HEADER IMMUNE SYSTEM 21-MAY-18 6GKH TITLE CRYOEM STRUCTURE OF THE MDA5-DSRNA FILAMENT IN COMPLEX WITH ADP-ALF4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERFERON-INDUCED HELICASE C DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HELICASE WITH 2 CARD DOMAINS,HELICARD,INTERFERON INDUCED COMPND 5 WITH HELICASE C DOMAIN PROTEIN 1,MELANOMA DIFFERENTIATION-ASSOCIATED COMPND 6 PROTEIN 5,MDA-5,RIG-I-LIKE RECEPTOR 2,RLR-2; COMPND 7 EC: 3.6.4.13; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: RNA (5'-R(P*GP*UP*CP*AP*AP*GP*CP*CP*GP*AP*GP*GP*AP*GP*A)- COMPND 12 3'); COMPND 13 CHAIN: X; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: RNA (5'-R(P*UP*CP*UP*CP*CP*UP*CP*GP*GP*CP*UP*UP*GP*AP*C)- COMPND 17 3'); COMPND 18 CHAIN: Y; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: IFIH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE PHI6; SOURCE 12 ORGANISM_TAXID: 10879; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: PSEUDOMONAS PHAGE PHI6; SOURCE 16 ORGANISM_TAXID: 10879 KEYWDS PROTEIN-RNA COMPLEX, HELICAL FILAMENT, ATPASE, INNATE IMMUNE KEYWDS 2 RECEPTOR, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR Q.YU,K.QU,Y.MODIS REVDAT 5 20-NOV-24 6GKH 1 REMARK REVDAT 4 18-NOV-20 6GKH 1 REMARK REVDAT 3 02-JAN-19 6GKH 1 JRNL REVDAT 2 28-NOV-18 6GKH 1 JRNL REVDAT 1 21-NOV-18 6GKH 0 JRNL AUTH Q.YU,K.QU,Y.MODIS JRNL TITL CRYO-EM STRUCTURES OF MDA5-DSRNA FILAMENTS AT DIFFERENT JRNL TITL 2 STAGES OF ATP HYDROLYSIS. JRNL REF MOL. CELL V. 72 999 2018 JRNL REFN ISSN 1097-4164 JRNL PMID 30449722 JRNL DOI 10.1016/J.MOLCEL.2018.10.012 REMARK 2 REMARK 2 RESOLUTION. 4.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, EPU, GCTF, COOT, PHENIX, REMARK 3 RELION, RELION, RELION, RELION REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 175.000 REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.060 REMARK 3 NUMBER OF PARTICLES : 31556 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 6GKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1200010091. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : HELICAL REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : HELICAL ARRAY REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : MDA5-DSRNA HELICAL FILAMENT IN REMARK 245 COMPLEX WITH ADP-ALF4; MDA5 REMARK 245 BOUND TO ADP-ALF4; DOUBLE- REMARK 245 STRANDED RNA FROM BACTERIOPHAGE REMARK 245 PHI6 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 REMARK 245 SAMPLE SUPPORT DETAILS : 25 MA REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.70 REMARK 245 SAMPLE DETAILS : DEXD/H-BOX HELICASE CONSISTING REMARK 245 OF HEL1, HEL2, HEL2I, AND PINCER DOMAINS, FOLLOWED BY A C- REMARK 245 TERMINAL DOMAIN REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : -1800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : -2700.