HEADER IMMUNE SYSTEM 16-APR-24 9F0J TITLE CRYO-EM STRUCTURE OF THE I923V MDA5-DSRNA FILAMENT WITHOUT NUCLEOTIDE 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 OTHER_DETAILS: N-TERMINAL HEXAHISTIDINE TAG AND TEV CLEAVAGE SITE; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: RNA (5'-UCCAUGCGCAUGACG-3'); COMPND 13 CHAIN: X; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: OLIGORIBONUCLEOTIDE; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: RNA (5'-CGUCAUGCGCAUGGA-3'); COMPND 18 CHAIN: Z; COMPND 19 ENGINEERED: YES; COMPND 20 OTHER_DETAILS: OLIGORIBONUCLEOTIDE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: IFIH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLYSS; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_TAXID: 10090; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 16 ORGANISM_TAXID: 10090 KEYWDS PROTEIN-RNA COMPLEX, HELICAL FILAMENT, ATPASE, INNATE IMMUNE KEYWDS 2 RECEPTOR, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR R.SINGH,A.HERRERO DEL VALLE,Y.MODIS REVDAT 2 18-JUN-25 9F0J 1 JRNL REVDAT 1 26-FEB-25 9F0J 0 JRNL AUTH R.SINGH,J.D.JOINER,A.HERRERO DEL VALLE,M.ZWAAGSTRA,I.JOBE, JRNL AUTH 2 B.J.FERGUSON,F.J.M.VAN KUPPEVELD,Y.MODIS JRNL TITL MOLECULAR BASIS OF AUTOIMMUNE DISEASE PROTECTION BY MDA5 JRNL TITL 2 VARIANTS. JRNL REF CELL REP V. 44 15754 2025 JRNL REFN ESSN 2211-1247 JRNL PMID 40450684 JRNL DOI 10.1016/J.CELREP.2025.115754 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.SINGH,A.HERRERO DEL VALLE,J.D.JOINER,M.ZWAAGSTRA, REMARK 1 AUTH 2 B.J.FERGUSON,F.J.M.VAN KUPPEVELD,Y.MODIS REMARK 1 TITL MOLECULAR BASIS OF AUTOIMMUNE DISEASE PROTECTION BY MDA5 REMARK 1 TITL 2 VARIANTS REMARK 1 REF BIORXIV 2024 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2024.10.03.616466 REMARK 2 REMARK 2 RESOLUTION. 3.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOLO, EPU, CTFFIND, UCSF CHIMERA, REMARK 3 RELION, RELION, RELION, RELION, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : BACK PROJECTION REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7BKQ REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CROSS-CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : 90.000 REMARK 3 REMARK 3 FITTING PROCEDURE : INITIAL LOCAL FITTING WITH FIT-IN-MAP IN REMARK 3 CHIMERA FOLLOWED BY REAL SPACE REFINEMENT IN PHENIX. 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) : 3.350 REMARK 3 NUMBER OF PARTICLES : 547562 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 9F0J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-APR-24. REMARK 100 THE DEPOSITION ID IS D_1292137476. 