HEADER TRANSCRIPTION/DNA 31-DEC-69 7MKD TITLE Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda TITLE 2 PR promoter DNA (class 1) COMPND MOL_ID: 5; COMPND 2 MOLECULE: RNA polymerase sigma factor RpoD; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; EXPDTA ELECTRON MICROSCOPY DBREF 7MKD L 1 613 UNP Q0P6L9 Q0P6L9_ECOL 1 613 SEQRES 1 L 32 ARG THR ILE ARG ILE PRO VAL HIS MET ILE GLU THR ILE SEQRES 2 L 32 ASN LYS LEU ASN ARG ILE SER ARG GLN MET LEU GLN GLU SEQRES 3 L 32 MET GLY ARG GLU PRO THR ATOM 1 N ARG L 448 130.695 121.852 104.134 1.00 84.55 ATOM 2 CA ARG L 448 130.829 121.079 105.356 1.00 84.55 ATOM 3 C ARG L 448 132.292 120.985 105.756 1.00 84.55 ATOM 4 O ARG L 448 133.167 120.841 104.900 1.00 84.55 ATOM 5 CB ARG L 448 130.256 119.684 105.161 1.00 84.55 ATOM 6 CG ARG L 448 128.787 119.662 104.813 1.00 84.55 ATOM 7 CD ARG L 448 127.967 119.780 106.065 1.00 84.55 ATOM 8 NE ARG L 448 128.343 118.747 107.017 1.00 84.55 ATOM 9 CZ ARG L 448 127.604 117.682 107.284 1.00 84.55 ATOM 10 NH1 ARG L 448 126.438 117.522 106.679 1.00 84.55 ATOM 11 NH2 ARG L 448 128.027 116.786 108.162 1.00 84.55 ATOM 12 N THR L 449 132.560 121.078 107.060 1.00 80.77 ATOM 13 CA THR L 449 133.930 120.908 107.532 1.00 80.77 ATOM 14 C THR L 449 134.404 119.480 107.328 1.00 80.77 ATOM 15 O THR L 449 135.549 119.249 106.934 1.00 80.77 ATOM 16 CB THR L 449 134.037 121.289 109.003 1.00 80.77 ATOM 17 OG1 THR L 449 133.433 122.568 109.207 1.00 80.77 ATOM 18 CG2 THR L 449 135.486 121.362 109.412 1.00 80.77 ATOM 19 N ILE L 450 133.540 118.517 107.602 1.00 80.79 ATOM 20 CA ILE L 450 133.789 117.107 107.357 1.00 80.79 ATOM 21 C ILE L 450 132.972 116.749 106.129 1.00 80.79 ATOM 22 O ILE L 450 131.751 116.600 106.212 1.00 80.79 ATOM 23 CB ILE L 450 133.398 116.247 108.559 1.00 80.79 ATOM 24 CG1 ILE L 450 134.251 116.601 109.761 1.00 80.79 ATOM 25 CG2 ILE L 450 133.561 114.803 108.240 1.00 80.79 ATOM 26 CD1 ILE L 450 133.839 115.882 110.984 1.00 80.79 ATOM 27 N ARG L 451 133.629 116.628 104.985 1.00 84.16 ATOM 28 CA ARG L 451 132.903 116.505 103.731 1.00 84.16 ATOM 29 C ARG L 451 132.194 115.167 103.657 1.00 84.16 ATOM 30 O ARG L 451 132.806 114.121 103.881 1.00 84.16 ATOM 31 CB ARG L 451 133.858 116.648 102.554 1.00 84.16 ATOM 32 CG ARG L 451 133.170 116.696 101.214 1.00 84.16 ATOM 33 CD ARG L 451 134.178 116.762 100.094 1.00 84.16 ATOM 34 NE ARG L 451 134.686 115.445 99.753 1.00 84.16 ATOM 35 CZ ARG L 451 134.105 114.645 98.874 1.00 84.16 ATOM 36 NH1 ARG L 451 133.003 115.041 98.261 1.00 84.16 ATOM 37 NH2 ARG L 451 134.620 113.457 98.608 1.00 84.16 ATOM 38 N ILE L 452 130.905 