HEADER TRANSCRIPTION, TRANSFERASE/DNA 31-DEC-69 6XLL TITLE Cryo-EM structure of E. coli RNAP-promoter initial transcribing TITLE 2 complex with 5-nt RNA transcript (RPitc-5nt) COMPND MOL_ID: 5; COMPND 2 MOLECULE: RNA polymerase sigma factor RpoD; COMPND 3 CHAIN: F; COMPND 4 ENGINEERED: YES; EXPDTA ELECTRON MICROSCOPY DBREF 6XLL 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 448 172.146 147.018 194.711 1.00 96.64 ATOM 2 CA ARG F 448 172.071 146.743 193.285 1.00 96.64 ATOM 3 C ARG F 448 170.641 146.892 192.792 1.00 96.64 ATOM 4 O ARG F 448 169.691 146.619 193.529 1.00 96.64 ATOM 5 CB ARG F 448 172.584 145.338 192.983 1.00 96.64 ATOM 6 CG ARG F 448 174.078 145.192 193.139 1.00 96.64 ATOM 7 CD ARG F 448 174.554 143.886 192.562 1.00 96.64 ATOM 8 NE ARG F 448 175.969 143.928 192.225 1.00 96.64 ATOM 9 CZ ARG F 448 176.433 143.958 190.984 1.00 96.64 ATOM 10 NH1 ARG F 448 175.592 143.953 189.962 1.00 96.64 ATOM 11 NH2 ARG F 448 177.738 143.993 190.765 1.00 96.64 ATOM 12 N THR F 449 170.492 147.338 191.544 1.00 90.97 ATOM 13 CA THR F 449 169.161 147.459 190.961 1.00 90.97 ATOM 14 C THR F 449 168.555 146.086 190.718 1.00 90.97 ATOM 15 O THR F 449 167.477 145.769 191.231 1.00 90.97 ATOM 16 CB THR F 449 169.220 148.253 189.660 1.00 90.97 ATOM 17 OG1 THR F 449 170.055 149.401 189.836 1.00 90.97 ATOM 18 CG2 THR F 449 167.837 148.708 189.273 1.00 90.97 ATOM 19 N ILE F 450 169.238 145.256 189.939 1.00 93.70 ATOM 20 CA ILE F 450 168.867 143.860 189.767 1.00 93.70 ATOM 21 C ILE F 450 169.593 143.083 190.856 1.00 93.70 ATOM 22 O ILE F 450 170.782 142.789 190.734 1.00 93.70 ATOM 23 CB ILE F 450 169.227 143.345 188.371 1.00 93.70 ATOM 24 CG1 ILE F 450 168.459 144.108 187.304 1.00 93.70 ATOM 25 CG2 ILE F 450 168.884 141.900 188.244 1.00 93.70 ATOM 26 CD1 ILE F 450 169.290 145.123 186.589 1.00 93.70 ATOM 27 N ARG F 451 168.883 142.773 191.931 1.00103.53 ATOM 28 CA ARG F 451 169.511 142.227 193.121 1.00103.53 ATOM 29 C ARG F 451 169.961 140.798 192.878 1.00103.53 ATOM 30 O ARG F 451 169.213 139.986 192.329 1.00103.53 ATOM 31 CB ARG F 451 168.543 142.277 194.295 1.00103.53 ATOM 32 CG ARG F 451 169.130 141.799 195.591 1.00103.53 ATOM 33 CD ARG F 451 168.035 141.315 196.497 1.00103.53 ATOM 34 NE ARG F 451 167.575 140.008 196.073 1.00103.53 ATOM 35 CZ ARG F 451 167.856 138.884 196.713 1.00103.53 ATOM 36 NH1 ARG F 451 168.588 138.917 197.814 1.00103.53 ATOM 37 NH2 ARG F 451 167.400 137.732 196.251 1.00103.53 ATOM 38 N ILE F 452 171.190 140.497 193.280 1.00107.55 ATOM 39 CA ILE F 452 171.741 139.152 193.168 1.00107.55 ATOM 40 C ILE F 452 171.955 138.646 