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 2985.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : 75000 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X, Y REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ILE A 3 REMARK 465 VAL A 4 REMARK 465 CYS A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 8 REMARK 465 ASP A 9 REMARK 465 SER A 10 REMARK 465 PHE A 11 REMARK 465 ARG A 12 REMARK 465 ASN A 13 REMARK 465 LEU A 14 REMARK 465 ILE A 15 REMARK 465 LEU A 16 REMARK 465 PHE A 17 REMARK 465 PHE A 18 REMARK 465 ARG A 19 REMARK 465 PRO A 20 REMARK 465 ARG A 21 REMARK 465 LEU A 22 REMARK 465 LYS A 23 REMARK 465 MET A 24 REMARK 465 TYR A 25 REMARK 465 ILE A 26 REMARK 465 GLN A 27 REMARK 465 VAL A 28 REMARK 465 GLU A 29 REMARK 465 PRO A 30 REMARK 465 VAL A 31 REMARK 465 LEU A 32 REMARK 465 ASP A 33 REMARK 465 HIS A 34 REMARK 465 LEU A 35 REMARK 465 ILE A 36 REMARK 465 PHE A 37 REMARK 465 LEU A 38 REMARK 465 SER A 39 REMARK 465 ALA A 40 REMARK 465 GLU A 41 REMARK 465 THR A 42 REMARK 465 LYS A 43 REMARK 465 GLU A 44 REMARK 465 GLN A 45 REMARK 465 ILE A 46 REMARK 465 LEU A 47 REMARK 465 LYS A 48 REMARK 465 LYS A 49 REMARK 465 ILE A 50 REMARK 465 ASN A 51 REMARK 465 THR A 52 REMARK 465 CYS A 53 REMARK 465 GLY A 54 REMARK 465 ASN A 55 REMARK 465 THR A 56 REMARK 465 SER A 57 REMARK 465 ALA A 58 REMARK 465 ALA A 59 REMARK 465 GLU A 60 REMARK 465 LEU A 61 REMARK 465 LEU A 62 REMARK 465 LEU A 63 REMARK 465 SER A 64 REMARK 465 THR A 65 REMARK 465 LEU A 66 REMARK 465 GLU A 67 REMARK 465 GLN A 68 REMARK 465 GLY A 69 REMARK 465 GLN A 70 REMARK 465 TRP A 71 REMARK 465 PRO A 72 REMARK 465 LEU A 73 REMARK 465 GLY A 74 REMARK 465 TRP A 75 REMARK 465 THR A 76 REMARK 465 GLN A 77 REMARK 465 MET A 78 REMARK 465 PHE A 79 REMARK 465 VAL A 80 REMARK 465 GLU A 81 REMARK 465 ALA A 82 REMARK 465 LEU A 83 REMARK 465 GLU A 84 REMARK 465 HIS A 85 REMARK 465 SER A 86 REMARK 465 GLY A 87 REMARK 465 ASN A 88 REMARK 465 PRO A 89 REMARK 465 LEU A 90 REMARK 465 ALA A 91 REMARK 465 ALA A 92 REMARK 465 ARG A 93 REMARK 465 TYR A 94 REMARK 465 VAL A 95 REMARK 465 LYS A 96 REMARK 465 PRO A 97 REMARK 465 THR A 98 REMARK 465 LEU A 99 REMARK 465 THR A 100 REMARK 465 ASP A 101 REMARK 465 LEU A 102 REMARK 465 PRO A 103 REMARK 465 SER A 104 REMARK 465 PRO A 105 REMARK 465 SER A 106 REMARK 465 SER A 107 REMARK 465 GLU A 108 REMARK 465 THR A 109 REMARK 465 ALA A 110 REMARK 465 HIS A 111 REMARK 465 ASP A 112 REMARK 465 GLU A 113 REMARK 465 CYS A 114 REMARK 465 LEU A 115 REMARK 465 HIS A 116 REMARK 465 LEU A 117 REMARK 465 LEU A 118 REMARK 465 THR A 119 REMARK 465 LEU A 120 REMARK 465 LEU A 121 REMARK 465 GLN A 122 REMARK 465 PRO A 123 REMARK 465 THR A 124 REMARK 465 LEU A 125 REMARK 465 VAL A 126 REMARK 465 ASP A 127 REMARK 465 LYS A 128 REMARK 465 LEU A 129 REMARK 465 LEU A 130 REMARK 465 ILE A 131 REMARK 465 ASN A 132 REMARK 