115.194 103.343 1.00 83.46 ATOM 39 CA ILE L 452 130.172 113.957 103.102 1.00 83.46 ATOM 40 C ILE L 452 129.825 113.927 101.619 1.00 83.46 ATOM 41 O ILE L 452 129.665 114.989 101.008 1.00 83.46 ATOM 42 CB ILE L 452 128.941 113.840 104.014 1.00 83.46 ATOM 43 CG1 ILE L 452 127.727 114.505 103.405 1.00 83.46 ATOM 44 CG2 ILE L 452 129.208 114.476 105.353 1.00 83.46 ATOM 45 CD1 ILE L 452 126.545 114.479 104.323 1.00 83.46 ATOM 46 N PRO L 453 129.743 112.761 100.994 1.00 86.45 ATOM 47 CA PRO L 453 129.625 112.713 99.536 1.00 86.45 ATOM 48 C PRO L 453 128.285 113.197 99.028 1.00 86.45 ATOM 49 O PRO L 453 127.430 113.614 99.809 1.00 86.45 ATOM 50 CB PRO L 453 129.824 111.229 99.225 1.00 86.45 ATOM 51 CG PRO L 453 130.486 110.687 100.395 1.00 86.45 ATOM 52 CD PRO L 453 129.947 111.423 101.547 1.00 86.45 ATOM 53 N VAL L 454 128.094 113.153 97.712 1.00 89.02 ATOM 54 CA VAL L 454 126.840 113.617 97.139 1.00 89.02 ATOM 55 C VAL L 454 125.709 112.646 97.445 1.00 89.02 ATOM 56 O VAL L 454 124.593 113.064 97.768 1.00 89.02 ATOM 57 CB VAL L 454 127.005 113.853 95.632 1.00 89.02 ATOM 58 CG1 VAL L 454 125.661 113.989 94.963 1.00 89.02 ATOM 59 CG2 VAL L 454 127.811 115.104 95.405 1.00 89.02 ATOM 60 N HIS L 455 125.964 111.340 97.351 1.00 94.05 ATOM 61 CA HIS L 455 124.876 110.382 97.514 1.00 94.05 ATOM 62 C HIS L 455 124.331 110.394 98.935 1.00 94.05 ATOM 63 O HIS L 455 123.113 110.328 99.142 1.00 94.05 ATOM 64 CB HIS L 455 125.329 108.981 97.106 1.00 94.05 ATOM 65 CG HIS L 455 126.322 108.360 98.035 1.00 94.05 ATOM 66 ND1 HIS L 455 125.953 107.530 99.070 1.00 94.05 ATOM 67 CD2 HIS L 455 127.672 108.427 98.071 1.00 94.05 ATOM 68 CE1 HIS L 455 127.032 107.121 99.710 1.00 94.05 ATOM 69 NE2 HIS L 455 128.088 107.655 99.126 1.00 94.05 ATOM 70 N MET L 456 125.208 110.511 99.929 1.00 91.26 ATOM 71 CA MET L 456 124.725 110.628 101.296 1.00 91.26 ATOM 72 C MET L 456 123.988 111.939 101.513 1.00 91.26 ATOM 73 O MET L 456 123.044 111.991 102.305 1.00 91.26 ATOM 74 CB MET L 456 125.876 110.497 102.281 1.00 91.26 ATOM 75 CG MET L 456 125.432 110.413 103.712 1.00 91.26 ATOM 76 SD MET L 456 124.200 109.134 103.960 1.00 91.26 ATOM 77 CE MET L 456 125.134 107.677 103.530 1.00 91.26 ATOM 78 N ILE L 457 124.374 112.999 100.804 1.00 89.83 ATOM 79 CA ILE L 457 123.651 114.260 100.927 1.00 89.83 ATOM 80 C ILE L 457 122.254 114.132 100.338 1.00 89.83 ATOM 81 O ILE L 457 121.286 114.665 100.887 1.00 89.83 ATOM 82 CB ILE L 457 124.451 115.400 100.281 1.00 89.83 ATOM 83 CG1 ILE L 457 125.235 116.136 101.350 1.00 89.83 ATOM 84 CG2 ILE L 457 123.550 116.369 99.579 1.00 89.83 ATOM 85 CD1 