194.588 1.00107.55 ATOM 41 O ILE F 452 172.129 139.459 195.505 1.00107.55 ATOM 42 CB ILE F 452 173.027 139.145 192.328 1.00107.55 ATOM 43 CG1 ILE F 452 174.142 139.881 193.046 1.00107.55 ATOM 44 CG2 ILE F 452 172.782 139.813 190.987 1.00107.55 ATOM 45 CD1 ILE F 452 175.324 140.139 192.176 1.00107.55 ATOM 46 N PRO F 453 171.895 137.343 194.833 1.00113.89 ATOM 47 CA PRO F 453 171.931 136.847 196.209 1.00113.89 ATOM 48 C PRO F 453 173.290 137.055 196.850 1.00113.89 ATOM 49 O PRO F 453 174.268 137.436 196.209 1.00113.89 ATOM 50 CB PRO F 453 171.607 135.362 196.051 1.00113.89 ATOM 51 CG PRO F 453 170.858 135.291 194.784 1.00113.89 ATOM 52 CD PRO F 453 171.533 136.272 193.899 1.00113.89 ATOM 53 N VAL F 454 173.336 136.796 198.156 1.00115.48 ATOM 54 CA VAL F 454 174.565 137.035 198.898 1.00115.48 ATOM 55 C VAL F 454 175.614 135.989 198.549 1.00115.48 ATOM 56 O VAL F 454 176.816 136.265 198.618 1.00115.48 ATOM 57 CB VAL F 454 174.264 137.088 200.407 1.00115.48 ATOM 58 CG1 VAL F 454 173.819 135.729 200.920 1.00115.48 ATOM 59 CG2 VAL F 454 175.457 137.609 201.181 1.00115.48 ATOM 60 N HIS F 455 175.195 134.794 198.123 1.00118.44 ATOM 61 CA HIS F 455 176.175 133.796 197.711 1.00118.44 ATOM 62 C HIS F 455 176.798 134.167 196.374 1.00118.44 ATOM 63 O HIS F 455 178.008 134.012 196.181 1.00118.44 ATOM 64 CB HIS F 455 175.541 132.402 197.668 1.00118.44 ATOM 65 CG HIS F 455 174.637 132.169 196.498 1.00118.44 ATOM 66 ND1 HIS F 455 175.106 131.806 195.256 1.00118.44 ATOM 67 CD2 HIS F 455 173.290 132.234 196.386 1.00118.44 ATOM 68 CE1 HIS F 455 174.089 131.669 194.426 1.00118.44 ATOM 69 NE2 HIS F 455 172.976 131.925 195.086 1.00118.44 ATOM 70 N MET F 456 175.999 134.700 195.450 1.00114.30 ATOM 71 CA MET F 456 176.566 135.180 194.199 1.00114.30 ATOM 72 C MET F 456 177.384 136.440 194.417 1.00114.30 ATOM 73 O MET F 456 178.344 136.684 193.685 1.00114.30 ATOM 74 CB MET F 456 175.462 135.425 193.180 1.00114.30 ATOM 75 CG MET F 456 175.956 135.593 191.760 1.00114.30 ATOM 76 SD MET F 456 176.784 134.134 191.122 1.00114.30 ATOM 77 CE MET F 456 175.552 132.882 191.433 1.00114.30 ATOM 78 N ILE F 457 177.044 137.233 195.431 1.00112.97 ATOM 79 CA ILE F 457 177.856 138.397 195.770 1.00112.97 ATOM 80 C ILE F 457 179.217 137.961 196.290 1.00112.97 ATOM 81 O ILE F 457 180.250 138.514 195.899 1.00112.97 ATOM 82 CB ILE F 457 177.109 139.281 196.783 1.00112.97 ATOM 83 CG1 ILE F 457 176.132 140.195 196.056 1.00112.97 ATOM 84 CG2 ILE F 457 178.076 140.103 197.610 1.00112.97 ATOM 85 CD1 ILE F 457 176.800 141.317 195.314 1.00112.97 ATOM 86 N GLU F 458 179.242 136.960 