465 ASP A 133 REMARK 465 VAL A 134 REMARK 465 LEU A 135 REMARK 465 ASP A 136 REMARK 465 THR A 137 REMARK 465 CYS A 138 REMARK 465 PHE A 139 REMARK 465 GLU A 140 REMARK 465 LYS A 141 REMARK 465 GLY A 142 REMARK 465 LEU A 143 REMARK 465 LEU A 144 REMARK 465 THR A 145 REMARK 465 VAL A 146 REMARK 465 GLU A 147 REMARK 465 ASP A 148 REMARK 465 ARG A 149 REMARK 465 ASN A 150 REMARK 465 ARG A 151 REMARK 465 ILE A 152 REMARK 465 SER A 153 REMARK 465 ALA A 154 REMARK 465 ALA A 155 REMARK 465 GLY A 156 REMARK 465 ASN A 157 REMARK 465 SER A 158 REMARK 465 GLY A 159 REMARK 465 ASN A 160 REMARK 465 GLU A 161 REMARK 465 SER A 162 REMARK 465 GLY A 163 REMARK 465 VAL A 164 REMARK 465 ARG A 165 REMARK 465 GLU A 166 REMARK 465 LEU A 167 REMARK 465 LEU A 168 REMARK 465 ARG A 169 REMARK 465 ARG A 170 REMARK 465 ILE A 171 REMARK 465 VAL A 172 REMARK 465 GLN A 173 REMARK 465 LYS A 174 REMARK 465 GLU A 175 REMARK 465 ASN A 176 REMARK 465 TRP A 177 REMARK 465 PHE A 178 REMARK 465 SER A 179 REMARK 465 THR A 180 REMARK 465 PHE A 181 REMARK 465 LEU A 182 REMARK 465 ASP A 183 REMARK 465 VAL A 184 REMARK 465 LEU A 185 REMARK 465 ARG A 186 REMARK 465 GLN A 187 REMARK 465 THR A 188 REMARK 465 GLY A 189 REMARK 465 ASN A 190 REMARK 465 ASP A 191 REMARK 465 ALA A 192 REMARK 465 LEU A 193 REMARK 465 PHE A 194 REMARK 465 GLN A 195 REMARK 465 GLU A 196 REMARK 465 LEU A 197 REMARK 465 THR A 198 REMARK 465 GLY A 199 REMARK 465 GLY A 200 REMARK 465 GLY A 201 REMARK 465 CYS A 202 REMARK 465 PRO A 203 REMARK 465 GLU A 204 REMARK 465 ASP A 205 REMARK 465 ASN A 206 REMARK 465 THR A 207 REMARK 465 ASP A 208 REMARK 465 LEU A 209 REMARK 465 ALA A 210 REMARK 465 ASN A 211 REMARK 465 SER A 212 REMARK 465 SER A 213 REMARK 465 HIS A 214 REMARK 465 ARG A 215 REMARK 465 ASP A 216 REMARK 465 GLY A 217 REMARK 465 PRO A 218 REMARK 465 ALA A 219 REMARK 465 ALA A 220 REMARK 465 ASN A 221 REMARK 465 GLU A 222 REMARK 465 CYS A 223 REMARK 465 LEU A 224 REMARK 465 LEU A 225 REMARK 465 PRO A 226 REMARK 465 ALA A 227 REMARK 465 VAL A 228 REMARK 465 ASP A 229 REMARK 465 GLU A 230 REMARK 465 SER A 231 REMARK 465 SER A 232 REMARK 465 LEU A 233 REMARK 465 GLU A 234 REMARK 465 THR A 235 REMARK 465 GLU A 236 REMARK 465 ALA A 237 REMARK 465 TRP A 238 REMARK 465 ASN A 239 REMARK 465 VAL A 240 REMARK 465 ASP A 241 REMARK 465 ASP A 242 REMARK 465 ILE A 243 REMARK 465 LEU A 244 REMARK 465 PRO A 245 REMARK 465 GLU A 246 REMARK 465 ALA A 247 REMARK 465 SER A 248 REMARK 465 CYS A 249 REMARK 465 THR A 250 REMARK 465 ASP A 251 REMARK 465 SER A 252 REMARK 465 SER A 253 REMARK 465 VAL A 254 REMARK 465 THR A 255 REMARK 465 THR A 256 REMARK 465 GLU A 257 REMARK 465 SER A 258 REMARK 465 ASP A 259 REMARK 465 THR A 260 REMARK 465 SER A 261 REMARK 465 LEU A 262 REMARK 465 ALA A 263 REMARK 465 GLU A 264 REMARK 465 GLY A 265 REMARK 465 SER A 266 REMARK 465 VAL A 