ILE L 457 126.035 117.273 100.830 1.00 89.83 ATOM 86 N GLU L 458 122.121 113.414 99.226 1.00 95.13 ATOM 87 CA GLU L 458 120.797 113.188 98.661 1.00 95.13 ATOM 88 C GLU L 458 119.939 112.357 99.600 1.00 95.13 ATOM 89 O GLU L 458 118.744 112.628 99.763 1.00 95.13 ATOM 90 CB GLU L 458 120.911 112.514 97.299 1.00 95.13 ATOM 91 CG GLU L 458 121.478 113.422 96.226 1.00 95.13 ATOM 92 CD GLU L 458 121.698 112.708 94.912 1.00 95.13 ATOM 93 OE1 GLU L 458 121.659 111.460 94.898 1.00 95.13 ATOM 94 OE2 GLU L 458 121.908 113.395 93.893 1.00 95.13 ATOM 95 N THR L 459 120.532 111.348 100.238 1.00 92.61 ATOM 96 CA THR L 459 119.780 110.564 101.213 1.00 92.61 ATOM 97 C THR L 459 119.341 111.422 102.392 1.00 92.61 ATOM 98 O THR L 459 118.208 111.302 102.867 1.00 92.61 ATOM 99 CB THR L 459 120.610 109.381 101.692 1.00 92.61 ATOM 100 OG1 THR L 459 120.826 108.484 100.600 1.00 92.61 ATOM 101 CG2 THR L 459 119.885 108.647 102.785 1.00 92.61 ATOM 102 N ILE L 460 120.214 112.309 102.865 1.00 93.86 ATOM 103 CA ILE L 460 119.856 113.182 103.979 1.00 93.86 ATOM 104 C ILE L 460 118.737 114.138 103.585 1.00 93.86 ATOM 105 O ILE L 460 117.810 114.378 104.365 1.00 93.86 ATOM 106 CB ILE L 460 121.097 113.935 104.481 1.00 93.86 ATOM 107 CG1 ILE L 460 121.955 113.017 105.338 1.00 93.86 ATOM 108 CG2 ILE L 460 120.704 115.151 105.269 1.00 93.86 ATOM 109 CD1 ILE L 460 123.135 113.704 105.942 1.00 93.86 ATOM 110 N ASN L 461 118.807 114.713 102.383 1.00101.77 ATOM 111 CA ASN L 461 117.751 115.620 101.942 1.00101.77 ATOM 112 C ASN L 461 116.424 114.895 101.812 1.00101.77 ATOM 113 O ASN L 461 115.382 115.423 102.212 1.00101.77 ATOM 114 CB ASN L 461 118.122 116.280 100.617 1.00101.77 ATOM 115 CG ASN L 461 119.146 117.386 100.781 1.00101.77 ATOM 116 OD1 ASN L 461 119.339 117.911 101.875 1.00101.77 ATOM 117 ND2 ASN L 461 119.804 117.749 99.690 1.00101.77 ATOM 118 N LYS L 462 116.438 113.678 101.268 1.00100.00 ATOM 119 CA LYS L 462 115.205 112.905 101.183 1.00100.00 ATOM 120 C LYS L 462 114.655 112.595 102.567 1.00100.00 ATOM 121 O LYS L 462 113.442 112.680 102.797 1.00100.00 ATOM 122 CB LYS L 462 115.448 111.617 100.407 1.00100.00 ATOM 123 CG LYS L 462 114.242 110.721 100.332 1.00100.00 ATOM 124 CD LYS L 462 114.565 109.430 99.613 1.00100.00 ATOM 125 CE LYS L 462 113.342 108.537 99.521 1.00100.00 ATOM 126 NZ LYS L 462 113.615 107.292 98.754 1.00100.00 ATOM 127 N LEU L 463 115.534 112.250 103.505 1.00100.46 ATOM 128 CA LEU L 463 115.095 111.939 104.860 1.00100.46 ATOM 129 C LEU L 463 114.473 113.153 105.530 1.00100.46 ATOM 130 O LEU L 463 113.422 113.052 106.169 1.00100.46 ATOM 131 CB LEU