HEADER BLOOD CLOTTING 03-OCT-23 8UF7 TITLE CRYO-EM STRUCTURE OF POMAB, A TYPE-I ANTI-PROTHROMBIN ANTIPHOSPHOLIPID TITLE 2 ANTIBODY, BOUND TO KRINGLE-1 OF HUMAN PROTHROMBIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POMAB LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: POMAB HEAVY CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROTHROMBIN; COMPND 11 CHAIN: C SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 13 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606 KEYWDS AUTOIMMUNITY, THROMBOSIS, COMPLEX, IMMUNOGLOBULIN, COAGULATION KEYWDS 2 FACTOR, ANTICOAGULATION, INHIBITOR, BLOOD CLOTTING EXPDTA ELECTRON MICROSCOPY AUTHOR S.KUMAR,B.SUMMERS,K.BASORE,N.POZZI REVDAT 3 22-MAY-24 8UF7 1 JRNL REVDAT 2 27-MAR-24 8UF7 1 JRNL REVDAT 1 14-FEB-24 8UF7 0 JRNL AUTH S.KUMAR,B.SUMMERS,K.BASORE,V.PENGO,R.FLAUMENHAFT,N.POZZI JRNL TITL CRYO-EM STRUCTURE AND FUNCTIONAL BASIS OF PROTHROMBIN JRNL TITL 2 RECOGNITION BY A TYPE I ANTIPROTHROMBIN ANTIPHOSPHOLIPID JRNL TITL 3 ANTIBODY. JRNL REF BLOOD V. 143 2005 2024 JRNL REFN ESSN 1528-0020 JRNL PMID 38437497 JRNL DOI 10.1182/BLOOD.2023022942 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, CRYOSPARC 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 : NULL 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 176744 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 8UF7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000277850. 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 : COMPLEX OF FAB FRAGMENT OF REMARK 245 POMAB WITH HUMAN PROTHROMBIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.33 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : FAB FRAGMENT GENERATED BY REMARK 245 PROTEOLYTIC CLEAVAGE OF POMAB IGG ANTIBODY IN COMPLEX WITH OPEN REMARK 245 CONFORMATION OF HUMAN PROTHROMBIN 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) : 2400.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 0.01 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6220.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 59000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLU B 216 REMARK 465 VAL B 217 REMARK 465 HIS B 218 REMARK 465 ALA C 1 REMARK 465 ASN C 2 REMARK 465 THR C 3 REMARK 465 PHE C 4 REMARK 465 LEU C 5 REMARK 465 GLU C 6 REMARK 465 GLU C 7 REMARK 465 VAL C 8 REMARK 465 ARG C 9 REMARK 465 LYS C 10 REMARK 465 GLY C 11 REMARK 465 ASN C 12 REMARK 465 LEU C 13 REMARK 465 GLU C 14 REMARK 465 ARG C 15 REMARK 465 GLU C 16 REMARK 465 CYS C 17 REMARK 465 VAL C 18 REMARK 465 GLU C 19 REMARK 465 GLU C 20 REMARK 465 THR C 21 