267 REMARK 465 SER A 268 REMARK 465 CYS A 269 REMARK 465 PHE A 270 REMARK 465 ASP A 271 REMARK 465 GLU A 272 REMARK 465 SER A 273 REMARK 465 LEU A 274 REMARK 465 GLY A 275 REMARK 465 HIS A 276 REMARK 465 ASN A 277 REMARK 465 SER A 278 REMARK 465 ASN A 279 REMARK 465 MET A 280 REMARK 465 GLY A 281 REMARK 465 ARG A 282 REMARK 465 ASP A 283 REMARK 465 SER A 284 REMARK 465 GLY A 285 REMARK 465 THR A 286 REMARK 465 MET A 287 REMARK 465 GLY A 288 REMARK 465 SER A 289 REMARK 465 ASP A 290 REMARK 465 SER A 291 REMARK 465 ASP A 292 REMARK 465 GLU A 293 REMARK 465 SER A 294 REMARK 465 VAL A 295 REMARK 465 ILE A 296 REMARK 465 GLN A 297 REMARK 465 THR A 298 REMARK 465 LYS A 299 REMARK 465 ARG A 300 REMARK 465 VAL A 301 REMARK 465 SER A 302 REMARK 465 PRO A 303 REMARK 465 GLU A 304 REMARK 465 PRO A 305 REMARK 465 SER A 663 REMARK 465 LYS A 664 REMARK 465 LYS A 945 REMARK 465 ALA A 946 REMARK 465 LEU A 947 REMARK 465 GLN A 948 REMARK 465 LYS A 949 REMARK 465 LYS A 950 REMARK 465 PHE A 951 REMARK 465 ALA A 952 REMARK 465 ASP A 953 REMARK 465 TYR A 954 REMARK 465 TYR A 1021 REMARK 465 SER A 1022 REMARK 465 ASP A 1023 REMARK 465 GLU A 1024 REMARK 465 ASP A 1025 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HG CYS A 907 ZN ZN A 1104 1.11 REMARK 500 C GLU A 793 H GLU A 794 1.30 REMARK 500 C LYS A 884 H LYS A 885 1.33 REMARK 500 C MET A 886 H LYS A 887 1.33 REMARK 500 C LYS A 451 H GLU A 452 1.34 REMARK 500 C LYS A 887 H VAL A 888 1.35 REMARK 500 C GLU A 827 H SER A 828 1.36 REMARK 500 C ILE A 399 H SER A 400 1.38 REMARK 500 C ALA A 497 H LYS A 498 1.44 REMARK 500 O2B ADP A 1101 F3 ALF A 1102 1.64 REMARK 500 O2B ADP A 1101 AL ALF A 1102 1.69 REMARK 500 OG1 THR A 790 O2' U Y 6 1.99 REMARK 500 OG SER A 392 OD1 ASP A 394 2.06 REMARK 500 O2B ADP A 1101 F2 ALF A 1102 2.08 REMARK 500 O VAL A 341 OG1 THR A 344 2.09 REMARK 500 O3B ADP A 1101 F4 ALF A 1102 2.11 REMARK 500 PB ADP A 1101 AL ALF A 1102 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER A 400 C - N - CA ANGL. DEV. = 19.0 DEGREES REMARK 500 LYS A 498 C - N - CA ANGL. DEV. = 26.8 DEGREES REMARK 500 SER A 828 C - N - CA ANGL. DEV. = 16.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 399 -76.45 -101.58 REMARK 500 SER A 400 177.04 173.24 REMARK 500 SER A 407 -55.65 -121.80 REMARK 500 ASP A 409 -14.31 74.56 REMARK 500 THR A 449 92.86 -69.53 REMARK 500 ALA A 496 61.90 62.58 REMARK 500 LYS A 520 66.05 61.37 REMARK 500 LYS A 523 -35.88 -130.78 REMARK 500 GLU A 548 10.21 80.52 REMARK 500 PHE A 551 -60.49 -95.25 REMARK 500 SER A 572 -169.20 -161.93 REMARK 500 LYS A 597 -7.25 71.84 REMARK 500 SER A 666 118.11 -160.93 REMARK 500 TYR A 696 70.01 -102.45 REMARK 500 ASN A 698 145.38 -172.68 REMARK 500 GLU A 716 68.49 61.23 REMARK 500 GLU A 717 -3.96 79.36 REMARK 500 SER A 718 34.12 -93.28 REMARK 500 HIS A 759 49.79 -83.92 REMARK 500 ASP A 797 78.10 -68.35 REMARK 500 LYS A 894 -16.03 70.18 REMARK 500 GLN A 895 106.52 -161.69 REMARK 500 VAL A 914 -62.74 -124.35 REMARK 500 LEU A 938 -35.48 -130.52 REMARK 500 LYS A1001 -9.62 73.