HEADER STRUCTURAL PROTEIN 08-FEB-23 8G3K TITLE CRYO-EM IMAGING SCAFFOLD SUBUNITS A AND B USED TO DISPLAY KRAS G12C TITLE 2 COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: COB_ADENO_TRANS DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CRYO-EM IMAGING SCAFFOLD SUBUNIT B WITH DARPIN - RCG-33; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOPLASMA ACIDOPHILUM; SOURCE 3 ORGANISM_TAXID: 2303; SOURCE 4 GENE: PH0671; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRYOEM IMAGING SCAFFOLD, CANCER, GTPASE, STRUCTURAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.CASTELLS-GRAELLS,M.R.SAWAYA,T.O.YEATES REVDAT 2 27-SEP-23 8G3K 1 JRNL REVDAT 1 09-AUG-23 8G3K 0 JRNL AUTH R.CASTELLS-GRAELLS,K.MEADOR,M.A.ARBING,M.R.SAWAYA,M.GEE, JRNL AUTH 2 D.CASCIO,E.GLEAVE,J.E.DEBRECZENI,J.BREED,K.LEOPOLD,A.PATEL, JRNL AUTH 3 D.JAHAGIRDAR,B.LYONS,S.SUBRAMANIAM,C.PHILLIPS,T.O.YEATES JRNL TITL CRYO-EM STRUCTURE DETERMINATION OF SMALL THERAPEUTIC PROTEIN JRNL TITL 2 TARGETS AT 3 ANGSTROM -RESOLUTION USING A RIGID IMAGING JRNL TITL 3 SCAFFOLD. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 94120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37669364 JRNL DOI 10.1073/PNAS.2305494120 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, COOT, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL 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) : 2.200 REMARK 3 NUMBER OF PARTICLES : 121441 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 8G3K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272093. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : CRYO-EM IMAGING SCAFFOLD REMARK 245 DISPLAYING KRAS G12C REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL 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 IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2250.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 155000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ARG A 2 REMARK 465 ILE A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 LYS A 6 REMARK 465 VAL A 7 REMARK 465 GLY A 8 REMARK 465 ASP A 9 REMARK 465 LYS A 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 THR A 13 REMARK 465 ARG A 14 REMARK 465 LEU A 15 REMARK 465 PHE A 16 REMARK 465 GLY A 17 REMARK 465 GLY A 18 REMARK 465 GLU A 19 REMARK 465 GLU A 20 REMARK 465 VAL A 21 REMARK 465 TRP A 22 REMARK 465 LYS A 23 REMARK 465 VAL A 97A REMARK 465 ASN A 97B REMARK 465 LYS A 97C REMARK 465 LEU A 97D REMARK 465 SER A 97E REMARK 465 PHE A 97F REMARK 465 VAL A 97G REMARK 465 LEU A 166 REMARK 465 LYS A 167 REMARK 465 GLU A 168 REMARK 465 VAL A 169 REMARK 465 ARG A 170 REMARK 465 SER A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 