REMARK 465 CYS C 22 REMARK 465 SER C 23 REMARK 465 TYR C 24 REMARK 465 GLU C 25 REMARK 465 GLU C 26 REMARK 465 ALA C 27 REMARK 465 PHE C 28 REMARK 465 GLU C 29 REMARK 465 ALA C 30 REMARK 465 LEU C 31 REMARK 465 GLU C 32 REMARK 465 SER C 33 REMARK 465 SER C 34 REMARK 465 THR C 35 REMARK 465 ALA C 36 REMARK 465 THR C 37 REMARK 465 ASP C 38 REMARK 465 VAL C 39 REMARK 465 PHE C 40 REMARK 465 TRP C 41 REMARK 465 ALA C 42 REMARK 465 LYS C 43 REMARK 465 TYR C 44 REMARK 465 THR C 45 REMARK 465 ALA C 46 REMARK 465 CYS C 47 REMARK 465 GLU C 48 REMARK 465 THR C 49 REMARK 465 ALA C 50 REMARK 465 ARG C 51 REMARK 465 THR C 52 REMARK 465 PRO C 53 REMARK 465 ARG C 54 REMARK 465 ASP C 55 REMARK 465 LYS C 56 REMARK 465 LEU C 57 REMARK 465 ALA C 58 REMARK 465 ALA C 59 REMARK 465 CYS C 60 REMARK 465 LEU C 61 REMARK 465 ASP C 146 REMARK 465 GLN C 147 REMARK 465 VAL C 148 REMARK 465 THR C 149 REMARK 465 VAL C 150 REMARK 465 ALA C 151 REMARK 465 MET C 152 REMARK 465 THR C 153 REMARK 465 PRO C 154 REMARK 465 ARG C 155 REMARK 465 SER C 156 REMARK 465 GLU C 157 REMARK 465 GLY C 158 REMARK 465 SER C 159 REMARK 465 SER C 160 REMARK 465 VAL C 161 REMARK 465 ASN C 162 REMARK 465 LEU C 163 REMARK 465 SER C 164 REMARK 465 PRO C 165 REMARK 465 PRO C 166 REMARK 465 LEU C 167 REMARK 465 GLU C 168 REMARK 465 GLN C 169 REMARK 465 CYS C 170 REMARK 465 VAL C 171 REMARK 465 PRO C 172 REMARK 465 ASP C 173 REMARK 465 ARG C 174 REMARK 465 GLY C 175 REMARK 465 GLN C 176 REMARK 465 GLN C 177 REMARK 465 TYR C 178 REMARK 465 GLN C 179 REMARK 465 GLY C 180 REMARK 465 ARG C 181 REMARK 465 LEU C 182 REMARK 465 ALA C 183 REMARK 465 VAL C 184 REMARK 465 THR C 185 REMARK 465 THR C 186 REMARK 465 HIS C 187 REMARK 465 GLY C 188 REMARK 465 LEU C 189 REMARK 465 PRO C 190 REMARK 465 CYS C 191 REMARK 465 LEU C 192 REMARK 465 ALA C 193 REMARK 465 TRP C 194 REMARK 465 ALA C 195 REMARK 465 SER C 196 REMARK 465 ALA C 197 REMARK 465 GLN C 198 REMARK 465 ALA C 199 REMARK 465 LYS C 200 REMARK 465 ALA C 201 REMARK 465 LEU C 202 REMARK 465 SER C 203 REMARK 465 LYS C 204 REMARK 465 HIS C 205 REMARK 465 GLN C 206 REMARK 465 ASP C 207 REMARK 465 PHE C 208 REMARK 465 ASN C 209 REMARK 465 SER C 210 REMARK 465 ALA C 211 REMARK 465 VAL C 212 REMARK 465 GLN C 213 REMARK 465 LEU C 214 REMARK 465 VAL C 215 REMARK 465 GLU C 216 REMARK 465 ASN C 217 REMARK 465 PHE C 218 REMARK 465 CYS C 219 REMARK 465 ARG C 220 REMARK 465 ASN C 221 REMARK 465 PRO C 222 REMARK 465 ASP C 223 REMARK 465 GLY C 224 REMARK 465 ASP C 225 REMARK 465 GLU C 226 REMARK 465 GLU C 227 REMARK 465 GLY C 228 REMARK 465 VAL