HEADER TRANSCRIPTION, TRANSFERASE/DNA 31-DEC-69 6XLJ TITLE Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex TITLE 2 with 4-nt RNA transcript (EcmrR-RPitc-4nt) COMPND MOL_ID: 5; COMPND 2 MOLECULE: RNA polymerase sigma factor RpoD; COMPND 3 CHAIN: F; COMPND 4 ENGINEERED: YES; EXPDTA ELECTRON MICROSCOPY DBREF 6XLJ 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 448 171.957 176.299 198.122 1.00 73.12 ATOM 2 CA ARG F 448 171.881 175.041 197.406 1.00 73.12 ATOM 3 C ARG F 448 170.450 174.791 196.982 1.00 73.12 ATOM 4 O ARG F 448 169.515 175.123 197.709 1.00 73.12 ATOM 5 CB ARG F 448 172.343 173.890 198.275 1.00 73.12 ATOM 6 CG ARG F 448 173.764 173.960 198.694 1.00 73.12 ATOM 7 CD ARG F 448 174.507 172.810 198.122 1.00 73.12 ATOM 8 NE ARG F 448 175.876 172.792 198.589 1.00 73.12 ATOM 9 CZ ARG F 448 176.776 171.918 198.173 1.00 73.12 ATOM 10 NH1 ARG F 448 176.434 171.002 197.285 1.00 73.12 ATOM 11 NH2 ARG F 448 178.011 171.958 198.642 1.00 73.12 ATOM 12 N THR F 449 170.275 174.191 195.809 1.00 70.84 ATOM 13 CA THR F 449 168.927 173.899 195.344 1.00 70.84 ATOM 14 C THR F 449 168.279 172.820 196.191 1.00 70.84 ATOM 15 O THR F 449 167.192 173.016 196.735 1.00 70.84 ATOM 16 CB THR F 449 168.943 173.492 193.886 1.00 70.84 ATOM 17 OG1 THR F 449 169.528 174.547 193.125 1.00 70.84 ATOM 18 CG2 THR F 449 167.546 173.290 193.411 1.00 70.84 ATOM 19 N ILE F 450 168.928 171.677 196.323 1.00 71.04 ATOM 20 CA ILE F 450 168.477 170.667 197.264 1.00 71.04 ATOM 21 C ILE F 450 169.297 170.825 198.532 1.00 71.04 ATOM 22 O ILE F 450 170.511 170.623 198.541 1.00 71.04 ATOM 23 CB ILE F 450 168.556 169.256 196.656 1.00 71.04 ATOM 24 CG1 ILE F 450 169.927 168.879 196.172 1.00 71.04 ATOM 25 CG2 ILE F 450 167.802 169.232 195.385 1.00 71.04 ATOM 26 CD1 ILE F 450 169.961 167.506 195.605 1.00 71.04 ATOM 27 N ARG F 451 168.646 171.281 199.584 1.00 71.28 ATOM 28 CA ARG F 451 169.336 171.811 200.743 1.00 71.28 ATOM 29 C ARG F 451 169.949 170.677 201.536 1.00 71.28 ATOM 30 O ARG F 451 169.291 169.666 201.784 1.00 71.28 ATOM 31 CB ARG F 451 168.371 172.600 201.614 1.00 71.28 ATOM 32 CG ARG F 451 169.019 173.290 202.759 1.00 71.28 ATOM 33 CD ARG F 451 167.988 173.695 203.743 1.00 71.28 ATOM 34 NE ARG F 451 167.213 172.557 204.167 1.00 71.28 ATOM 35 CZ ARG F 451 167.377 171.957 205.328 1.00 71.28 ATOM 36 NH1 ARG F 451 168.280 172.410 206.170 1.00 71.28 ATOM 37 NH2 ARG F 451 166.630 170.919 205.647 1.00 71.28 ATOM 38 N ILE F 452 171.208 170.838 201.921 1.00 73.02 ATOM 39 CA ILE F 452 171.845 169.887 202.819 1.00 73.02 ATOM 40 C ILE F 452 172.002 170.575 204.166 