB ARG F 468 134.568 147.981 167.187 1.00111.58 ATOM 173 CG ARG F 468 135.500 149.013 166.623 1.00111.58 ATOM 174 CD ARG F 468 134.783 150.339 166.455 1.00111.58 ATOM 175 NE ARG F 468 133.657 150.235 165.537 1.00111.58 ATOM 176 CZ ARG F 468 133.725 150.502 164.238 1.00111.58 ATOM 177 NH1 ARG F 468 134.868 150.893 163.697 1.00111.58 ATOM 178 NH2 ARG F 468 132.650 150.373 163.479 1.00111.58 ATOM 179 N GLN F 469 133.302 145.536 168.533 1.00113.99 ATOM 180 CA GLN F 469 132.219 145.024 169.358 1.00113.99 ATOM 181 C GLN F 469 132.713 143.984 170.352 1.00113.99 ATOM 182 O GLN F 469 132.186 143.904 171.467 1.00113.99 ATOM 183 CB GLN F 469 131.096 144.473 168.478 1.00113.99 ATOM 184 CG GLN F 469 131.185 143.005 168.112 1.00113.99 ATOM 185 CD GLN F 469 130.305 142.655 166.927 1.00113.99 ATOM 186 OE1 GLN F 469 129.861 143.535 166.190 1.00113.99 ATOM 187 NE2 GLN F 469 130.050 141.367 166.738 1.00113.99 ATOM 188 N MET F 470 133.748 143.217 170.008 1.00117.80 ATOM 189 CA MET F 470 134.293 142.305 171.008 1.00117.80 ATOM 190 C MET F 470 134.993 143.061 172.130 1.00117.80 ATOM 191 O MET F 470 134.994 142.602 173.278 1.00117.80 ATOM 192 CB MET F 470 135.249 141.307 170.367 1.00117.80 ATOM 193 CG MET F 470 134.563 140.204 169.595 1.00117.80 ATOM 194 SD MET F 470 135.713 138.921 169.092 1.00117.80 ATOM 195 CE MET F 470 136.155 138.262 170.689 1.00117.80 ATOM 196 N LEU F 471 135.571 144.226 171.828 1.00116.55 ATOM 197 CA LEU F 471 136.187 145.042 172.866 1.00116.55 ATOM 198 C LEU F 471 135.137 145.684 173.758 1.00116.55 ATOM 199 O LEU F 471 135.323 145.778 174.975 1.00116.55 ATOM 200 CB LEU F 471 137.071 146.106 172.222 1.00116.55 ATOM 201 CG LEU F 471 137.539 147.294 173.055 1.00116.55 ATOM 202 CD1 LEU F 471 138.752 146.925 173.860 1.00116.55 ATOM 203 CD2 LEU F 471 137.848 148.456 172.144 1.00116.55 ATOM 204 N GLN F 472 134.029 146.138 173.172 1.00114.76 ATOM 205 CA GLN F 472 132.932 146.652 173.984 1.00114.76 ATOM 206 C GLN F 472 132.322 145.569 174.860 1.00114.76 ATOM 207 O GLN F 472 131.866 145.859 175.968 1.00114.76 ATOM 208 CB GLN F 472 131.847 147.253 173.098 1.00114.76 ATOM 209 CG GLN F 472 132.179 148.594 172.504 1.00114.76 ATOM 210 CD GLN F 472 132.349 149.654 173.556 1.00114.76 ATOM 211 OE1 GLN F 472 133.286 150.447 173.508 1.00114.76 ATOM 212 NE2 GLN F 472 131.453 149.666 174.526 1.00114.76 ATOM 213 N GLU F 473 132.299 144.324 174.385 1.00121.20 ATOM 214 CA GLU F 473 131.598 143.271 175.112 1.00121.20 ATOM 215 C GLU F 473 132.464 142.632 176.192 1.00121.20 ATOM 216 O GLU F 473 131.973 142.346 177.286 1.00121.20 ATOM 217 CB GLU F 473 131.097 142.217 174.125 1.00121.20 ATOM 218 CG GLU F 473 130.198 141.159 174.724 1.00121.20 ATOM 219 CD GLU F 473 130.964 139.951 175.221 1.00121.20 ATOM 