C 229 REMARK 465 TRP C 230 REMARK 465 CYS C 231 REMARK 465 TYR C 232 REMARK 465 VAL C 233 REMARK 465 ALA C 234 REMARK 465 GLY C 235 REMARK 465 LYS C 236 REMARK 465 PRO C 237 REMARK 465 GLY C 238 REMARK 465 ASP C 239 REMARK 465 PHE C 240 REMARK 465 GLY C 241 REMARK 465 TYR C 242 REMARK 465 CYS C 243 REMARK 465 ASP C 244 REMARK 465 LEU C 245 REMARK 465 ASN C 246 REMARK 465 TYR C 247 REMARK 465 CYS C 248 REMARK 465 GLU C 249 REMARK 465 GLU C 250 REMARK 465 ALA C 251 REMARK 465 VAL C 252 REMARK 465 GLU C 253 REMARK 465 GLU C 254 REMARK 465 GLU C 255 REMARK 465 THR C 256 REMARK 465 GLY C 257 REMARK 465 ASP C 258 REMARK 465 GLY C 259 REMARK 465 LEU C 260 REMARK 465 ASP C 261 REMARK 465 GLU C 262 REMARK 465 ASP C 263 REMARK 465 SER C 264 REMARK 465 ASP C 265 REMARK 465 ARG C 266 REMARK 465 ALA C 267 REMARK 465 ILE C 268 REMARK 465 GLU C 269 REMARK 465 GLY C 270 REMARK 465 ARG C 271 REMARK 465 THR C 272 REMARK 465 ALA C 273 REMARK 465 THR C 274 REMARK 465 SER C 275 REMARK 465 GLU C 276 REMARK 465 TYR C 277 REMARK 465 GLN C 278 REMARK 465 THR C 279 REMARK 465 PHE C 280 REMARK 465 PHE C 281 REMARK 465 ASN C 282 REMARK 465 PRO C 283 REMARK 465 ARG C 284 REMARK 465 THR C 285 REMARK 465 PHE C 286 REMARK 465 GLY C 287 REMARK 465 SER C 288 REMARK 465 GLY C 289 REMARK 465 GLU C 290 REMARK 465 ALA C 291 REMARK 465 ASP C 292 REMARK 465 CYS C 293 REMARK 465 GLY C 294 REMARK 465 LEU C 295 REMARK 465 ARG C 296 REMARK 465 PRO C 297 REMARK 465 LEU C 298 REMARK 465 PHE C 299 REMARK 465 GLU C 300 REMARK 465 LYS C 301 REMARK 465 LYS C 302 REMARK 465 SER C 303 REMARK 465 LEU C 304 REMARK 465 GLU C 305 REMARK 465 ASP C 306 REMARK 465 LYS C 307 REMARK 465 THR C 308 REMARK 465 GLU C 309 REMARK 465 ARG C 310 REMARK 465 GLU C 311 REMARK 465 LEU C 312 REMARK 465 LEU C 313 REMARK 465 GLU C 314 REMARK 465 SER C 315 REMARK 465 TYR C 316 REMARK 465 ILE C 317 REMARK 465 ASP C 318 REMARK 465 GLY C 319 REMARK 465 ARG C 320 REMARK 465 ILE C 321 REMARK 465 VAL C 322 REMARK 465 GLU C 323 REMARK 465 GLY C 324 REMARK 465 SER C 325 REMARK 465 ASP C 326 REMARK 465 ALA C 327 REMARK 465 GLU C 328 REMARK 465 ILE C 329 REMARK 465 GLY C 330 REMARK 465 MET C 331 REMARK 465 SER C 332 REMARK 465 PRO C 333 REMARK 465 TRP C 334 REMARK 465 GLN C 335 REMARK 465 VAL C 336 REMARK 465 MET C 337 REMARK 465 LEU C 338 REMARK 465 PHE C 339 REMARK 465 ARG C 340 REMARK 465 LYS C 341 REMARK 465 SER C 342 REMARK 465 PRO C 343 REMARK 465 GLN C 344 REMARK 465 GLU C 345 REMARK 465 LEU C 346 REMARK 465 LEU C 347 REMARK 465 CYS C 348 REMARK 465 GLY C 349 REMARK 465 ALA C 350 REMARK 465 