1.00 73.02 ATOM 41 O ILE F 452 172.138 171.800 204.219 1.00 73.02 ATOM 42 CB ILE F 452 173.176 169.380 202.255 1.00 73.02 ATOM 43 CG1 ILE F 452 174.110 170.525 201.999 1.00 73.02 ATOM 44 CG2 ILE F 452 172.954 168.715 200.941 1.00 73.02 ATOM 45 CD1 ILE F 452 175.317 170.096 201.259 1.00 73.02 ATOM 46 N PRO F 453 171.951 169.849 205.261 1.00 74.61 ATOM 47 CA PRO F 453 171.955 170.479 206.580 1.00 74.61 ATOM 48 C PRO F 453 173.277 171.117 206.932 1.00 74.61 ATOM 49 O PRO F 453 174.242 170.986 206.185 1.00 74.61 ATOM 50 CB PRO F 453 171.641 169.307 207.503 1.00 74.61 ATOM 51 CG PRO F 453 170.945 168.375 206.652 1.00 74.61 ATOM 52 CD PRO F 453 171.631 168.432 205.373 1.00 74.61 ATOM 53 N VAL F 454 173.345 171.820 208.058 1.00 77.33 ATOM 54 CA VAL F 454 174.596 172.478 208.395 1.00 77.33 ATOM 55 C VAL F 454 175.634 171.468 208.837 1.00 77.33 ATOM 56 O VAL F 454 176.834 171.709 208.699 1.00 77.33 ATOM 57 CB VAL F 454 174.376 173.544 209.469 1.00 77.33 ATOM 58 CG1 VAL F 454 175.486 174.537 209.423 1.00 77.33 ATOM 59 CG2 VAL F 454 173.064 174.223 209.262 1.00 77.33 ATOM 60 N HIS F 455 175.214 170.327 209.372 1.00 80.12 ATOM 61 CA HIS F 455 176.198 169.315 209.718 1.00 80.12 ATOM 62 C HIS F 455 176.822 168.725 208.464 1.00 80.12 ATOM 63 O HIS F 455 178.038 168.532 208.404 1.00 80.12 ATOM 64 CB HIS F 455 175.575 168.243 210.613 1.00 80.12 ATOM 65 CG HIS F 455 174.795 167.191 209.885 1.00 80.12 ATOM 66 ND1 HIS F 455 175.379 166.060 209.362 1.00 80.12 ATOM 67 CD2 HIS F 455 173.473 167.082 209.623 1.00 80.12 ATOM 68 CE1 HIS F 455 174.455 165.311 208.794 1.00 80.12 ATOM 69 NE2 HIS F 455 173.290 165.910 208.936 1.00 80.12 ATOM 70 N MET F 456 176.028 168.499 207.425 1.00 80.46 ATOM 71 CA MET F 456 176.613 167.982 206.200 1.00 80.46 ATOM 72 C MET F 456 177.365 169.066 205.457 1.00 80.46 ATOM 73 O MET F 456 178.337 168.770 204.768 1.00 80.46 ATOM 74 CB MET F 456 175.546 167.371 205.310 1.00 80.46 ATOM 75 CG MET F 456 176.094 166.508 204.217 1.00 80.46 ATOM 76 SD MET F 456 177.256 165.293 204.830 1.00 80.46 ATOM 77 CE MET F 456 176.188 164.335 205.886 1.00 80.46 ATOM 78 N ILE F 457 176.951 170.320 205.599 1.00 79.26 ATOM 79 CA ILE F 457 177.704 171.428 205.021 1.00 79.26 ATOM 80 C ILE F 457 179.086 171.509 205.642 1.00 79.26 ATOM 81 O ILE F 457 180.092 171.660 204.943 1.00 79.26 ATOM 82 CB ILE F 457 176.930 172.741 205.188 1.00 79.26 ATOM 83 CG1 ILE F 457 175.956 172.907 204.042 1.00 79.26 ATOM 84 CG2 ILE F 457 177.856 173.905 205.255 1.00 79.26 ATOM 85 CD1 ILE F 457 176.645 173.105 202.755 1.00 79.26 ATOM 86 N GLU F 458 179.163 171.385 206.960 