220 OE1 GLU F 473 132.012 139.628 174.629 1.00121.20 ATOM 221 OE2 GLU F 473 130.521 139.326 176.207 1.00121.20 ATOM 222 N MET F 474 133.744 142.387 175.912 1.00123.87 ATOM 223 CA MET F 474 134.603 141.715 176.880 1.00123.87 ATOM 224 C MET F 474 135.288 142.663 177.853 1.00123.87 ATOM 225 O MET F 474 135.665 142.232 178.947 1.00123.87 ATOM 226 CB MET F 474 135.681 140.899 176.162 1.00123.87 ATOM 227 CG MET F 474 135.151 139.875 175.189 1.00123.87 ATOM 228 SD MET F 474 134.788 138.306 175.991 1.00123.87 ATOM 229 CE MET F 474 136.438 137.688 176.286 1.00123.87 ATOM 230 N GLY F 475 135.468 143.928 177.488 1.00121.16 ATOM 231 CA GLY F 475 136.249 144.841 178.297 1.00121.16 ATOM 232 C GLY F 475 137.738 144.794 178.044 1.00121.16 ATOM 233 O GLY F 475 138.488 145.510 178.715 1.00121.16 ATOM 234 N ARG F 476 138.187 143.974 177.097 1.00128.40 ATOM 235 CA ARG F 476 139.592 143.834 176.749 1.00128.40 ATOM 236 C ARG F 476 139.714 143.808 175.236 1.00128.40 ATOM 237 O ARG F 476 138.717 143.838 174.512 1.00128.40 ATOM 238 CB ARG F 476 140.195 142.550 177.311 1.00128.40 ATOM 239 CG ARG F 476 140.314 142.463 178.806 1.00128.40 ATOM 240 CD ARG F 476 140.950 141.131 179.143 1.00128.40 ATOM 241 NE ARG F 476 140.056 140.033 178.785 1.00128.40 ATOM 242 CZ ARG F 476 140.255 139.209 177.764 1.00128.40 ATOM 243 NH1 ARG F 476 141.312 139.362 176.982 1.00128.40 ATOM 244 NH2 ARG F 476 139.388 138.245 177.515 1.00128.40 ATOM 245 N GLU F 477 140.949 143.722 174.752 1.00132.40 ATOM 246 CA GLU F 477 141.185 143.514 173.336 1.00132.40 ATOM 247 C GLU F 477 141.328 142.028 173.062 1.00132.40 ATOM 248 O GLU F 477 142.080 141.347 173.776 1.00132.40 ATOM 249 CB GLU F 477 142.430 144.256 172.888 1.00132.40 ATOM 250 CG GLU F 477 142.462 145.687 173.359 1.00132.40 ATOM 251 CD GLU F 477 143.434 146.530 172.572 1.00132.40 ATOM 252 OE1 GLU F 477 144.221 145.952 171.794 1.00132.40 ATOM 253 OE2 GLU F 477 143.408 147.768 172.727 1.00132.40 ATOM 254 N PRO F 478 140.641 141.484 172.066 1.00132.92 ATOM 255 CA PRO F 478 140.700 140.040 171.835 1.00132.92 ATOM 256 C PRO F 478 141.982 139.619 171.139 1.00132.92 ATOM 257 O PRO F 478 142.513 140.320 170.276 1.00132.92 ATOM 258 CB PRO F 478 139.485 139.782 170.944 1.00132.92 ATOM 259 CG PRO F 478 139.295 141.055 170.221 1.00132.92 ATOM 260 CD PRO F 478 139.665 142.141 171.184 1.00132.92 ATOM 261 N THR F 479 142.476 138.452 171.530 1.00133.75 ATOM 262 CA THR F 479 143.608 137.839 170.863 1.00133.75 ATOM 263 C THR F 479 143.172 137.303 169.507 1.00133.75 ATOM 264 O THR F 479 141.988 137.036 169.294 1.00133.75 ATOM 265 CB THR F 479 144.169 136.710 171.717 1.00133.75 ATOM 266 OG1 THR F 479 143.278 135.591 171.667 1.00133.75 ATOM 267 CG2 THR F 479 144.322 137.161 173.155 1.00133.75 TER