HIS A 175 REMARK 465 HIS A 176 REMARK 465 HIS A 177 REMARK 465 MET B 1 REMARK 465 PHE B 2 REMARK 465 THR B 3 REMARK 465 ARG B 4 REMARK 465 ARG B 5 REMARK 465 GLY B 6 REMARK 465 ASP B 7 REMARK 465 GLN B 8 REMARK 465 GLY B 9 REMARK 465 GLU B 10 REMARK 465 THR B 11 REMARK 465 ASP B 12 REMARK 465 LEU B 13 REMARK 465 ALA B 14 REMARK 465 ASN B 15 REMARK 465 ARG B 16 REMARK 465 ALA B 17 REMARK 465 ARG B 18 REMARK 465 VAL B 19 REMARK 465 GLY B 20 REMARK 465 LYS B 21 REMARK 465 ASP B 22 REMARK 465 LEU B 172 REMARK 465 GLU B 173 REMARK 465 ALA B 174 REMARK 465 ALA B 175 REMARK 465 ARG B 176 REMARK 465 ALA B 177 REMARK 465 GLY B 178 REMARK 465 GLN B 179 REMARK 465 ASP B 180 REMARK 465 ASP B 181 REMARK 465 GLU B 182 REMARK 465 VAL B 183 REMARK 465 ALA B 184 REMARK 465 ALA B 185 REMARK 465 LEU B 186 REMARK 465 LEU B 187 REMARK 465 ALA B 188 REMARK 465 LYS B 189 REMARK 465 GLY B 190 REMARK 465 ALA B 191 REMARK 465 ASP B 192 REMARK 465 VAL B 193 REMARK 465 ASN B 194 REMARK 465 ALA B 195 REMARK 465 HIS B 196 REMARK 465 ASP B 197 REMARK 465 THR B 198 REMARK 465 PHE B 199 REMARK 465 GLY B 200 REMARK 465 PHE B 201 REMARK 465 THR B 202 REMARK 465 PRO B 203 REMARK 465 LEU B 204 REMARK 465 HIS B 205 REMARK 465 LEU B 206 REMARK 465 ALA B 207 REMARK 465 ALA B 208 REMARK 465 LEU B 209 REMARK 465 TYR B 210 REMARK 465 GLY B 211 REMARK 465 HIS B 212 REMARK 465 LEU B 213 REMARK 465 GLU B 214 REMARK 465 ILE B 215 REMARK 465 VAL B 216 REMARK 465 GLU B 217 REMARK 465 VAL B 218 REMARK 465 LEU B 219 REMARK 465 LEU B 220 REMARK 465 LYS B 221 REMARK 465 ARG B 222 REMARK 465 GLY B 223 REMARK 465 ALA B 224 REMARK 465 ASP B 225 REMARK 465 ILE B 226 REMARK 465 ASN B 227 REMARK 465 ALA B 228 REMARK 465 ASP B 229 REMARK 465 ASP B 230 REMARK 465 SER B 231 REMARK 465 TYR B 232 REMARK 465 GLY B 233 REMARK 465 ARG B 234 REMARK 465 THR B 235 REMARK 465 PRO B 236 REMARK 465 LEU B 237 REMARK 465 HIS B 238 REMARK 465 LEU B 239 REMARK 465 ALA B 240 REMARK 465 ALA B 241 REMARK 465 MET B 242 REMARK 465 ARG B 243 REMARK 465 GLY B 244 REMARK 465 HIS B 245 REMARK 465 LEU B 246 REMARK 465 GLU B 247 REMARK 465 ILE B 248 REMARK 465 VAL B 249 REMARK 465 GLU B 250 REMARK 465 LEU B 251 REMARK 465 LEU B 252 REMARK 465 LEU B 253 REMARK 465 ARG B 254 REMARK 465 TRP B 255 REMARK 465 GLY B 256 REMARK 465 ALA B 257 REMARK 465 ASP B 258 REMARK 465 VAL B 259 REMARK 465 ASN B 260 REMARK 465 ALA B 261 REMARK 465 ALA B 262 REMARK 465 ASP B 263 REMARK 465 GLU B 264 REMARK 465 GLU B 265 REMARK 465 GLY B 266 REMARK 465 ARG B 267 REMARK 465 THR B 268 REMARK 465 PRO B 269 REMARK 465 LEU B 270 REMARK 465 HIS B 271 REMARK 465 LEU B 272 REMARK 465 ALA B 273 REMARK 465 ALA B 274 REMARK 465 LYS B 275 