1.00 82.38 ATOM 87 CA GLU F 458 180.460 171.406 207.609 1.00 82.38 ATOM 88 C GLU F 458 181.287 170.176 207.295 1.00 82.38 ATOM 89 O GLU F 458 182.505 170.291 207.174 1.00 82.38 ATOM 90 CB GLU F 458 180.289 171.553 209.105 1.00 82.38 ATOM 91 CG GLU F 458 179.863 172.933 209.501 1.00 82.38 ATOM 92 CD GLU F 458 179.527 173.021 210.958 1.00 82.38 ATOM 93 OE1 GLU F 458 179.894 172.089 211.703 1.00 82.38 ATOM 94 OE2 GLU F 458 178.890 174.013 211.361 1.00 82.38 ATOM 95 N THR F 459 180.661 169.014 207.132 1.00 82.25 ATOM 96 CA THR F 459 181.411 167.831 206.733 1.00 82.25 ATOM 97 C THR F 459 181.961 167.958 205.323 1.00 82.25 ATOM 98 O THR F 459 183.102 167.577 205.068 1.00 82.25 ATOM 99 CB THR F 459 180.539 166.597 206.842 1.00 82.25 ATOM 100 OG1 THR F 459 180.024 166.510 208.170 1.00 82.25 ATOM 101 CG2 THR F 459 181.339 165.379 206.569 1.00 82.25 ATOM 102 N ILE F 460 181.187 168.524 204.403 1.00 82.47 ATOM 103 CA ILE F 460 181.672 168.724 203.045 1.00 82.47 ATOM 104 C ILE F 460 182.789 169.751 203.019 1.00 82.47 ATOM 105 O ILE F 460 183.778 169.586 202.301 1.00 82.47 ATOM 106 CB ILE F 460 180.514 169.131 202.131 1.00 82.47 ATOM 107 CG1 ILE F 460 179.577 167.958 201.959 1.00 82.47 ATOM 108 CG2 ILE F 460 181.024 169.513 200.793 1.00 82.47 ATOM 109 CD1 ILE F 460 178.458 168.239 201.060 1.00 82.47 ATOM 110 N ASN F 461 182.670 170.813 203.814 1.00 85.61 ATOM 111 CA ASN F 461 183.736 171.806 203.860 1.00 85.61 ATOM 112 C ASN F 461 185.009 171.217 204.440 1.00 85.61 ATOM 113 O ASN F 461 186.105 171.478 203.935 1.00 85.61 ATOM 114 CB ASN F 461 183.289 173.015 204.664 1.00 85.61 ATOM 115 CG ASN F 461 182.244 173.822 203.949 1.00 85.61 ATOM 116 OD1 ASN F 461 181.998 173.626 202.766 1.00 85.61 ATOM 117 ND2 ASN F 461 181.622 174.741 204.659 1.00 85.61 ATOM 118 N LYS F 462 184.885 170.409 205.488 1.00 87.68 ATOM 119 CA LYS F 462 186.055 169.767 206.062 1.00 87.68 ATOM 120 C LYS F 462 186.686 168.803 205.080 1.00 87.68 ATOM 121 O LYS F 462 187.913 168.729 204.975 1.00 87.68 ATOM 122 CB LYS F 462 185.673 169.050 207.347 1.00 87.68 ATOM 123 CG LYS F 462 186.750 168.145 207.852 1.00 87.68 ATOM 124 CD LYS F 462 186.614 167.866 209.320 1.00 87.68 ATOM 125 CE LYS F 462 187.868 167.173 209.823 1.00 87.68 ATOM 126 NZ LYS F 462 187.764 166.715 211.230 1.00 87.68 ATOM 127 N LEU F 463 185.869 168.068 204.337 1.00 88.46 ATOM 128 CA LEU F 463 186.405 167.148 203.346 1.00 88.46 ATOM 129 C LEU F 463 187.139 167.890 202.247 1.00 88.46 ATOM 130 O LEU F 463 188.189 167.443 201.789 1.00 88.46 ATOM 131 CB LEU F 463 185.280 166.322 202.747 1.00 88.46 ATOM 132 CG LEU