197.173 1.00113.85 ATOM 87 CA GLU F 458 180.511 136.426 197.653 1.00113.85 ATOM 88 C GLU F 458 181.317 135.820 196.515 1.00113.85 ATOM 89 O GLU F 458 182.543 135.966 196.468 1.00113.85 ATOM 90 CB GLU F 458 180.262 135.389 198.744 1.00113.85 ATOM 91 CG GLU F 458 179.741 135.966 200.049 1.00113.85 ATOM 92 CD GLU F 458 178.904 134.971 200.836 1.00113.85 ATOM 93 OE1 GLU F 458 178.621 133.875 200.306 1.00113.85 ATOM 94 OE2 GLU F 458 178.529 135.282 201.986 1.00113.85 ATOM 95 N THR F 459 180.639 135.154 195.578 1.00112.87 ATOM 96 CA THR F 459 181.321 134.585 194.420 1.00112.87 ATOM 97 C THR F 459 181.945 135.669 193.551 1.00112.87 ATOM 98 O THR F 459 183.097 135.546 193.128 1.00112.87 ATOM 99 CB THR F 459 180.343 133.745 193.604 1.00112.87 ATOM 100 OG1 THR F 459 179.955 132.595 194.361 1.00112.87 ATOM 101 CG2 THR F 459 180.976 133.298 192.314 1.00112.87 ATOM 102 N ILE F 460 181.206 136.748 193.291 1.00111.40 ATOM 103 CA ILE F 460 181.723 137.834 192.466 1.00111.40 ATOM 104 C ILE F 460 182.875 138.541 193.167 1.00111.40 ATOM 105 O ILE F 460 183.853 138.940 192.526 1.00111.40 ATOM 106 CB ILE F 460 180.585 138.805 192.106 1.00111.40 ATOM 107 CG1 ILE F 460 179.623 138.145 191.125 1.00111.40 ATOM 108 CG2 ILE F 460 181.122 140.086 191.511 1.00111.40 ATOM 109 CD1 ILE F 460 178.483 139.017 190.722 1.00111.40 ATOM 110 N ASN F 461 182.800 138.683 194.491 1.00112.21 ATOM 111 CA ASN F 461 183.901 139.306 195.222 1.00112.21 ATOM 112 C ASN F 461 185.153 138.443 195.179 1.00112.21 ATOM 113 O ASN F 461 186.260 138.958 194.981 1.00112.21 ATOM 114 CB ASN F 461 183.495 139.570 196.667 1.00112.21 ATOM 115 CG ASN F 461 182.541 140.725 196.795 1.00112.21 ATOM 116 OD1 ASN F 461 182.498 141.605 195.938 1.00112.21 ATOM 117 ND2 ASN F 461 181.765 140.733 197.869 1.00112.21 ATOM 118 N LYS F 462 184.998 137.130 195.367 1.00113.35 ATOM 119 CA LYS F 462 186.136 136.226 195.254 1.00113.35 ATOM 120 C LYS F 462 186.721 136.259 193.851 1.00113.35 ATOM 121 O LYS F 462 187.944 136.242 193.679 1.00113.35 ATOM 122 CB LYS F 462 185.708 134.811 195.629 1.00113.35 ATOM 123 CG LYS F 462 186.781 133.768 195.443 1.00113.35 ATOM 124 CD LYS F 462 186.334 132.427 195.985 1.00113.35 ATOM 125 CE LYS F 462 187.486 131.443 196.023 1.00113.35 ATOM 126 NZ LYS F 462 187.164 130.240 196.835 1.00113.35 ATOM 127 N LEU F 463 185.860 136.339 192.838 1.00113.45 ATOM 128 CA LEU F 463 186.321 136.423 191.458 1.00113.45 ATOM 129 C LEU F 463 187.118 137.695 191.214 1.00113.45 ATOM 130 O LEU F 463 188.178 137.658 190.581 1.00113.45 ATOM 131 CB LEU F 463 185.124 136.363 190.518 1.00113.45 ATOM 132 CG