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 413 THR A 414 149.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1103 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 444 OD1 REMARK 620 2 ADP A1101 O3B 145.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 907 SG REMARK 620 2 CYS A 910 SG 94.8 REMARK 620 3 CYS A 962 SG 136.9 128.3 REMARK 620 4 CYS A 964 SG 107.7 89.8 78.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ALF A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-4338 RELATED DB: EMDB REMARK 900 MDA5-DSRNA COMPLEX FORMED WITH 1MM AMPPNP, LOW HELICAL TWIST CLASS REMARK 900 RELATED ID: EMD-4340 RELATED DB: EMDB REMARK 900 MDA5-DSRNA COMPLEX FORMED WITH 1MM AMPPNP, INTERMEDIATE HELICAL REMARK 900 TWIST CLASS REMARK 900 RELATED ID: EMD-4341 RELATED DB: EMDB REMARK 900 MDA5-DSRNA COMPLEX FORMED WITH 1MM AMPPNP, HIGH HELICAL TWIST CLASS REMARK 900 RELATED ID: EMD-0012 RELATED DB: EMDB REMARK 900 MDA5-DSRNA COMPLEX FORMED WITH 2.5MM AMPPNP, LOW HELICAL TWIST CLASS REMARK 900 RELATED ID: 6G19 RELATED DB: PDB REMARK 900 MDA5-DSRNA COMPLEX FORMED WITH 1MM AMPPNP, LOW HELICAL TWIST CLASS REMARK 900 RELATED ID: 6G1S RELATED DB: PDB REMARK 900 MDA5-DSRNA COMPLEX FORMED WITH 1MM AMPPNP, INTERMEDIATE HELICAL REMARK 900 TWIST CLASS REMARK 900 RELATED ID: 6G1X RELATED DB: PDB REMARK 900 MDA5-DSRNA COMPLEX FORMED WITH 1MM AMPPNP, HIGH HELICAL TWIST CLASS REMARK 900 RELATED ID: 6GJZ RELATED DB: PDB REMARK 900 MDA5-DSRNA COMPLEX FORMED WITH 2.5MM AMPPNP, LOW HELICAL TWIST CLASS REMARK 900 RELATED ID: EMD-0023 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF THE MDA5-DSRNA FILAMENT IN COMPLEX WITH ADP-ALF4 DBREF 6GKH A 1 1025 UNP Q8R5F7 IFIH1_MOUSE 1 1025 DBREF 6GKH X 1 15 PDB 6GKH 6GKH 1 15 DBREF 6GKH Y 1 15 PDB 6GKH 6GKH 1 15 SEQADV 6GKH A UNP Q8R5F7 ASP 646 DELETION SEQADV 6GKH A UNP Q8R5F7 LYS 647 DELETION SEQADV 6GKH A UNP Q8R5F7 SER 648 DELETION SEQADV 6GKH A UNP Q8R5F7 ASP 649 DELETION SEQADV 6GKH A UNP Q8R5F7 ASP 650 DELETION SEQADV 6GKH A UNP Q8R5F7 GLU 651 DELETION SEQADV 6GKH A UNP Q8R5F7 ALA 652 DELETION SEQADV 6GKH A UNP Q8R5F7 SER 653 DELETION SEQADV 6GKH A UNP Q8R5F7 SER 654 DELETION SEQADV 6GKH A UNP Q8R5F7 CYS 655 DELETION SEQADV 6GKH A UNP Q8R5F7 ASN 656 DELETION SEQADV 6GKH A UNP Q8R5F7 ASP 657 DELETION SEQADV 6GKH A UNP Q8R5F7 GLN 658 DELETION SEQADV 6GKH A UNP Q8R5F7 LEU 659 DELETION SEQADV 6GKH A UNP Q8R5F7 LYS 660 DELETION SEQADV 6GKH A UNP Q8R5F7 GLY 661 DELETION SEQADV 6GKH A UNP Q8R5F7 ASP 662 DELETION SEQADV 6GKH A UNP Q8R5F7 VAL 663 DELETION SEQRES 1 A 1007 MET SER ILE VAL CYS SER ALA GLU ASP SER PHE ARG ASN SEQRES 2 A 1007 LEU ILE LEU