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 : FILAMENT REMARK 245 PARTICLE TYPE : HELICAL REMARK 245 NAME OF SAMPLE : MOUSE MDA5 I923V IN COMPLEX REMARK 245 WITH DOUBLE STRANDED RNA; MOUSE REMARK 245 MDA5 I923V; DOUBLE STRANDED RNA REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.50 REMARK 245 SAMPLE SUPPORT DETAILS : 30 MA, EDWARDS 12E6/531 GLOW REMARK 245 DISCHARGER REMARK 245 SAMPLE VITRIFICATION DETAILS : 2-4 S BLOTTING, 15 S WAIT TIME REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.70 REMARK 245 SAMPLE DETAILS : HELICAL FILAMENT. STRUCTURE REMARK 245 DETERMINED WITH HELICAL SYMMETRY AVERAGING. 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 : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : DARK FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4400.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 REMARK 245 CALIBRATED MAGNIFICATION : NULL 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X, Z 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 350 BIOMT1 2 -0.028400 0.999500 0.013420 1.50300 REMARK 350 BIOMT2 2 -0.999600 -0.028400 -0.000367 234.50000 REMARK 350 BIOMT3 2 0.000015 -0.013430 0.999900 -43.28000 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 -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 ARG A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 GLY A 0 REMARK 465 HIS A 1 REMARK 465 MET 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 GLU A 306 REMARK 465 GLU A 535 REMARK 465 PRO A 536 REMARK 465 CYS A 537 REMARK 465 LYS A 538 REMARK 465 ASP A 544 REMARK 465 ASP A 545 REMARK 465 THR A 546 REMARK 465 ARG A 547 REMARK 465 GLU A 548 REMARK 465 SER A 663 REMARK 465 LYS A 664 REMARK 465 LYS A 665 REMARK 465 SER A 666 REMARK 465 LEU A 667 REMARK 465 LYS A 695 REMARK 465 TYR A 696 REMARK 465 GLU A 697 REMARK 465 ASN A 698 REMARK 465 GLU A 716 REMARK 465 GLU A 717 REMARK 465 VAL A 810 REMARK 465 THR A 811 REMARK 465 ASN A 812 REMARK 465 GLU A 813 REMARK 465 ILE A 814 REMARK 465 ALA A 815 REMARK 465 MET A 816 REMARK 465 VAL A 817 REMARK 465 GLN A 818 REMARK 465 ALA A 819 REMARK 465 ARG A 820 REMARK 465 GLY A 821 REMARK 465 ARG A 822 REMARK 465 ALA A 823 REMARK 465 ARG A 824 REMARK 465 ALA A 825 REMARK 465 ASP A 826 REMARK 465 GLU A 827 REMARK 465 SER A 835 REMARK 465 SER A 836 REMARK 465 GLY A 837 REMARK 465 SER A 838 REMARK 465 GLY A 839 REMARK 465 VAL A 840 REMARK 465 THR A 841 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 GLN A 955 REMARK 465 THR A 956 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 353 CG CD OE1 NE2 REMARK 470 ARG A 599 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 689 CG CD CE NZ REMARK 470 VAL A 749 CG1 CG2 REMARK 470 LEU A 796 CG CD1 CD2 REMARK 470 TYR A 896 CG CD1 CD2 CE1 CE2 CZ OH 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 O ARG A 728 HG1 THR A 731 1.59 REMARK 500 O LEU A 472 H ASN A 476 1.59 REMARK 500 NH2 ARG A 779 OD1 ASP A 797 2.08 