F 463 185.689 165.199 201.821 1.00 88.46 ATOM 133 CD1 LEU F 463 185.966 163.969 202.622 1.00 88.46 ATOM 134 CD2 LEU F 463 184.610 164.954 200.812 1.00 88.46 ATOM 135 N ASN F 464 186.608 169.026 201.809 1.00 89.78 ATOM 136 CA ASN F 464 187.263 169.768 200.741 1.00 89.78 ATOM 137 C ASN F 464 188.566 170.385 201.216 1.00 89.78 ATOM 138 O ASN F 464 189.542 170.437 200.464 1.00 89.78 ATOM 139 CB ASN F 464 186.333 170.840 200.201 1.00 89.78 ATOM 140 CG ASN F 464 185.287 170.277 199.290 1.00 89.78 ATOM 141 OD1 ASN F 464 185.287 169.089 198.995 1.00 89.78 ATOM 142 ND2 ASN F 464 184.381 171.124 198.836 1.00 89.78 ATOM 143 N ARG F 465 188.616 170.838 202.459 1.00 93.16 ATOM 144 CA ARG F 465 189.869 171.375 202.966 1.00 93.16 ATOM 145 C ARG F 465 190.916 170.281 203.123 1.00 93.16 ATOM 146 O ARG F 465 192.072 170.458 202.721 1.00 93.16 ATOM 147 CB ARG F 465 189.624 172.085 204.287 1.00 93.16 ATOM 148 CG ARG F 465 190.797 172.871 204.763 1.00 93.16 ATOM 149 CD ARG F 465 190.570 173.361 206.162 1.00 93.16 ATOM 150 NE ARG F 465 190.221 172.273 207.059 1.00 93.16 ATOM 151 CZ ARG F 465 189.099 172.231 207.761 1.00 93.16 ATOM 152 NH1 ARG F 465 188.220 173.220 207.667 1.00 93.16 ATOM 153 NH2 ARG F 465 188.858 171.205 208.559 1.00 93.16 ATOM 154 N ILE F 466 190.529 169.141 203.695 1.00 94.21 ATOM 155 CA ILE F 466 191.433 168.002 203.816 1.00 94.21 ATOM 156 C ILE F 466 191.918 167.552 202.446 1.00 94.21 ATOM 157 O ILE F 466 193.090 167.208 202.264 1.00 94.21 ATOM 158 CB ILE F 466 190.722 166.862 204.562 1.00 94.21 ATOM 159 CG1 ILE F 466 190.626 167.186 206.041 1.00 94.21 ATOM 160 CG2 ILE F 466 191.440 165.566 204.369 1.00 94.21 ATOM 161 CD1 ILE F 466 191.960 167.357 206.689 1.00 94.21 ATOM 162 N SER F 467 191.031 167.569 201.458 1.00 95.42 ATOM 163 CA SER F 467 191.390 167.122 200.122 1.00 95.42 ATOM 164 C SER F 467 192.330 168.096 199.435 1.00 95.42 ATOM 165 O SER F 467 193.229 167.675 198.707 1.00 95.42 ATOM 166 CB SER F 467 190.132 166.921 199.292 1.00 95.42 ATOM 167 OG SER F 467 190.470 166.627 197.958 1.00 95.42 ATOM 168 N ARG F 468 192.154 169.397 199.642 1.00 97.41 ATOM 169 CA ARG F 468 193.117 170.304 199.036 1.00 97.41 ATOM 170 C ARG F 468 194.426 170.345 199.802 1.00 97.41 ATOM 171 O ARG F 468 195.415 170.848 199.271 1.00 97.41 ATOM 172 CB ARG F 468 192.554 171.721 198.902 1.00 97.41 ATOM 173 CG ARG F 468 192.888 172.642 200.048 1.00 97.41 ATOM 174 CD ARG F 468 192.256 174.002 199.865 1.00 97.41 ATOM 175 NE ARG F 468 190.828 173.870 199.603 1.00 97.41 ATOM 176 CZ ARG F 468 189.945 174.857 199.692 1.00 97.41 ATOM 177 NH1 ARG F 468 190.329 