PHE PHE ARG PRO ARG LEU LYS MET TYR ILE SEQRES 3 A 1007 GLN VAL GLU PRO VAL LEU ASP HIS LEU ILE PHE LEU SER SEQRES 4 A 1007 ALA GLU THR LYS GLU GLN ILE LEU LYS LYS ILE ASN THR SEQRES 5 A 1007 CYS GLY ASN THR SER ALA ALA GLU LEU LEU LEU SER THR SEQRES 6 A 1007 LEU GLU GLN GLY GLN TRP PRO LEU GLY TRP THR GLN MET SEQRES 7 A 1007 PHE VAL GLU ALA LEU GLU HIS SER GLY ASN PRO LEU ALA SEQRES 8 A 1007 ALA ARG TYR VAL LYS PRO THR LEU THR ASP LEU PRO SER SEQRES 9 A 1007 PRO SER SER GLU THR ALA HIS ASP GLU CYS LEU HIS LEU SEQRES 10 A 1007 LEU THR LEU LEU GLN PRO THR LEU VAL ASP LYS LEU LEU SEQRES 11 A 1007 ILE ASN ASP VAL LEU ASP THR CYS PHE GLU LYS GLY LEU SEQRES 12 A 1007 LEU THR VAL GLU ASP ARG ASN ARG ILE SER ALA ALA GLY SEQRES 13 A 1007 ASN SER GLY ASN GLU SER GLY VAL ARG GLU LEU LEU ARG SEQRES 14 A 1007 ARG ILE VAL GLN LYS GLU ASN TRP PHE SER THR PHE LEU SEQRES 15 A 1007 ASP VAL LEU ARG GLN THR GLY ASN ASP ALA LEU PHE GLN SEQRES 16 A 1007 GLU LEU THR GLY GLY GLY CYS PRO GLU ASP ASN THR ASP SEQRES 17 A 1007 LEU ALA ASN SER SER HIS ARG ASP GLY PRO ALA ALA ASN SEQRES 18 A 1007 GLU CYS LEU LEU PRO ALA VAL ASP GLU SER SER LEU GLU SEQRES 19 A 1007 THR GLU ALA TRP ASN VAL ASP ASP ILE LEU PRO GLU ALA SEQRES 20 A 1007 SER CYS THR ASP SER SER VAL THR THR GLU SER ASP THR SEQRES 21 A 1007 SER LEU ALA GLU GLY SER VAL SER CYS PHE ASP GLU SER SEQRES 22 A 1007 LEU GLY HIS ASN SER ASN MET GLY ARG ASP SER GLY THR SEQRES 23 A 1007 MET GLY SER ASP SER ASP GLU SER VAL ILE GLN THR LYS SEQRES 24 A 1007 ARG VAL SER PRO GLU PRO GLU LEU GLN LEU ARG PRO TYR SEQRES 25 A 1007 GLN MET GLU VAL ALA GLN PRO ALA LEU ASP GLY LYS ASN SEQRES 26 A 1007 ILE ILE ILE CYS LEU PRO THR GLY SER GLY LYS THR ARG SEQRES 27 A 1007 VAL ALA VAL TYR ILE THR LYS ASP HIS LEU ASP LYS LYS SEQRES 28 A 1007 LYS GLN ALA SER GLU SER GLY LYS VAL ILE VAL LEU VAL SEQRES 29 A 1007 ASN LYS VAL MET LEU ALA GLU GLN LEU PHE ARG LYS GLU SEQRES 30 A 1007 PHE ASN PRO TYR LEU LYS LYS TRP TYR ARG ILE ILE GLY SEQRES 31 A 1007 LEU SER GLY ASP THR GLN LEU LYS ILE SER PHE PRO GLU SEQRES 32 A 1007 VAL VAL LYS SER TYR ASP VAL ILE ILE SER THR ALA GLN SEQRES 33 A 1007 ILE LEU GLU ASN SER LEU LEU ASN LEU GLU SER GLY ASP SEQRES 34 A 1007 ASP ASP GLY VAL GLN LEU SER ASP PHE SER LEU ILE ILE SEQRES 35 A 1007 ILE ASP GLU CYS HIS HIS THR ASN LYS GLU ALA VAL TYR SEQRES 36 A 1007 ASN ASN ILE MET ARG ARG TYR LEU LYS GLN LYS LEU ARG SEQRES 37 A 1007 ASN ASN ASP LEU LYS LYS GLN ASN LYS PRO ALA ILE PRO SEQRES 38 A 1007 LEU PRO GLN ILE LEU GLY LEU THR ALA SER PRO GLY VAL SEQRES 39 A 1007 GLY ALA ALA LYS LYS GLN SER GLU ALA GLU LYS HIS ILE SEQRES 40 A 1007 LEU ASN ILE CYS ALA ASN LEU ASP ALA PHE THR ILE LYS SEQRES 41 A 1007 THR VAL LYS GLU ASN LEU GLY GLN LEU LYS HIS GLN ILE SEQRES 42 A 1007 LYS GLU PRO CYS LYS LYS PHE VAL ILE ALA ASP ASP THR SEQRES 43 A 1007 ARG GLU ASN PRO