LEU F 463 185.420 136.392 189.028 1.00113.45 ATOM 133 CD1 LEU F 463 185.663 134.989 188.541 1.00113.45 ATOM 134 CD2 LEU F 463 184.285 137.046 188.268 1.00113.45 ATOM 135 N ASN F 464 186.621 138.832 191.706 1.00113.82 ATOM 136 CA ASN F 464 187.322 140.097 191.513 1.00113.82 ATOM 137 C ASN F 464 188.658 140.107 192.242 1.00113.82 ATOM 138 O ASN F 464 189.658 140.589 191.703 1.00113.82 ATOM 139 CB ASN F 464 186.450 141.260 191.978 1.00113.82 ATOM 140 CG ASN F 464 185.335 141.575 191.006 1.00113.82 ATOM 141 OD1 ASN F 464 185.328 141.092 189.879 1.00113.82 ATOM 142 ND2 ASN F 464 184.389 142.397 191.437 1.00113.82 ATOM 143 N ARG F 465 188.699 139.553 193.455 1.00116.43 ATOM 144 CA ARG F 465 189.955 139.461 194.193 1.00116.43 ATOM 145 C ARG F 465 190.969 138.585 193.468 1.00116.43 ATOM 146 O ARG F 465 192.149 138.947 193.344 1.00116.43 ATOM 147 CB ARG F 465 189.686 138.908 195.588 1.00116.43 ATOM 148 CG ARG F 465 190.924 138.696 196.407 1.00116.43 ATOM 149 CD ARG F 465 190.586 138.133 197.769 1.00116.43 ATOM 150 NE ARG F 465 190.083 136.765 197.701 1.00116.43 ATOM 151 CZ ARG F 465 188.875 136.391 198.111 1.00116.43 ATOM 152 NH1 ARG F 465 188.035 137.284 198.617 1.00116.43 ATOM 153 NH2 ARG F 465 188.507 135.122 198.017 1.00116.43 ATOM 154 N ILE F 466 190.527 137.427 192.982 1.00115.94 ATOM 155 CA ILE F 466 191.435 136.503 192.318 1.00115.94 ATOM 156 C ILE F 466 191.943 137.094 191.011 1.00115.94 ATOM 157 O ILE F 466 193.132 136.990 190.692 1.00115.94 ATOM 158 CB ILE F 466 190.736 135.149 192.109 1.00115.94 ATOM 159 CG1 ILE F 466 190.602 134.417 193.438 1.00115.94 ATOM 160 CG2 ILE F 466 191.508 134.300 191.156 1.00115.94 ATOM 161 CD1 ILE F 466 191.880 134.352 194.221 1.00115.94 ATOM 162 N SER F 467 191.066 137.746 190.245 1.00115.25 ATOM 163 CA SER F 467 191.514 138.371 189.008 1.00115.25 ATOM 164 C SER F 467 192.430 139.554 189.280 1.00115.25 ATOM 165 O SER F 467 193.333 139.824 188.485 1.00115.25 ATOM 166 CB SER F 467 190.319 138.807 188.170 1.00115.25 ATOM 167 OG SER F 467 189.617 139.853 188.806 1.00115.25 ATOM 168 N ARG F 468 192.267 140.179 190.440 1.00114.48 ATOM 169 CA ARG F 468 193.127 141.283 190.833 1.00114.48 ATOM 170 C ARG F 468 194.534 140.748 191.066 1.00114.48 ATOM 171 O ARG F 468 195.502 141.306 190.567 1.00114.48 ATOM 172 CB ARG F 468 192.619 141.941 192.113 1.00114.48 ATOM 173 CG ARG F 468 193.610 142.910 192.732 1.00114.48 ATOM 174 CD ARG F 468 193.402 143.039 194.231 1.00114.48 ATOM 175 NE ARG F 468 194.374 143.944 194.838 1.00114.48 ATOM 176 CZ ARG F 468 195.656 143.648 195.027 1.00114.48 ATOM 177 NH1 ARG F 468 