SER C 351 REMARK 465 LEU C 352 REMARK 465 ILE C 353 REMARK 465 SER C 354 REMARK 465 ASP C 355 REMARK 465 ARG C 356 REMARK 465 TRP C 357 REMARK 465 VAL C 358 REMARK 465 LEU C 359 REMARK 465 THR C 360 REMARK 465 ALA C 361 REMARK 465 ALA C 362 REMARK 465 HIS C 363 REMARK 465 CYS C 364 REMARK 465 LEU C 365 REMARK 465 LEU C 366 REMARK 465 TYR C 367 REMARK 465 PRO C 368 REMARK 465 PRO C 369 REMARK 465 TRP C 370 REMARK 465 ASP C 371 REMARK 465 LYS C 372 REMARK 465 ASN C 373 REMARK 465 PHE C 374 REMARK 465 THR C 375 REMARK 465 GLU C 376 REMARK 465 ASN C 377 REMARK 465 ASP C 378 REMARK 465 LEU C 379 REMARK 465 LEU C 380 REMARK 465 VAL C 381 REMARK 465 ARG C 382 REMARK 465 ILE C 383 REMARK 465 GLY C 384 REMARK 465 LYS C 385 REMARK 465 HIS C 386 REMARK 465 SER C 387 REMARK 465 ARG C 388 REMARK 465 THR C 389 REMARK 465 ARG C 390 REMARK 465 TYR C 391 REMARK 465 GLU C 392 REMARK 465 ARG C 393 REMARK 465 ASN C 394 REMARK 465 ILE C 395 REMARK 465 GLU C 396 REMARK 465 LYS C 397 REMARK 465 ILE C 398 REMARK 465 SER C 399 REMARK 465 MET C 400 REMARK 465 LEU C 401 REMARK 465 GLU C 402 REMARK 465 LYS C 403 REMARK 465 ILE C 404 REMARK 465 TYR C 405 REMARK 465 ILE C 406 REMARK 465 HIS C 407 REMARK 465 PRO C 408 REMARK 465 ARG C 409 REMARK 465 TYR C 410 REMARK 465 ASN C 411 REMARK 465 TRP C 412 REMARK 465 ARG C 413 REMARK 465 GLU C 414 REMARK 465 ASN C 415 REMARK 465 LEU C 416 REMARK 465 ASP C 417 REMARK 465 ARG C 418 REMARK 465 ASP C 419 REMARK 465 ILE C 420 REMARK 465 ALA C 421 REMARK 465 LEU C 422 REMARK 465 MET C 423 REMARK 465 LYS C 424 REMARK 465 LEU C 425 REMARK 465 LYS C 426 REMARK 465 LYS C 427 REMARK 465 PRO C 428 REMARK 465 VAL C 429 REMARK 465 ALA C 430 REMARK 465 PHE C 431 REMARK 465 SER C 432 REMARK 465 ASP C 433 REMARK 465 TYR C 434 REMARK 465 ILE C 435 REMARK 465 HIS C 436 REMARK 465 PRO C 437 REMARK 465 VAL C 438 REMARK 465 CYS C 439 REMARK 465 LEU C 440 REMARK 465 PRO C 441 REMARK 465 ASP C 442 REMARK 465 ARG C 443 REMARK 465 GLU C 444 REMARK 465 THR C 445 REMARK 465 ALA C 446 REMARK 465 ALA C 447 REMARK 465 SER C 448 REMARK 465 LEU C 449 REMARK 465 LEU C 450 REMARK 465 GLN C 451 REMARK 465 ALA C 452 REMARK 465 GLY C 453 REMARK 465 TYR C 454 REMARK 465 LYS C 455 REMARK 465 GLY C 456 REMARK 465 ARG C 457 REMARK 465 VAL C 458 REMARK 465 THR C 459 REMARK 465 GLY C 460 REMARK 465 TRP C 461 REMARK 465 GLY C 462 REMARK 465 ASN C 463 REMARK 465 LEU C 464 REMARK 465 LYS C 465 REMARK 465 GLU C 466 REMARK 465 THR C 467 REMARK 465 TRP C 468 REMARK 465 THR C 469 REMARK 465 ALA C 470 REMARK 465 ASN C 471 REMARK 465 VAL C 472 REMARK 