PHE LYS GLU LYS LEU LEU GLU ILE MET SEQRES 44 A 1007 ALA SER ILE GLN THR TYR CYS GLN LYS SER PRO MET SER SEQRES 45 A 1007 ASP PHE GLY THR GLN HIS TYR GLU GLN TRP ALA ILE GLN SEQRES 46 A 1007 MET GLU LYS LYS ALA ALA LYS ASP GLY ASN ARG LYS ASP SEQRES 47 A 1007 ARG VAL CYS ALA GLU HIS LEU ARG LYS TYR ASN GLU ALA SEQRES 48 A 1007 LEU GLN ILE ASN ASP THR ILE ARG MET ILE ASP ALA TYR SEQRES 49 A 1007 SER HIS LEU GLU THR PHE TYR THR ASP GLU LYS GLU LYS SEQRES 50 A 1007 LYS PHE ALA VAL LEU ASN ASP SER LYS LYS SER LEU LYS SEQRES 51 A 1007 LEU ASP GLU THR ASP GLU PHE LEU MET ASN LEU PHE PHE SEQRES 52 A 1007 ASP ASN LYS LYS MET LEU LYS LYS LEU ALA GLU ASN PRO SEQRES 53 A 1007 LYS TYR GLU ASN GLU LYS LEU ILE LYS LEU ARG ASN THR SEQRES 54 A 1007 ILE LEU GLU GLN PHE THR ARG SER GLU GLU SER SER ARG SEQRES 55 A 1007 GLY ILE ILE PHE THR LYS THR ARG GLN SER THR TYR ALA SEQRES 56 A 1007 LEU SER GLN TRP ILE MET GLU ASN ALA LYS PHE ALA GLU SEQRES 57 A 1007 VAL GLY VAL LYS ALA HIS HIS LEU ILE GLY ALA GLY HIS SEQRES 58 A 1007 SER SER GLU VAL LYS PRO MET THR GLN THR GLU GLN LYS SEQRES 59 A 1007 GLU VAL ILE SER LYS PHE ARG THR GLY GLU ILE ASN LEU SEQRES 60 A 1007 LEU ILE ALA THR THR VAL ALA GLU GLU GLY LEU ASP ILE SEQRES 61 A 1007 LYS GLU CYS ASN ILE VAL ILE ARG TYR GLY LEU VAL THR SEQRES 62 A 1007 ASN GLU ILE ALA MET VAL GLN ALA ARG GLY ARG ALA ARG SEQRES 63 A 1007 ALA ASP GLU SER THR TYR VAL LEU VAL THR SER SER GLY SEQRES 64 A 1007 SER GLY VAL THR GLU ARG GLU ILE VAL ASN ASP PHE ARG SEQRES 65 A 1007 GLU LYS MET MET TYR LYS ALA ILE ASN ARG VAL GLN ASN SEQRES 66 A 1007 MET LYS PRO GLU GLU TYR ALA HIS LYS ILE LEU GLU LEU SEQRES 67 A 1007 GLN VAL GLN SER ILE LEU GLU LYS LYS MET LYS VAL LYS SEQRES 68 A 1007 ARG SER ILE ALA LYS GLN TYR ASN ASP ASN PRO SER LEU SEQRES 69 A 1007 ILE THR LEU LEU CYS LYS ASN CYS SER MET LEU VAL CYS SEQRES 70 A 1007 SER GLY GLU ASN ILE HIS VAL ILE GLU LYS MET HIS HIS SEQRES 71 A 1007 VAL ASN MET THR PRO GLU PHE LYS GLY LEU TYR ILE VAL SEQRES 72 A 1007 ARG GLU ASN LYS ALA LEU GLN LYS LYS PHE ALA ASP TYR SEQRES 73 A 1007 GLN THR ASN GLY GLU ILE ILE CYS LYS CYS GLY GLN ALA SEQRES 74 A 1007 TRP GLY THR MET MET VAL HIS LYS GLY LEU ASP LEU PRO SEQRES 75 A 1007 CYS LEU LYS ILE ARG ASN PHE VAL VAL ASN PHE LYS ASN SEQRES 76 A 1007 ASN SER PRO LYS LYS GLN TYR LYS LYS TRP VAL GLU LEU SEQRES 77 A 1007 PRO ILE ARG PHE PRO ASP LEU ASP TYR SER GLU TYR CYS SEQRES 78 A 1007 LEU TYR SER ASP GLU ASP SEQRES 1 X 15 G U C A A G C C G A G G A SEQRES 2 X 15 G A SEQRES 1 Y 15 U C U C C U C G G C U U G SEQRES 2 Y 15 A C HET ADP A1101 39 HET ALF A1102 5 HET MG A1103 1 HET ZN A1104 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ALF TETRAFLUOROALUMINATE ION HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 ALF AL F4 1- FORMUL 6 MG MG 2+ FORMUL 7 ZN ZN 2+ HELIX 1 AA1 ARG A 310 GLN A 318 1 9 