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 ASP A 430 -4.97 75.38 REMARK 500 GLU A 452 25.17 -78.29 REMARK 500 MET A 571 -4.29 70.66 REMARK 500 LYS A1001 -8.12 73.24 REMARK 500 TYR A1018 -6.48 75.71 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 ZN A1101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 907 SG REMARK 620 2 CYS A 910 SG 108.1 REMARK 620 3 CYS A 962 SG 110.3 114.0 REMARK 620 4 CYS A 964 SG 110.9 105.6 108.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-50111 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE I923V MDA5-DSRNA FILAMENT WITHOUT REMARK 900 NUCLEOTIDE DBREF 9F0J A 3 1025 UNP Q8R5F7 IFIH1_MOUSE 3 1025 DBREF 9F0J X 1 15 PDB 9F0J 9F0J 1 15 DBREF 9F0J Z 1 15 PDB 9F0J 9F0J 1 15 SEQADV 9F0J MET A -20 UNP Q8R5F7 INITIATING METHIONINE SEQADV 9F0J GLY A -19 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J SER A -18 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J SER A -17 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J HIS A -16 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J HIS A -15 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J HIS A -14 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J HIS A -13 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J HIS A -12 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J HIS A -11 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J SER A -10 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J SER A -9 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J GLY A -8 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J ARG A -7 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J GLU A -6 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J ASN A -5 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J LEU A -4 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J TYR A -3 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J PHE A -2 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J GLN A -1 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J GLY A 0 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J HIS A 1 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J MET A 2 UNP Q8R5F7 EXPRESSION TAG SEQADV 9F0J A UNP Q8R5F7 ASP 646 DELETION SEQADV 9F0J A UNP Q8R5F7 LYS 647 DELETION SEQADV 9F0J A UNP Q8R5F7 SER 648 DELETION SEQADV 9F0J A UNP Q8R5F7 ASP 649 DELETION SEQADV 9F0J A UNP Q8R5F7 ASP 650 DELETION SEQADV 9F0J A UNP Q8R5F7 GLU 651 DELETION SEQADV 9F0J A UNP Q8R5F7 ALA 652 DELETION SEQADV 9F0J A UNP Q8R5F7 SER 653 DELETION SEQADV 9F0J A UNP Q8R5F7 SER 654 DELETION SEQADV 9F0J A UNP Q8R5F7 CYS 655 DELETION SEQADV 9F0J A UNP Q8R5F7 ASN 656 DELETION SEQADV 9F0J A UNP Q8R5F7 ASP 657 DELETION SEQADV 9F0J A UNP Q8R5F7 GLN 658 DELETION SEQADV 9F0J A UNP Q8R5F7 LEU 659 DELETION SEQADV 