465 GLY C 473 REMARK 465 LYS C 474 REMARK 465 GLY C 475 REMARK 465 GLN C 476 REMARK 465 PRO C 477 REMARK 465 SER C 478 REMARK 465 VAL C 479 REMARK 465 LEU C 480 REMARK 465 GLN C 481 REMARK 465 VAL C 482 REMARK 465 VAL C 483 REMARK 465 ASN C 484 REMARK 465 LEU C 485 REMARK 465 PRO C 486 REMARK 465 ILE C 487 REMARK 465 VAL C 488 REMARK 465 GLU C 489 REMARK 465 ARG C 490 REMARK 465 PRO C 491 REMARK 465 VAL C 492 REMARK 465 CYS C 493 REMARK 465 LYS C 494 REMARK 465 ASP C 495 REMARK 465 SER C 496 REMARK 465 THR C 497 REMARK 465 ARG C 498 REMARK 465 ILE C 499 REMARK 465 ARG C 500 REMARK 465 ILE C 501 REMARK 465 THR C 502 REMARK 465 ASP C 503 REMARK 465 ASN C 504 REMARK 465 MET C 505 REMARK 465 PHE C 506 REMARK 465 CYS C 507 REMARK 465 ALA C 508 REMARK 465 GLY C 509 REMARK 465 TYR C 510 REMARK 465 LYS C 511 REMARK 465 PRO C 512 REMARK 465 ASP C 513 REMARK 465 GLU C 514 REMARK 465 GLY C 515 REMARK 465 LYS C 516 REMARK 465 ARG C 517 REMARK 465 GLY C 518 REMARK 465 ASP C 519 REMARK 465 ALA C 520 REMARK 465 CYS C 521 REMARK 465 GLU C 522 REMARK 465 GLY C 523 REMARK 465 ASP C 524 REMARK 465 SER C 525 REMARK 465 GLY C 526 REMARK 465 GLY C 527 REMARK 465 PRO C 528 REMARK 465 PHE C 529 REMARK 465 VAL C 530 REMARK 465 MET C 531 REMARK 465 LYS C 532 REMARK 465 SER C 533 REMARK 465 PRO C 534 REMARK 465 PHE C 535 REMARK 465 ASN C 536 REMARK 465 ASN C 537 REMARK 465 ARG C 538 REMARK 465 TRP C 539 REMARK 465 TYR C 540 REMARK 465 GLN C 541 REMARK 465 MET C 542 REMARK 465 GLY C 543 REMARK 465 ILE C 544 REMARK 465 VAL C 545 REMARK 465 SER C 546 REMARK 465 TRP C 547 REMARK 465 GLY C 548 REMARK 465 GLU C 549 REMARK 465 GLY C 550 REMARK 465 CYS C 551 REMARK 465 ASP C 552 REMARK 465 ARG C 553 REMARK 465 ASP C 554 REMARK 465 GLY C 555 REMARK 465 LYS C 556 REMARK 465 TYR C 557 REMARK 465 GLY C 558 REMARK 465 PHE C 559 REMARK 465 TYR C 560 REMARK 465 THR C 561 REMARK 465 HIS C 562 REMARK 465 VAL C 563 REMARK 465 PHE C 564 REMARK 465 ARG C 565 REMARK 465 LEU C 566 REMARK 465 LYS C 567 REMARK 465 LYS C 568 REMARK 465 TRP C 569 REMARK 465 ILE C 570 REMARK 465 GLN C 571 REMARK 465 LYS C 572 REMARK 465 VAL C 573 REMARK 465 ILE C 574 REMARK 465 ASP C 575 REMARK 465 GLN C 576 REMARK 465 PHE C 577 REMARK 465 GLY C 578 REMARK 465 GLU C 579 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 2 -62.49 59.62 REMARK 500 SER A 27 -5.65 75.91 REMARK 500 PRO A 41 98.63 -69.14 REMARK 500 SER A 43 175.22 177.18 REMARK 500 SER A 52 -143.51 61.75 REMARK 500 THR A 70 -5.02 66.00 REMARK 500 ASP A 83 0.07 -68.24 REMARK 500 ARG A 93 33.70 -143.42 REMARK 500 ARG