REMARK 465 ARG B 276 REMARK 465 GLY B 277 REMARK 465 HIS B 278 REMARK 465 LEU B 279 REMARK 465 GLU B 280 REMARK 465 ILE B 281 REMARK 465 VAL B 282 REMARK 465 GLU B 283 REMARK 465 VAL B 284 REMARK 465 LEU B 285 REMARK 465 LEU B 286 REMARK 465 LYS B 287 REMARK 465 ASN B 288 REMARK 465 GLY B 289 REMARK 465 ALA B 290 REMARK 465 ASP B 291 REMARK 465 VAL B 292 REMARK 465 ASN B 293 REMARK 465 ALA B 294 REMARK 465 GLN B 295 REMARK 465 ASP B 296 REMARK 465 LYS B 297 REMARK 465 PHE B 298 REMARK 465 GLY B 299 REMARK 465 LYS B 300 REMARK 465 THR B 301 REMARK 465 ALA B 302 REMARK 465 PHE B 303 REMARK 465 ASP B 304 REMARK 465 ILE B 305 REMARK 465 SER B 306 REMARK 465 ILE B 307 REMARK 465 ASP B 308 REMARK 465 ASN B 309 REMARK 465 GLY B 310 REMARK 465 ASN B 311 REMARK 465 GLU B 312 REMARK 465 ASP B 313 REMARK 465 LEU B 314 REMARK 465 ALA B 315 REMARK 465 GLU B 316 REMARK 465 ILE B 317 REMARK 465 LEU B 318 REMARK 465 GLN B 319 REMARK 465 LYS B 320 REMARK 465 LEU B 321 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8G42 RELATED DB: PDB REMARK 900 FOCUSED REFINEMENT ON A DIFFERENT PART OF THE TETRAHEDRAL ASSEMBLY REMARK 900 RELATED ID: EMD-29700 RELATED DB: EMDB REMARK 900 CRYO-EM IMAGING SCAFFOLD SUBUNITS A AND B USED TO DISPLAY KRAS G12C REMARK 900 COMPLEX WITH GDP DBREF 8G3K A 1 171 UNP O58404 O58404_PYRHO 1 172 DBREF 8G3K B 1 321 PDB 8G3K 8G3K 1 321 SEQADV 8G3K ASP A 25 UNP O58404 SER 25 CONFLICT SEQADV 8G3K ALA A 88 UNP O58404 GLU 88 CONFLICT SEQADV 8G3K GLU A 92 UNP O58404 SER 92 CONFLICT SEQADV 8G3K SER A 95 UNP O58404 GLU 95 CONFLICT SEQADV 8G3K LYS A 97C UNP O58404 LEU 100 CONFLICT SEQADV 8G3K LEU A 97D UNP O58404 LYS 101 CONFLICT SEQADV 8G3K THR A 139 UNP O58404 LYS 140 CONFLICT SEQADV 8G3K LEU A 140 UNP O58404 GLU 141 CONFLICT SEQADV 8G3K ALA A 142 UNP O58404 LEU 143 CONFLICT SEQADV 8G3K ILE A 143 UNP O58404 VAL 144 CONFLICT SEQADV 8G3K ALA A 146 UNP O58404 ASN 147 CONFLICT SEQADV 8G3K LEU A 147 UNP O58404 ARG 148 CONFLICT SEQADV 8G3K ARG A 150 UNP O58404 ASP 151 CONFLICT SEQADV 8G3K HIS A 172 UNP O58404 EXPRESSION TAG SEQADV 8G3K HIS A 173 UNP O58404 EXPRESSION TAG SEQADV 8G3K HIS A 174 UNP O58404 EXPRESSION TAG SEQADV 8G3K HIS A 175 UNP O58404 EXPRESSION TAG SEQADV 8G3K HIS A 176 UNP O58404 EXPRESSION TAG SEQADV 8G3K HIS A 177 UNP O58404 EXPRESSION TAG SEQRES 1 A 178 MET ARG ILE THR THR LYS VAL GLY ASP LYS GLY SER THR SEQRES 2 A 178 ARG LEU PHE GLY GLY GLU GLU VAL TRP LYS ASP ASP PRO SEQRES 3 A 178 ILE ILE GLU ALA ASN GLY THR LEU ASP GLU LEU THR SER SEQRES 4 A 178 PHE ILE GLY GLU ALA LYS HIS TYR VAL ASP GLU GLU MET SEQRES 5 A 178 LYS GLY ILE LEU GLU GLU ILE GLN ASN ASP ILE TYR LYS SEQRES 6 A 178 ILE MET GLY GLU ILE GLY SER LYS GLY