9F0J A UNP Q8R5F7 LYS 660 DELETION SEQADV 9F0J A UNP Q8R5F7 GLY 661 DELETION SEQADV 9F0J A UNP Q8R5F7 ASP 662 DELETION SEQADV 9F0J A UNP Q8R5F7 VAL 663 DELETION SEQADV 9F0J VAL A 923 UNP Q8R5F7 ILE 923 ENGINEERED MUTATION SEQRES 1 A 1028 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 1028 ARG GLU ASN LEU TYR PHE GLN GLY HIS MET ILE VAL CYS SEQRES 3 A 1028 SER ALA GLU ASP SER PHE ARG ASN LEU ILE LEU PHE PHE SEQRES 4 A 1028 ARG PRO ARG LEU LYS MET TYR ILE GLN VAL GLU PRO VAL SEQRES 5 A 1028 LEU ASP HIS LEU ILE PHE LEU SER ALA GLU THR LYS GLU SEQRES 6 A 1028 GLN ILE LEU LYS LYS ILE ASN THR CYS GLY ASN THR SER SEQRES 7 A 1028 ALA ALA GLU LEU LEU LEU SER THR LEU GLU GLN GLY GLN SEQRES 8 A 1028 TRP PRO LEU GLY TRP THR GLN MET PHE VAL GLU ALA LEU SEQRES 9 A 1028 GLU HIS SER GLY ASN PRO LEU ALA ALA ARG TYR VAL LYS SEQRES 10 A 1028 PRO THR LEU THR ASP LEU PRO SER PRO SER SER GLU THR SEQRES 11 A 1028 ALA HIS ASP GLU CYS LEU HIS LEU LEU THR LEU LEU GLN SEQRES 12 A 1028 PRO THR LEU VAL ASP LYS LEU LEU ILE ASN ASP VAL LEU SEQRES 13 A 1028 ASP THR CYS PHE GLU LYS GLY LEU LEU THR VAL GLU ASP SEQRES 14 A 1028 ARG ASN ARG ILE SER ALA ALA GLY ASN SER GLY ASN GLU SEQRES 15 A 1028 SER GLY VAL ARG GLU LEU LEU ARG ARG ILE VAL GLN LYS SEQRES 16 A 1028 GLU ASN TRP PHE SER THR PHE LEU ASP VAL LEU ARG GLN SEQRES 17 A 1028 THR GLY ASN ASP ALA LEU PHE GLN GLU LEU THR GLY GLY SEQRES 18 A 1028 GLY CYS PRO GLU ASP ASN THR ASP LEU ALA ASN SER SER SEQRES 19 A 1028 HIS ARG ASP GLY PRO ALA ALA ASN GLU CYS LEU LEU PRO SEQRES 20 A 1028 ALA VAL ASP GLU SER SER LEU GLU THR GLU ALA TRP ASN SEQRES 21 A 1028 VAL ASP ASP ILE LEU PRO GLU ALA SER CYS THR ASP SER SEQRES 22 A 1028 SER VAL THR THR GLU SER ASP THR SER LEU ALA GLU GLY SEQRES 23 A 1028 SER VAL SER CYS PHE ASP GLU SER LEU GLY HIS ASN SER SEQRES 24 A 1028 ASN MET GLY ARG ASP SER GLY THR MET GLY SER ASP SER SEQRES 25 A 1028 ASP GLU SER VAL ILE GLN THR LYS ARG VAL SER PRO GLU SEQRES 26 A 1028 PRO GLU LEU GLN LEU ARG PRO TYR GLN MET GLU VAL ALA SEQRES 27 A 1028 GLN PRO ALA LEU ASP GLY LYS ASN ILE ILE ILE CYS LEU SEQRES 28 A 1028 PRO THR GLY SER GLY LYS THR ARG VAL ALA VAL TYR ILE SEQRES 29 A 1028 THR LYS ASP HIS LEU ASP LYS LYS LYS GLN ALA SER GLU SEQRES 30 A 1028 SER GLY LYS VAL ILE VAL LEU VAL ASN LYS VAL MET LEU SEQRES 31 A 1028 ALA GLU GLN LEU PHE ARG LYS GLU PHE ASN PRO TYR LEU SEQRES 32 A 1028 LYS LYS TRP TYR ARG ILE ILE GLY LEU SER GLY ASP THR SEQRES 33 A 1028 GLN LEU LYS ILE SER PHE PRO GLU VAL VAL LYS SER TYR SEQRES 34 A 1028 ASP VAL ILE ILE SER THR ALA GLN ILE LEU GLU ASN SER SEQRES 35 A 1028 LEU LEU ASN LEU GLU SER GLY ASP ASP ASP GLY VAL GLN SEQRES 36 A 1028 LEU SER ASP PHE SER LEU ILE ILE ILE ASP GLU CYS HIS SEQRES 37 A 1028 HIS THR ASN LYS GLU ALA VAL TYR ASN ASN ILE MET ARG SEQRES 