A 94 -130.54 64.72 REMARK 500 ASN A 139 63.78 60.39 REMARK 500 LYS A 170 -60.02 -93.80 REMARK 500 THR A 181 58.08 -91.71 REMARK 500 LEU B 226 -168.66 -161.45 REMARK 500 GLU B 257 46.34 -84.93 REMARK 500 LYS B 258 48.53 39.16 REMARK 500 ALA B 264 170.76 63.85 REMARK 500 THR B 265 146.61 -170.16 REMARK 500 ASP B 314 -71.54 -61.65 REMARK 500 GLU B 316 0.64 59.33 REMARK 500 ARG B 317 172.75 60.81 REMARK 500 SER B 334 30.53 -90.99 REMARK 500 LYS B 336 140.85 70.17 REMARK 500 GLU B 369 143.16 70.60 REMARK 500 LEU B 380 41.98 -103.84 REMARK 500 GLN B 392 -61.92 -95.28 REMARK 500 VAL B 427 52.07 26.75 REMARK 500 SER C 101 48.36 -82.16 REMARK 500 GLU C 111 -133.17 49.96 REMARK 500 PRO C 141 -168.36 -73.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42185 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF POMAB, A TYPE-I ANTI-PROTHROMBIN REMARK 900 ANTIPHOSPHOLIPID ANTIBODY, BOUND TO KRINGLE-1 OF HUMAN PROTHROMBIN DBREF 8UF7 A 1 215 PDB 8UF7 8UF7 1 215 DBREF 8UF7 B 216 433 PDB 8UF7 8UF7 216 433 DBREF 8UF7 C 1 579 UNP P00734 THRB_HUMAN 44 622 SEQRES 1 A 215 GLN ILE VAL LEU THR GLN SER PRO ALA ILE MET SER VAL SEQRES 2 A 215 SER LEU GLY GLU ARG VAL THR MET THR CYS ILE VAL SER SEQRES 3 A 215 SER SER VAL SER SER THR TYR LEU HIS TRP TYR GLN GLN SEQRES 4 A 215 LYS PRO GLY SER SER PRO LYS LEU TRP ILE TYR SER SER SEQRES 5 A 215 SER ASN LEU ALA SER GLY VAL PRO THR ARG PHE SER GLY SEQRES 6 A 215 SER GLY SER GLY THR SER HIS SER LEU THR ILE SER SER SEQRES 7 A 215 MET GLU ALA GLU ASP ALA ALA ALA TYR TYR CYS GLN LEU SEQRES 8 A 215 TYR ARG ARG SER PRO LEU THR PHE GLY ALA GLY THR LYS SEQRES 9 A 215 LEU GLU LEU LYS ARG ALA ASP ALA ALA PRO THR VAL SER SEQRES 10 A 215 ILE PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY SEQRES 11 A 215 ALA SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS SEQRES 12 A 215 ASP ILE ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG SEQRES 13 A 215 GLN ASN GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER SEQRES 14 A 215 LYS ASP SER THR TYR SER MET SER SER THR LEU THR LEU SEQRES 15 A 215 THR LYS ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS SEQRES 16 A 215 GLU ALA THR HIS LYS THR SER THR SER PRO ILE VAL LYS SEQRES 17 A 215 SER PHE ASN ARG ASN GLU CYS SEQRES 1 B 218 GLU VAL HIS LEU VAL GLU SER GLY GLY GLY LEU VAL LYS SEQRES 2 B 218 PRO GLY GLY SER LEU LYS LEU SER CYS ALA ALA SER GLY SEQRES 3 B 218 PHE THR PHE SER SER TYR TYR MET TYR TRP VAL ARG GLN SEQRES 4 B 218 THR PRO GLU LYS ARG LEU GLU TRP VAL ALA THR ILE SER SEQRES 5 B 218 ASN GLY GLY ILE TYR THR TYR TYR LEU ASP