LYS ILE GLU GLY SEQRES 7 A 178 ILE SER GLU GLU ARG ILE LYS TRP LEU ALA GLY LEU ILE SEQRES 8 A 178 GLU ARG TYR SER GLU MET VAL ASN LYS LEU SER PHE VAL SEQRES 9 A 178 LEU PRO GLY GLY THR LEU GLU SER ALA LYS LEU ASP VAL SEQRES 10 A 178 CYS ARG THR ILE ALA ARG ARG ALA GLU ARG LYS VAL ALA SEQRES 11 A 178 THR VAL LEU ARG GLU PHE GLY ILE GLY THR LEU ALA ALA SEQRES 12 A 178 ILE TYR LEU ALA LEU LEU SER ARG LEU LEU PHE LEU LEU SEQRES 13 A 178 ALA ARG VAL ILE GLU ILE GLU LYS ASN LYS LEU LYS GLU SEQRES 14 A 178 VAL ARG SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 321 MET PHE THR ARG ARG GLY ASP GLN GLY GLU THR ASP LEU SEQRES 2 B 321 ALA ASN ARG ALA ARG VAL GLY LYS ASP SER PRO VAL VAL SEQRES 3 B 321 GLU VAL GLN GLY THR ILE ASP GLU LEU ASN SER PHE ILE SEQRES 4 B 321 GLY TYR ALA LEU VAL LEU SER ARG TRP ASP ASP ILE ARG SEQRES 5 B 321 ASN ASP LEU PHE ARG ILE GLN ASN ASP LEU PHE VAL LEU SEQRES 6 B 321 GLY GLU ASP VAL SER THR GLY GLY LYS GLY ARG THR VAL SEQRES 7 B 321 THR MET ASP MET ILE ILE TYR LEU ILE LYS ARG SER VAL SEQRES 8 B 321 GLU MET LYS ALA GLU ILE GLY LYS ILE GLU LEU PHE VAL SEQRES 9 B 321 VAL PRO GLY GLY SER VAL GLU SER ALA SER LEU HIS MET SEQRES 10 B 321 ALA ARG ALA VAL SER ARG ARG LEU GLU ARG ARG ILE LYS SEQRES 11 B 321 ALA ALA SER GLU LEU THR GLU ILE ASN ALA ASN VAL LEU SEQRES 12 B 321 LEU TYR ALA ASN MET LEU SER ASN ILE LEU PHE MET HIS SEQRES 13 B 321 ALA LEU ILE SER ASN LYS ARG LYS GLU GLU LEU ASP LYS SEQRES 14 B 321 LYS LEU LEU GLU ALA ALA ARG ALA GLY GLN ASP ASP GLU SEQRES 15 B 321 VAL ALA ALA LEU LEU ALA LYS GLY ALA ASP VAL ASN ALA SEQRES 16 B 321 HIS ASP THR PHE GLY PHE THR PRO LEU HIS LEU ALA ALA SEQRES 17 B 321 LEU TYR GLY HIS LEU GLU ILE VAL GLU VAL LEU LEU LYS SEQRES 18 B 321 ARG GLY ALA ASP ILE ASN ALA ASP ASP SER TYR GLY ARG SEQRES 19 B 321 THR PRO LEU HIS LEU ALA ALA MET ARG GLY HIS LEU GLU SEQRES 20 B 321 ILE VAL GLU LEU LEU LEU ARG TRP GLY ALA ASP VAL ASN SEQRES 21 B 321 ALA ALA ASP GLU GLU GLY ARG THR PRO LEU HIS LEU ALA SEQRES 22 B 321 ALA LYS ARG GLY HIS LEU GLU ILE VAL GLU VAL LEU LEU SEQRES 23 B 321 LYS ASN GLY ALA ASP VAL ASN ALA GLN ASP LYS PHE GLY SEQRES 24 B 321 LYS THR ALA PHE ASP ILE SER ILE ASP ASN GLY ASN GLU SEQRES 25 B 321 ASP LEU ALA GLU ILE LEU GLN LYS LEU HELIX 1 AA1 ASP A 24 LYS A 45 1 22 HELIX 2 AA2 HIS A 46 VAL A 48 5 3 HELIX 3 AA3 ASP A 49 SER A 72 1 24 HELIX 4 AA4 SER A 80 GLU A 96 1 17 HELIX 5 AA5 THR A 108 GLY A 136 1 29 HELIX 6 AA6 GLY A 138 LYS A 165 1 28 HELIX 7 AA7 PRO B 24 SER B 46 1 23 HELIX 8 AA8 TRP B 48 GLY B 72 1 25 HELIX 9 AA9 THR B 79 GLY B 98 1 20 HELIX 10 AB1 SER B 109 GLU B 134 1 26 HELIX 11 AB2 ASN B 139 LEU B 171 1 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