176.070 200.058 1.00 97.41 ATOM 178 NH2 ARG F 468 188.668 174.624 199.428 1.00 97.41 ATOM 179 N GLN F 469 194.473 169.830 201.023 1.00 97.51 ATOM 180 CA GLN F 469 195.783 169.651 201.636 1.00 97.51 ATOM 181 C GLN F 469 196.466 168.392 201.125 1.00 97.51 ATOM 182 O GLN F 469 197.671 168.402 200.851 1.00 97.51 ATOM 183 CB GLN F 469 195.652 169.607 203.150 1.00 97.51 ATOM 184 CG GLN F 469 195.169 170.909 203.731 1.00 97.51 ATOM 185 CD GLN F 469 194.943 170.825 205.217 1.00 97.51 ATOM 186 OE1 GLN F 469 195.130 169.772 205.823 1.00 97.51 ATOM 187 NE2 GLN F 469 194.541 171.936 205.817 1.00 97.51 ATOM 188 N MET F 470 195.717 167.303 200.983 1.00100.45 ATOM 189 CA MET F 470 196.301 166.078 200.455 1.00100.45 ATOM 190 C MET F 470 196.734 166.235 199.011 1.00100.45 ATOM 191 O MET F 470 197.716 165.618 198.598 1.00100.45 ATOM 192 CB MET F 470 195.320 164.920 200.552 1.00100.45 ATOM 193 CG MET F 470 195.053 164.419 201.936 1.00100.45 ATOM 194 SD MET F 470 194.432 162.744 201.845 1.00100.45 ATOM 195 CE MET F 470 195.898 161.815 202.274 1.00100.45 ATOM 196 N LEU F 471 196.009 167.023 198.220 1.00 97.37 ATOM 197 CA LEU F 471 196.417 167.250 196.840 1.00 97.37 ATOM 198 C LEU F 471 197.725 168.017 196.772 1.00 97.37 ATOM 199 O LEU F 471 198.567 167.746 195.914 1.00 97.37 ATOM 200 CB LEU F 471 195.327 168.002 196.100 1.00 97.37 ATOM 201 CG LEU F 471 195.731 168.705 194.823 1.00 97.37 ATOM 202 CD1 LEU F 471 195.951 167.684 193.778 1.00 97.37 ATOM 203 CD2 LEU F 471 194.638 169.636 194.416 1.00 97.37 ATOM 204 N GLN F 472 197.919 168.973 197.672 1.00 97.62 ATOM 205 CA GLN F 472 199.173 169.706 197.691 1.00 97.62 ATOM 206 C GLN F 472 200.315 168.826 198.155 1.00 97.62 ATOM 207 O GLN F 472 201.431 168.935 197.642 1.00 97.62 ATOM 208 CB GLN F 472 199.046 170.925 198.589 1.00 97.62 ATOM 209 CG GLN F 472 198.368 172.072 197.915 1.00 97.62 ATOM 210 CD GLN F 472 199.244 172.694 196.874 1.00 97.62 ATOM 211 OE1 GLN F 472 200.459 172.637 196.974 1.00 97.62 ATOM 212 NE2 GLN F 472 198.638 173.290 195.864 1.00 97.62 ATOM 213 N GLU F 473 200.063 167.948 199.124 1.00100.68 ATOM 214 CA GLU F 473 201.130 167.070 199.594 1.00100.68 ATOM 215 C GLU F 473 201.404 165.952 198.599 1.00100.68 ATOM 216 O GLU F 473 202.516 165.834 198.078 1.00100.68 ATOM 217 CB GLU F 473 200.775 166.489 200.956 1.00100.68 ATOM 218 CG GLU F 473 200.774 167.495 202.081 1.00100.68 ATOM 219 CD GLU F 473 199.855 167.083 203.211 1.00100.68 ATOM 220 OE1 GLU F 473 199.164 167.958 203.772 1.00100.68 ATOM 221 OE2 GLU F 473 199.814 165.878 203.533 1.00100.68 ATOM 222 N MET F 474 200.403 165.134 198.303 