L 463 116.274 111.429 105.678 1.00100.46 ATOM 132 CG LEU L 463 115.943 110.899 107.061 1.00100.46 ATOM 133 CD1 LEU L 463 115.539 109.458 106.941 1.00100.46 ATOM 134 CD2 LEU L 463 117.132 111.047 107.969 1.00100.46 ATOM 135 N ASN L 464 115.107 114.315 105.394 1.00101.76 ATOM 136 CA ASN L 464 114.568 115.518 106.017 1.00101.76 ATOM 137 C ASN L 464 113.252 115.928 105.382 1.00101.76 ATOM 138 O ASN L 464 112.341 116.383 106.076 1.00101.76 ATOM 139 CB ASN L 464 115.574 116.661 105.938 1.00101.76 ATOM 140 CG ASN L 464 116.542 116.655 107.091 1.00101.76 ATOM 141 OD1 ASN L 464 117.587 117.297 107.037 1.00101.76 ATOM 142 ND2 ASN L 464 116.207 115.923 108.142 1.00101.76 ATOM 143 N ARG L 465 113.128 115.779 104.064 1.00105.34 ATOM 144 CA ARG L 465 111.871 116.121 103.413 1.00105.34 ATOM 145 C ARG L 465 110.745 115.203 103.869 1.00105.34 ATOM 146 O ARG L 465 109.631 115.665 104.143 1.00105.34 ATOM 147 CB ARG L 465 112.038 116.063 101.900 1.00105.34 ATOM 148 CG ARG L 465 110.792 116.396 101.129 1.00105.34 ATOM 149 CD ARG L 465 111.116 116.605 99.667 1.00105.34 ATOM 150 NE ARG L 465 111.859 115.481 99.114 1.00105.34 ATOM 151 CZ ARG L 465 111.293 114.388 98.620 1.00105.34 ATOM 152 NH1 ARG L 465 109.975 114.272 98.611 1.00105.34 ATOM 153 NH2 ARG L 465 112.044 113.411 98.135 1.00105.34 ATOM 154 N ILE L 466 111.017 113.903 103.979 1.00106.21 ATOM 155 CA ILE L 466 109.983 112.984 104.440 1.00106.21 ATOM 156 C ILE L 466 109.625 113.259 105.895 1.00106.21 ATOM 157 O ILE L 466 108.454 113.187 106.281 1.00106.21 ATOM 158 CB ILE L 466 110.427 111.530 104.230 1.00106.21 ATOM 159 CG1 ILE L 466 110.493 111.221 102.741 1.00106.21 ATOM 160 CG2 ILE L 466 109.468 110.585 104.893 1.00106.21 ATOM 161 CD1 ILE L 466 109.165 111.317 102.051 1.00106.21 ATOM 162 N SER L 467 110.614 113.590 106.723 1.00108.24 ATOM 163 CA SER L 467 110.323 113.904 108.118 1.00108.24 ATOM 164 C SER L 467 109.504 115.179 108.243 1.00108.24 ATOM 165 O SER L 467 108.617 115.269 109.095 1.00108.24 ATOM 166 CB SER L 467 111.615 114.028 108.914 1.00108.24 ATOM 167 OG SER L 467 111.351 114.543 110.202 1.00108.24 ATOM 168 N ARG L 468 109.800 116.183 107.419 1.00109.95 ATOM 169 CA ARG L 468 109.007 117.406 107.413 1.00109.95 ATOM 170 C ARG L 468 107.576 117.123 106.988 1.00109.95 ATOM 171 O ARG L 468 106.627 117.670 107.553 1.00109.95 ATOM 172 CB ARG L 468 109.651 118.433 106.483 1.00109.95 ATOM 173 CG ARG L 468 108.757 119.587 106.096 1.00109.95 ATOM 174 CD ARG L 468 109.260 120.248 104.825 1.00109.95 ATOM 175 NE ARG L 468 110.694 120.514 104.885 1.00109.95 ATOM 176 CZ ARG L 468 111.439 120.840 103.833 