38 A 1028 ARG TYR LEU LYS GLN LYS LEU ARG ASN ASN ASP LEU LYS SEQRES 39 A 1028 LYS GLN ASN LYS PRO ALA ILE PRO LEU PRO GLN ILE LEU SEQRES 40 A 1028 GLY LEU THR ALA SER PRO GLY VAL GLY ALA ALA LYS LYS SEQRES 41 A 1028 GLN SER GLU ALA GLU LYS HIS ILE LEU ASN ILE CYS ALA SEQRES 42 A 1028 ASN LEU ASP ALA PHE THR ILE LYS THR VAL LYS GLU ASN SEQRES 43 A 1028 LEU GLY GLN LEU LYS HIS GLN ILE LYS GLU PRO CYS LYS SEQRES 44 A 1028 LYS PHE VAL ILE ALA ASP ASP THR ARG GLU ASN PRO PHE SEQRES 45 A 1028 LYS GLU LYS LEU LEU GLU ILE MET ALA SER ILE GLN THR SEQRES 46 A 1028 TYR CYS GLN LYS SER PRO MET SER ASP PHE GLY THR GLN SEQRES 47 A 1028 HIS TYR GLU GLN TRP ALA ILE GLN MET GLU LYS LYS ALA SEQRES 48 A 1028 ALA LYS ASP GLY ASN ARG LYS ASP ARG VAL CYS ALA GLU SEQRES 49 A 1028 HIS LEU ARG LYS TYR ASN GLU ALA LEU GLN ILE ASN ASP SEQRES 50 A 1028 THR ILE ARG MET ILE ASP ALA TYR SER HIS LEU GLU THR SEQRES 51 A 1028 PHE TYR THR ASP GLU LYS GLU LYS LYS PHE ALA VAL LEU SEQRES 52 A 1028 ASN ASP SER LYS LYS SER LEU LYS LEU ASP GLU THR ASP SEQRES 53 A 1028 GLU PHE LEU MET ASN LEU PHE PHE ASP ASN LYS LYS MET SEQRES 54 A 1028 LEU LYS LYS LEU ALA GLU ASN PRO LYS TYR GLU ASN GLU SEQRES 55 A 1028 LYS LEU ILE LYS LEU ARG ASN THR ILE LEU GLU GLN PHE SEQRES 56 A 1028 THR ARG SER GLU GLU SER SER ARG GLY ILE ILE PHE THR SEQRES 57 A 1028 LYS THR ARG GLN SER THR TYR ALA LEU SER GLN TRP ILE SEQRES 58 A 1028 MET GLU ASN ALA LYS PHE ALA GLU VAL GLY VAL LYS ALA SEQRES 59 A 1028 HIS HIS LEU ILE GLY ALA GLY HIS SER SER GLU VAL LYS SEQRES 60 A 1028 PRO MET THR GLN THR GLU GLN LYS GLU VAL ILE SER LYS SEQRES 61 A 1028 PHE ARG THR GLY GLU ILE ASN LEU LEU ILE ALA THR THR SEQRES 62 A 1028 VAL ALA GLU GLU GLY LEU ASP ILE LYS GLU CYS ASN ILE SEQRES 63 A 1028 VAL ILE ARG TYR GLY LEU VAL THR ASN GLU ILE ALA MET SEQRES 64 A 1028 VAL GLN ALA ARG GLY ARG ALA ARG ALA ASP GLU SER THR SEQRES 65 A 1028 TYR VAL LEU VAL THR SER SER GLY SER GLY VAL THR GLU SEQRES 66 A 1028 ARG GLU ILE VAL ASN ASP PHE ARG GLU LYS MET MET TYR SEQRES 67 A 1028 LYS ALA ILE ASN ARG VAL GLN ASN MET LYS PRO GLU GLU SEQRES 68 A 1028 TYR ALA HIS LYS ILE LEU GLU LEU GLN VAL GLN SER ILE SEQRES 69 A 1028 LEU GLU LYS LYS MET LYS VAL LYS ARG SER ILE ALA LYS SEQRES 70 A 1028 GLN TYR ASN ASP ASN PRO SER LEU ILE THR LEU LEU CYS SEQRES 71 A 1028 LYS ASN CYS SER MET LEU VAL CYS SER GLY GLU ASN ILE SEQRES 72 A 1028 HIS VAL VAL GLU LYS MET HIS HIS VAL ASN MET THR PRO SEQRES 73 A 1028 GLU PHE LYS GLY LEU TYR ILE VAL ARG GLU ASN LYS ALA SEQRES 74 A 1028 LEU GLN LYS LYS PHE ALA ASP TYR GLN THR ASN GLY GLU SEQRES 75 A 1028 ILE ILE CYS LYS CYS GLY GLN ALA TRP GLY THR MET MET SEQRES 76 A 1028 VAL HIS LYS GLY LEU ASP LEU PRO CYS LEU LYS ILE ARG SEQRES 77 A 1028 ASN PHE VAL VAL ASN PHE LYS ASN ASN SER PRO LYS LYS SEQRES 78 A 