196.131 142.469 194.651 1.00114.48 ATOM 178 NH2 ARG F 468 196.467 144.533 195.587 1.00114.48 ATOM 179 N GLN F 469 194.645 139.663 191.827 1.00115.09 ATOM 180 CA GLN F 469 195.951 139.067 192.103 1.00115.09 ATOM 181 C GLN F 469 196.589 138.511 190.836 1.00115.09 ATOM 182 O GLN F 469 197.808 138.620 190.646 1.00115.09 ATOM 183 CB GLN F 469 195.823 137.973 193.156 1.00115.09 ATOM 184 CG GLN F 469 195.294 138.468 194.477 1.00115.09 ATOM 185 CD GLN F 469 195.294 137.393 195.533 1.00115.09 ATOM 186 OE1 GLN F 469 195.854 136.316 195.336 1.00115.09 ATOM 187 NE2 GLN F 469 194.665 137.677 196.665 1.00115.09 ATOM 188 N MET F 470 195.783 137.920 189.954 1.00116.89 ATOM 189 CA MET F 470 196.324 137.377 188.713 1.00116.89 ATOM 190 C MET F 470 196.836 138.482 187.802 1.00116.89 ATOM 191 O MET F 470 197.890 138.335 187.179 1.00116.89 ATOM 192 CB MET F 470 195.269 136.538 188.000 1.00116.89 ATOM 193 CG MET F 470 194.944 135.249 188.713 1.00116.89 ATOM 194 SD MET F 470 193.655 134.316 187.889 1.00116.89 ATOM 195 CE MET F 470 194.628 133.406 186.700 1.00116.89 ATOM 196 N LEU F 471 196.106 139.594 187.712 1.00113.13 ATOM 197 CA LEU F 471 196.592 140.742 186.958 1.00113.13 ATOM 198 C LEU F 471 197.882 141.283 187.556 1.00113.13 ATOM 199 O LEU F 471 198.782 141.712 186.827 1.00113.13 ATOM 200 CB LEU F 471 195.515 141.820 186.928 1.00113.13 ATOM 201 CG LEU F 471 195.887 143.218 186.465 1.00113.13 ATOM 202 CD1 LEU F 471 195.947 143.246 184.964 1.00113.13 ATOM 203 CD2 LEU F 471 194.864 144.207 186.971 1.00113.13 ATOM 204 N GLN F 472 198.002 141.245 188.883 1.00113.01 ATOM 205 CA GLN F 472 199.219 141.732 189.519 1.00113.01 ATOM 206 C GLN F 472 200.402 140.810 189.279 1.00113.01 ATOM 207 O GLN F 472 201.546 141.273 189.275 1.00113.01 ATOM 208 CB GLN F 472 199.007 141.899 191.019 1.00113.01 ATOM 209 CG GLN F 472 198.189 143.104 191.390 1.00113.01 ATOM 210 CD GLN F 472 198.785 144.384 190.874 1.00113.01 ATOM 211 OE1 GLN F 472 200.002 144.558 190.849 1.00113.01 ATOM 212 NE2 GLN F 472 197.926 145.300 190.464 1.00113.01 ATOM 213 N GLU F 473 200.162 139.512 189.095 1.00117.99 ATOM 214 CA GLU F 473 201.288 138.597 188.949 1.00117.99 ATOM 215 C GLU F 473 201.692 138.353 187.501 1.00117.99 ATOM 216 O GLU F 473 202.848 137.996 187.250 1.00117.99 ATOM 217 CB GLU F 473 200.986 137.254 189.617 1.00117.99 ATOM 218 CG GLU F 473 199.928 136.433 188.920 1.00117.99 ATOM 219 CD GLU F 473 199.654 135.125 189.625 1.00117.99 ATOM 220 OE1 GLU F 473 200.268 134.883 190.684 1.00117.99 ATOM 221 OE2 GLU F 473 198.830 134.336 189.118 1.00117.99 ATOM 222 N MET F 474 200.786 138.531 