1.00109.95 ATOM 177 NH1 ARG L 468 110.887 120.935 102.633 1.00109.95 ATOM 178 NH2 ARG L 468 112.738 121.059 103.979 1.00109.95 ATOM 179 N GLN L 469 107.404 116.266 105.984 1.00111.74 ATOM 180 CA GLN L 469 106.060 115.914 105.544 1.00111.74 ATOM 181 C GLN L 469 105.292 115.163 106.625 1.00111.74 ATOM 182 O GLN L 469 104.102 115.416 106.836 1.00111.74 ATOM 183 CB GLN L 469 106.136 115.090 104.263 1.00111.74 ATOM 184 CG GLN L 469 104.885 114.311 103.948 1.00111.74 ATOM 185 CD GLN L 469 105.041 113.481 102.701 1.00111.74 ATOM 186 OE1 GLN L 469 104.515 112.374 102.607 1.00111.74 ATOM 187 NE2 GLN L 469 105.771 114.012 101.730 1.00111.74 ATOM 188 N MET L 470 105.951 114.236 107.322 1.00115.69 ATOM 189 CA MET L 470 105.264 113.473 108.358 1.00115.69 ATOM 190 C MET L 470 105.047 114.276 109.626 1.00115.69 ATOM 191 O MET L 470 104.306 113.828 110.504 1.00115.69 ATOM 192 CB MET L 470 106.039 112.208 108.710 1.00115.69 ATOM 193 CG MET L 470 106.156 111.215 107.585 1.00115.69 ATOM 194 SD MET L 470 107.103 109.772 108.081 1.00115.69 ATOM 195 CE MET L 470 105.895 108.908 109.070 1.00115.69 ATOM 196 N LEU L 471 105.691 115.435 109.756 1.00112.21 ATOM 197 CA LEU L 471 105.501 116.244 110.952 1.00112.21 ATOM 198 C LEU L 471 104.098 116.818 111.015 1.00112.21 ATOM 199 O LEU L 471 103.539 116.970 112.104 1.00112.21 ATOM 200 CB LEU L 471 106.529 117.368 110.996 1.00112.21 ATOM 201 CG LEU L 471 106.645 118.070 112.339 1.00112.21 ATOM 202 CD1 LEU L 471 107.013 117.060 113.384 1.00112.21 ATOM 203 CD2 LEU L 471 107.682 119.159 112.273 1.00112.21 ATOM 204 N GLN L 472 103.509 117.135 109.866 1.00111.53 ATOM 205 CA GLN L 472 102.174 117.708 109.814 1.00111.53 ATOM 206 C GLN L 472 101.117 116.703 109.389 1.00111.53 ATOM 207 O GLN L 472 99.954 117.078 109.224 1.00111.53 ATOM 208 CB GLN L 472 102.161 118.907 108.877 1.00111.53 ATOM 209 CG GLN L 472 103.196 119.921 109.235 1.00111.53 ATOM 210 CD GLN L 472 103.101 121.141 108.380 1.00111.53 ATOM 211 OE1 GLN L 472 102.278 121.205 107.474 1.00111.53 ATOM 212 NE2 GLN L 472 103.942 122.125 108.655 1.00111.53 ATOM 213 N GLU L 473 101.487 115.443 109.193 1.00118.97 ATOM 214 CA GLU L 473 100.487 114.408 108.980 1.00118.97 ATOM 215 C GLU L 473 99.971 113.849 110.294 1.00118.97 ATOM 216 O GLU L 473 98.779 113.554 110.417 1.00118.97 ATOM 217 CB GLU L 473 101.060 113.269 108.137 1.00118.97 ATOM 218 CG GLU L 473 100.692 113.316 106.669 1.00118.97 ATOM 219 CD GLU L 473 100.893 111.976 105.988 1.00118.97 ATOM 220 OE1 GLU L 473 101.035 110.965 106.706 1.00118.97 ATOM 221 OE2 GLU L 473 100.912 111.929 104.741 1.00118.97 ATOM 222 N MET L 474 