1028 GLN TYR LYS LYS TRP VAL GLU LEU PRO ILE ARG PHE PRO SEQRES 79 A 1028 ASP LEU ASP TYR SER GLU TYR CYS LEU TYR SER ASP GLU SEQRES 80 A 1028 ASP SEQRES 1 X 15 U C C A U G C G C A U G A SEQRES 2 X 15 C G SEQRES 1 Z 15 C G U C A U G C G C A U G SEQRES 2 Z 15 G A HET ZN A1101 1 HETNAM ZN ZINC ION FORMUL 4 ZN ZN 2+ HELIX 1 AA1 ARG A 310 GLN A 318 1 9 HELIX 2 AA2 PRO A 319 GLY A 323 5 5 HELIX 3 AA3 GLY A 335 SER A 355 1 21 HELIX 4 AA4 LYS A 366 GLU A 377 1 12 HELIX 5 AA5 GLU A 377 LYS A 383 1 7 HELIX 6 AA6 SER A 400 SER A 407 1 8 HELIX 7 AA7 ALA A 415 SER A 427 1 13 HELIX 8 AA8 GLU A 445 THR A 449 5 5 HELIX 9 AA9 ALA A 453 ASN A 476 1 24 HELIX 10 AB1 LYS A 499 ASP A 515 1 17 HELIX 11 AB2 LEU A 526 ILE A 533 1 8 HELIX 12 AB3 PRO A 550 GLN A 567 1 18 HELIX 13 AB4 THR A 576 GLY A 594 1 19 HELIX 14 AB5 ASP A 598 ILE A 618 1 21 HELIX 15 AB6 ARG A 619 ASN A 643 1 25 HELIX 16 AB7 ASP A 670 GLU A 692 1 23 HELIX 17 AB8 LYS A 700 PHE A 712 1 13 HELIX 18 AB9 THR A 727 ASN A 741 1 15 HELIX 19 AC1 ALA A 742 GLY A 748 1 7 HELIX 20 AC2 THR A 767 GLY A 781 1 15 HELIX 21 AC3 THR A 790 GLU A 794 5 5 HELIX 22 AC4 ARG A 843 ASN A 863 1 21 HELIX 23 AC5 LYS A 865 GLN A 895 1 31 HELIX 24 AC6 THR A 932 GLY A 937 1 6 HELIX 25 AC7 LYS A 1002 LEU A 1006 5 5 SHEET 1 AA1 6 ILE A 328 CYS A 329 0 SHEET 2 AA1 6 GLN A 484 THR A 489 1 O GLY A 487 N ILE A 328 SHEET 3 AA1 6 LEU A 440 ILE A 443 1 N ILE A 441 O LEU A 486 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 362 SHEET 6 AA1 6 ILE A 388 GLY A 390 1 N ILE A 389 O ILE A 412 SHEET 1 AA2 5 ALA A 751 LEU A 754 0 SHEET 2 AA2 5 LEU A 785 ALA A 788 1 O ILE A 787 N HIS A 752 SHEET 3 AA2 5 GLY A 721 PHE A 724 1 N ILE A 723 O ALA A 788 SHEET 4 AA2 5 ILE A 803 TYR A 807 1 O ILE A 805 N PHE A 724 SHEET 5 AA2 5 THR A 829 VAL A 833 1 O VAL A 831 N VAL A 804 SHEET 1 AA3 3 LEU A 913 SER A 916 0 SHEET 2 AA3 3 ILE A 903 CYS A 907 -1 N LEU A 905 O VAL A 914 SHEET 3 AA3 3 PHE A 987 PHE A 991 -1 O VAL A 988 N LEU A 906 SHEET 1 AA4 2 ILE A 920 VAL A 923 0 SHEET 2 AA4 2 HIS A 927 ASN A 930 -1 O HIS A 927 N VAL A 923 SHEET 1 AA5 4 ILE A 940 ARG A 942 0 SHEET 2 AA5 4 GLU A 959 ILE A 961 -1 O ILE A 961 N ILE A 940 SHEET 3 AA5 4 ALA A 967 HIS A 974 -1 O TRP A 968 N ILE A 960 SHEET 4 AA5 4 LEU A 977 LEU A 982 -1 O LEU A 979 N MET A 972 LINK SG CYS A 907 ZN ZN A1101 1555 1555 2.33 LINK SG CYS A 910 ZN ZN A1101 1555 1555 2.33 LINK SG CYS A 962 ZN ZN A1101 1555 1555 2.33 LINK SG CYS A 964 ZN ZN A1101 1555 1555 2.33 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 TER 10404 LEU A1020 TER 10885 G X 15 TER 11370 A Z 15 HETATM11371 ZN ZN A1101 145.479 118.187 114.722 1.00138.07 ZN CONECT 873111371 CONECT 877711371 CONECT 942611371 CONECT 945811371 CONECT11371 8731 8777 9426 9458 MASTER 571 0 1 25 20 0 0 6 5782 3 5 84 END