186.538 1.00117.69 ATOM 223 CA MET F 474 201.111 138.276 185.143 1.00117.69 ATOM 224 C MET F 474 200.902 139.470 184.224 1.00117.69 ATOM 225 O MET F 474 201.100 139.330 183.013 1.00117.69 ATOM 226 CB MET F 474 200.302 137.084 184.604 1.00117.69 ATOM 227 CG MET F 474 198.844 137.376 184.316 1.00117.69 ATOM 228 SD MET F 474 197.931 135.912 183.802 1.00117.69 ATOM 229 CE MET F 474 197.930 134.963 185.318 1.00117.69 ATOM 230 N GLY F 475 200.508 140.626 184.750 1.00112.22 ATOM 231 CA GLY F 475 200.506 141.842 183.964 1.00112.22 ATOM 232 C GLY F 475 199.486 141.917 182.854 1.00112.22 ATOM 233 O GLY F 475 199.706 142.641 181.879 1.00112.22 ATOM 234 N ARG F 476 198.378 141.194 182.970 1.00116.66 ATOM 235 CA ARG F 476 197.302 141.256 181.992 1.00116.66 ATOM 236 C ARG F 476 196.049 140.687 182.635 1.00116.66 ATOM 237 O ARG F 476 196.117 139.967 183.634 1.00116.66 ATOM 238 CB ARG F 476 197.643 140.482 180.717 1.00116.66 ATOM 239 CG ARG F 476 197.507 138.989 180.882 1.00116.66 ATOM 240 CD ARG F 476 197.764 138.236 179.597 1.00116.66 ATOM 241 NE ARG F 476 197.234 136.879 179.678 1.00116.66 ATOM 242 CZ ARG F 476 197.829 135.877 180.316 1.00116.66 ATOM 243 NH1 ARG F 476 198.988 136.064 180.932 1.00116.66 ATOM 244 NH2 ARG F 476 197.265 134.680 180.336 1.00116.66 ATOM 245 N GLU F 477 194.907 141.029 182.064 1.00118.03 ATOM 246 CA GLU F 477 193.652 140.508 182.581 1.00118.03 ATOM 247 C GLU F 477 193.556 139.018 182.283 1.00118.03 ATOM 248 O GLU F 477 193.732 138.609 181.129 1.00118.03 ATOM 249 CB GLU F 477 192.465 141.254 181.982 1.00118.03 ATOM 250 CG GLU F 477 192.348 142.688 182.458 1.00118.03 ATOM 251 CD GLU F 477 192.058 142.781 183.941 1.00118.03 ATOM 252 OE1 GLU F 477 191.383 141.878 184.478 1.00118.03 ATOM 253 OE2 GLU F 477 192.510 143.757 184.573 1.00118.03 ATOM 254 N PRO F 478 193.304 138.179 183.285 1.00119.47 ATOM 255 CA PRO F 478 193.273 136.732 183.047 1.00119.47 ATOM 256 C PRO F 478 192.032 136.319 182.269 1.00119.47 ATOM 257 O PRO F 478 190.939 136.844 182.485 1.00119.47 ATOM 258 CB PRO F 478 193.276 136.143 184.461 1.00119.47 ATOM 259 CG PRO F 478 192.714 137.217 185.306 1.00119.47 ATOM 260 CD PRO F 478 193.177 138.505 184.713 1.00119.47 ATOM 261 N THR F 479 192.225 135.381 181.347 1.00121.77 ATOM 262 CA THR F 479 191.132 134.785 180.601 1.00121.77 ATOM 263 C THR F 479 190.236 133.997 181.558 1.00121.77 ATOM 264 O THR F 479 190.713 133.478 182.570 1.00121.77 ATOM 265 CB THR F 479 191.714 133.873 179.516 1.00121.77 ATOM 266 OG1 THR F 479 192.564 134.645 178.660 1.00121.77 ATOM 267 CG2 THR F 479 190.644 133.204 178.662 1.00121.77 TER