100.853 113.692 111.276 1.00120.09 ATOM 223 CA MET L 474 100.493 113.110 112.558 1.00120.09 ATOM 224 C MET L 474 100.627 114.076 113.721 1.00120.09 ATOM 225 O MET L 474 100.122 113.785 114.805 1.00120.09 ATOM 226 CB MET L 474 101.344 111.866 112.831 1.00120.09 ATOM 227 CG MET L 474 102.837 112.114 112.778 1.00120.09 ATOM 228 SD MET L 474 103.763 110.640 112.325 1.00120.09 ATOM 229 CE MET L 474 103.191 109.494 113.569 1.00120.09 ATOM 230 N GLY L 475 101.292 115.209 113.528 1.00113.96 ATOM 231 CA GLY L 475 101.311 116.272 114.502 1.00113.96 ATOM 232 C GLY L 475 102.521 116.297 115.411 1.00113.96 ATOM 233 O GLY L 475 102.746 117.307 116.084 1.00113.96 ATOM 234 N ARG L 476 103.306 115.227 115.453 1.00118.51 ATOM 235 CA ARG L 476 104.476 115.188 116.316 1.00118.51 ATOM 236 C ARG L 476 105.644 114.594 115.544 1.00118.51 ATOM 237 O ARG L 476 105.491 114.117 114.419 1.00118.51 ATOM 238 CB ARG L 476 104.196 114.405 117.602 1.00118.51 ATOM 239 CG ARG L 476 104.432 112.911 117.524 1.00118.51 ATOM 240 CD ARG L 476 103.390 112.198 116.693 1.00118.51 ATOM 241 NE ARG L 476 103.138 110.859 117.207 1.00118.51 ATOM 242 CZ ARG L 476 103.952 109.825 117.032 1.00118.51 ATOM 243 NH1 ARG L 476 105.082 109.966 116.353 1.00118.51 ATOM 244 NH2 ARG L 476 103.636 108.644 117.540 1.00118.51 ATOM 245 N GLU L 477 106.824 114.645 116.157 1.00119.42 ATOM 246 CA GLU L 477 108.038 114.198 115.490 1.00119.42 ATOM 247 C GLU L 477 107.942 112.714 115.144 1.00119.42 ATOM 248 O GLU L 477 107.399 111.928 115.927 1.00119.42 ATOM 249 CB GLU L 477 109.256 114.442 116.380 1.00119.42 ATOM 250 CG GLU L 477 109.868 115.823 116.253 1.00119.42 ATOM 251 CD GLU L 477 110.688 115.984 114.986 1.00119.42 ATOM 252 OE1 GLU L 477 110.890 117.135 114.544 1.00119.42 ATOM 253 OE2 GLU L 477 111.132 114.958 114.433 1.00119.42 ATOM 254 N PRO L 478 108.434 112.314 113.969 1.00116.59 ATOM 255 CA PRO L 478 108.329 110.932 113.533 1.00116.59 ATOM 256 C PRO L 478 109.553 110.175 113.919 1.00116.59 ATOM 257 O PRO L 478 110.626 110.654 113.660 1.00116.59 ATOM 258 CB PRO L 478 108.326 111.077 112.042 1.00116.59 ATOM 259 CG PRO L 478 109.276 112.181 111.832 1.00116.59 ATOM 260 CD PRO L 478 109.238 113.083 113.027 1.00116.59 ATOM 261 N THR L 479 109.374 109.031 114.561 1.00117.27 ATOM 262 CA THR L 479 110.437 108.152 115.019 1.00117.27 ATOM 263 C THR L 479 111.081 107.374 113.903 1.00117.27 ATOM 264 O THR L 479 110.426 107.076 112.925 1.00117.27 ATOM 265 CB THR L 479 109.828 107.113 115.937 1.00117.27 ATOM 266 OG1 THR L 479 108.626 106.627 115.338 1.00117.27 ATOM 267 CG2 THR L 479 109.470 107.745 117.237 1.00117.27 TER