SER VAL ARG SEQRES 6 B 218 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN ILE SEQRES 7 B 218 LEU TYR LEU GLN MET SER GLY LEU SER SER ALA ASP SER SEQRES 8 B 218 ALA ILE TYR TYR CYS THR ARG ASP GLY GLU ARG GLN GLY SEQRES 9 B 218 ALA MET ASP TYR TRP GLY GLN GLY THR SER VAL THR VAL SEQRES 10 B 218 SER SER ALA LYS THR THR PRO PRO SER VAL TYR PRO LEU SEQRES 11 B 218 ALA PRO GLY SER ALA ALA GLN THR ASN SER MET VAL THR SEQRES 12 B 218 LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL SEQRES 13 B 218 THR VAL THR TRP ASN SER GLY SER LEU SER SER GLY VAL SEQRES 14 B 218 HIS THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR THR SEQRES 15 B 218 LEU SER SER SER VAL THR VAL PRO SER SER THR TRP PRO SEQRES 16 B 218 SER GLU THR VAL THR CYS ASN VAL ALA HIS PRO ALA SER SEQRES 17 B 218 SER THR LYS VAL ASP LYS LYS ILE VAL PRO SEQRES 1 C 579 ALA ASN THR PHE LEU GLU GLU VAL ARG LYS GLY ASN LEU SEQRES 2 C 579 GLU ARG GLU CYS VAL GLU GLU THR CYS SER TYR GLU GLU SEQRES 3 C 579 ALA PHE GLU ALA LEU GLU SER SER THR ALA THR ASP VAL SEQRES 4 C 579 PHE TRP ALA LYS TYR THR ALA CYS GLU THR ALA ARG THR SEQRES 5 C 579 PRO ARG ASP LYS LEU ALA ALA CYS LEU GLU GLY ASN CYS SEQRES 6 C 579 ALA GLU GLY LEU GLY THR ASN TYR ARG GLY HIS VAL ASN SEQRES 7 C 579 ILE THR ARG SER GLY ILE GLU CYS GLN LEU TRP ARG SER SEQRES 8 C 579 ARG TYR PRO HIS LYS PRO GLU ILE ASN SER THR THR HIS SEQRES 9 C 579 PRO GLY ALA ASP LEU GLN GLU ASN PHE CYS ARG ASN PRO SEQRES 10 C 579 ASP SER SER THR THR GLY PRO TRP CYS TYR THR THR ASP SEQRES 11 C 579 PRO THR VAL ARG ARG GLN GLU CYS SER ILE PRO VAL CYS SEQRES 12 C 579 GLY GLN ASP GLN VAL THR VAL ALA MET THR PRO ARG SER SEQRES 13 C 579 GLU GLY SER SER VAL ASN LEU SER PRO PRO LEU GLU GLN SEQRES 14 C 579 CYS VAL PRO ASP ARG GLY GLN GLN TYR GLN GLY ARG LEU SEQRES 15 C 579 ALA VAL THR THR HIS GLY LEU PRO CYS LEU ALA TRP ALA SEQRES 16 C 579 SER ALA GLN ALA LYS ALA LEU SER LYS HIS GLN ASP PHE SEQRES 17 C 579 ASN SER ALA VAL GLN LEU VAL GLU ASN PHE CYS ARG ASN SEQRES 18 C 579 PRO ASP GLY ASP GLU GLU GLY VAL TRP CYS TYR VAL ALA SEQRES 19 C 579 GLY LYS PRO GLY ASP PHE GLY TYR CYS ASP LEU ASN TYR SEQRES 20 C 579 CYS GLU GLU ALA VAL GLU GLU GLU THR GLY ASP GLY LEU SEQRES 21 C 579 ASP GLU ASP SER ASP ARG ALA ILE GLU GLY ARG THR ALA SEQRES 22 C 579 THR SER GLU TYR GLN THR PHE PHE ASN PRO ARG THR PHE SEQRES 23 C 579 GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO LEU PHE SEQRES 24 C 579 GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG GLU LEU SEQRES 25 C 579 LEU GLU SER TYR ILE ASP GLY ARG ILE VAL GLU GLY SER SEQRES 