1.00101.31 ATOM 223 CA MET F 474 200.633 163.965 197.468 1.00101.31 ATOM 224 C MET F 474 200.874 164.310 196.010 1.00101.31 ATOM 225 O MET F 474 201.283 163.434 195.246 1.00101.31 ATOM 226 CB MET F 474 199.449 163.002 197.560 1.00101.31 ATOM 227 CG MET F 474 198.988 162.716 198.972 1.00101.31 ATOM 228 SD MET F 474 197.647 161.519 199.041 1.00101.31 ATOM 229 CE MET F 474 198.561 160.027 199.393 1.00101.31 ATOM 230 N GLY F 475 200.631 165.548 195.602 1.00 97.91 ATOM 231 CA GLY F 475 200.824 165.901 194.217 1.00 97.91 ATOM 232 C GLY F 475 199.805 165.315 193.279 1.00 97.91 ATOM 233 O GLY F 475 200.033 165.293 192.074 1.00 97.91 ATOM 234 N ARG F 476 198.682 164.843 193.796 1.00100.52 ATOM 235 CA ARG F 476 197.637 164.248 192.980 1.00100.52 ATOM 236 C ARG F 476 196.358 164.255 193.795 1.00100.52 ATOM 237 O ARG F 476 196.373 164.521 194.996 1.00100.52 ATOM 238 CB ARG F 476 197.995 162.829 192.560 1.00100.52 ATOM 239 CG ARG F 476 198.090 161.907 193.738 1.00100.52 ATOM 240 CD ARG F 476 198.155 160.469 193.324 1.00100.52 ATOM 241 NE ARG F 476 198.011 159.592 194.477 1.00100.52 ATOM 242 CZ ARG F 476 199.012 159.249 195.277 1.00100.52 ATOM 243 NH1 ARG F 476 200.234 159.706 195.049 1.00100.52 ATOM 244 NH2 ARG F 476 198.792 158.445 196.304 1.00100.52 ATOM 245 N GLU F 477 195.256 163.969 193.137 1.00102.28 ATOM 246 CA GLU F 477 193.980 163.936 193.831 1.00102.28 ATOM 247 C GLU F 477 193.950 162.750 194.783 1.00102.28 ATOM 248 O GLU F 477 194.332 161.644 194.394 1.00102.28 ATOM 249 CB GLU F 477 192.836 163.836 192.839 1.00102.28 ATOM 250 CG GLU F 477 192.643 165.069 191.987 1.00102.28 ATOM 251 CD GLU F 477 191.958 166.186 192.729 1.00102.28 ATOM 252 OE1 GLU F 477 191.432 165.934 193.833 1.00102.28 ATOM 253 OE2 GLU F 477 191.946 167.320 192.210 1.00102.28 ATOM 254 N PRO F 478 193.539 162.937 196.033 1.00101.83 ATOM 255 CA PRO F 478 193.480 161.807 196.959 1.00101.83 ATOM 256 C PRO F 478 192.274 160.934 196.664 1.00101.83 ATOM 257 O PRO F 478 191.159 161.427 196.497 1.00101.83 ATOM 258 CB PRO F 478 193.370 162.479 198.327 1.00101.83 ATOM 259 CG PRO F 478 192.782 163.777 198.048 1.00101.83 ATOM 260 CD PRO F 478 193.261 164.209 196.708 1.00101.83 ATOM 261 N THR F 479 192.511 159.632 196.577 1.00103.57 ATOM 262 CA THR F 479 191.419 158.697 196.420 1.00103.57 ATOM 263 C THR F 479 190.646 158.616 197.737 1.00103.57 ATOM 264 O THR F 479 191.216 158.838 198.808 1.00103.57 ATOM 265 CB THR F 479 191.952 157.327 195.992 1.00103.57 ATOM 266 OG1 THR F 479 190.876 156.493 195.553 1.00103.57 ATOM 267 CG2 THR F 479 192.679 156.634 197.120 1.00103.57 TER