HELIX 2 AA2 PRO A 319 ASP A 322 5 4 HELIX 3 AA3 GLY A 335 ALA A 354 1 20 HELIX 4 AA4 VAL A 367 LYS A 376 1 10 HELIX 5 AA5 PHE A 378 LYS A 383 1 6 HELIX 6 AA6 SER A 400 LYS A 406 1 7 HELIX 7 AA7 ALA A 415 GLY A 428 1 14 HELIX 8 AA8 GLN A 434 PHE A 438 5 5 HELIX 9 AA9 CYS A 446 THR A 449 5 4 HELIX 10 AB1 ALA A 453 LYS A 474 1 22 HELIX 11 AB2 LYS A 499 ASN A 513 1 15 HELIX 12 AB3 ASN A 525 ILE A 533 1 9 HELIX 13 AB4 PHE A 551 GLN A 567 1 17 HELIX 14 AB5 THR A 576 GLY A 594 1 19 HELIX 15 AB6 ASP A 598 ASP A 616 1 19 HELIX 16 AB7 ARG A 619 ASN A 643 1 25 HELIX 17 AB8 GLU A 671 GLU A 692 1 22 HELIX 18 AB9 ASN A 698 GLU A 716 1 19 HELIX 19 AC1 ARG A 728 ASN A 741 1 14 HELIX 20 AC2 ALA A 742 VAL A 747 1 6 HELIX 21 AC3 THR A 767 THR A 780 1 14 HELIX 22 AC4 THR A 789 GLU A 793 5 5 HELIX 23 AC5 ASN A 812 GLY A 821 1 10 HELIX 24 AC6 GLY A 839 ASN A 863 1 25 HELIX 25 AC7 LYS A 865 ARG A 890 1 26 HELIX 26 AC8 THR A 932 GLY A 937 1 6 SHEET 1 AA1 6 ILE A 326 CYS A 329 0 SHEET 2 AA1 6 GLN A 484 THR A 489 1 O GLY A 487 N ILE A 326 SHEET 3 AA1 6 LEU A 440 ASP A 444 1 N ILE A 441 O GLN A 484 SHEET 4 AA1 6 VAL A 360 VAL A 364 1 N LEU A 363 O ILE A 442 SHEET 5 AA1 6 VAL A 410 THR A 414 1 O ILE A 411 N VAL A 360 SHEET 6 AA1 6 ILE A 389 GLY A 390 1 N ILE A 389 O VAL A 410 SHEET 1 AA2 2 PHE A 540 ALA A 543 0 SHEET 2 AA2 2 LEU A 832 SER A 835 1 O THR A 834 N VAL A 541 SHEET 1 AA3 4 ALA A 751 HIS A 752 0 SHEET 2 AA3 4 LEU A 785 ALA A 788 1 O ILE A 787 N HIS A 752 SHEET 3 AA3 4 GLY A 721 PHE A 724 1 N ILE A 723 O LEU A 786 SHEET 4 AA3 4 ILE A 803 VAL A 804 1 O ILE A 803 N ILE A 722 SHEET 1 AA4 3 LEU A 913 CYS A 915 0 SHEET 2 AA4 3 ILE A 903 CYS A 907 -1 N LEU A 905 O CYS A 915 SHEET 3 AA4 3 PHE A 987 PHE A 991 -1 O VAL A 988 N LEU A 906 SHEET 1 AA5 2 ILE A 920 ILE A 923 0 SHEET 2 AA5 2 HIS A 927 ASN A 930 -1 O VAL A 929 N HIS A 921 SHEET 1 AA6 4 ILE A 940 ARG A 942 0 SHEET 2 AA6 4 GLU A 959 ILE A 961 -1 O ILE A 961 N ILE A 940 SHEET 3 AA6 4 ALA A 967 HIS A 974 -1 O GLY A 969 N ILE A 960 SHEET 4 AA6 4 LEU A 977 LEU A 982 -1 O LEU A 977 N HIS A 974 SSBOND 1 CYS A 962 CYS A 964 1555 1555 2.85 LINK OD1 ASP A 444 MG MG A1103 1555 1555 2.95 LINK SG CYS A 907 ZN ZN A1104 1555 1555 2.25 LINK SG CYS A 910 ZN ZN A1104 1555 1555 2.25 LINK SG CYS A 962 ZN ZN A1104 1555 1555 2.18 LINK SG CYS A 964 ZN ZN A1104 1555 1555 2.31 LINK O3B ADP A1101 MG MG A1103 1555 1555 2.16 SITE 1 AC1 13 GLN A 308 LEU A 309 ARG A 310 GLN A 313 SITE 2 AC1 13 GLY A 333 GLY A 335 LYS A 336 THR A 337 SITE 3 AC1 13 ARG A 338 ASP A 797 ARG A 824 ALF A1102 SITE 4 AC1 13 MG A1103 SITE 1 AC2 7 THR A 332 LYS A 336 ASP A 444 ARG A 822 SITE 2 AC2 7 ARG A 824 ADP A1101 MG A1103 SITE 1 AC3 3 ASP A 444 ADP A1101 ALF A1102 SITE 1 AC4 5 CYS A 907 CYS A 910 MET A 912 CYS A 962 SITE 2 AC4 5 CYS A 964 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000