26 C 579 ASP ALA GLU ILE GLY MET SER PRO TRP GLN VAL MET LEU SEQRES 27 C 579 PHE ARG LYS SER PRO GLN GLU LEU LEU CYS GLY ALA SER SEQRES 28 C 579 LEU ILE SER ASP ARG TRP VAL LEU THR ALA ALA HIS CYS SEQRES 29 C 579 LEU LEU TYR PRO PRO TRP ASP LYS ASN PHE THR GLU ASN SEQRES 30 C 579 ASP LEU LEU VAL ARG ILE GLY LYS HIS SER ARG THR ARG SEQRES 31 C 579 TYR GLU ARG ASN ILE GLU LYS ILE SER MET LEU GLU LYS SEQRES 32 C 579 ILE TYR ILE HIS PRO ARG TYR ASN TRP ARG GLU ASN LEU SEQRES 33 C 579 ASP ARG ASP ILE ALA LEU MET LYS LEU LYS LYS PRO VAL SEQRES 34 C 579 ALA PHE SER ASP TYR ILE HIS PRO VAL CYS LEU PRO ASP SEQRES 35 C 579 ARG GLU THR ALA ALA SER LEU LEU GLN ALA GLY TYR LYS SEQRES 36 C 579 GLY ARG VAL THR GLY TRP GLY ASN LEU LYS GLU THR TRP SEQRES 37 C 579 THR ALA ASN VAL GLY LYS GLY GLN PRO SER VAL LEU GLN SEQRES 38 C 579 VAL VAL ASN LEU PRO ILE VAL GLU ARG PRO VAL CYS LYS SEQRES 39 C 579 ASP SER THR ARG ILE ARG ILE THR ASP ASN MET PHE CYS SEQRES 40 C 579 ALA GLY TYR LYS PRO ASP GLU GLY LYS ARG GLY ASP ALA SEQRES 41 C 579 CYS GLU GLY ASP SER GLY GLY PRO PHE VAL MET LYS SER SEQRES 42 C 579 PRO PHE ASN ASN ARG TRP TYR GLN MET GLY ILE VAL SER SEQRES 43 C 579 TRP GLY GLU GLY CYS ASP ARG ASP GLY LYS TYR GLY PHE SEQRES 44 C 579 TYR THR HIS VAL PHE ARG LEU LYS LYS TRP ILE GLN LYS SEQRES 45 C 579 VAL ILE ASP GLN PHE GLY GLU HELIX 1 AA1 SER A 122 GLY A 129 1 8 HELIX 2 AA2 THR A 183 HIS A 190 1 8 HELIX 3 AA3 SER B 302 SER B 306 5 5 HELIX 4 AA4 GLY B 348 GLN B 352 5 5 SHEET 1 AA1 2 ILE A 10 SER A 12 0 SHEET 2 AA1 2 LYS A 104 GLU A 106 1 O GLU A 106 N MET A 11 SHEET 1 AA2 2 VAL A 19 MET A 21 0 SHEET 2 AA2 2 LEU A 74 ILE A 76 -1 O ILE A 76 N VAL A 19 SHEET 1 AA3 3 LYS A 46 ILE A 49 0 SHEET 2 AA3 3 LEU A 34 GLN A 38 -1 N TRP A 36 O ILE A 49 SHEET 3 AA3 3 CYS A 89 LEU A 91 -1 O GLN A 90 N HIS A 35 SHEET 1 AA4 4 THR A 115 PHE A 119 0 SHEET 2 AA4 4 VAL A 134 PHE A 140 -1 O ASN A 138 N THR A 115 SHEET 3 AA4 4 TYR A 174 LEU A 180 -1 O MET A 176 N LEU A 137 SHEET 4 AA4 4 VAL A 160 TRP A 164 -1 N LEU A 161 O THR A 179 SHEET 1 AA5 4 SER A 154 GLU A 155 0 SHEET 2 AA5 4 LYS A 148 ILE A 151 -1 N ILE A 151 O SER A 154 SHEET 3 AA5 4 SER A 192 ALA A 197 -1 O GLU A 196 N LYS A 148 SHEET 4 AA5 4 ILE A 206 ASN A 211 -1 O PHE A 210 N TYR A 193 SHEET 1 AA6 2 VAL B 220 GLU B 221 0 SHEET 2 AA6 2 ALA B 239 SER B 240 -1 O SER B 240 N VAL B 220 SHEET 1 AA7 3 LEU B 233 CYS B 237 0 SHEET 2 AA7 3 ILE B 293 MET B 298 -1 O LEU B 294 N CYS B 237 SHEET 3 AA7 3 THR B 284 ASP B 288 -1 N ASP B 288 O ILE B 293 SHEET 1 AA8 5 THR B 273 TYR B 274 0 SHEET 2 AA8 5 ARG B 259 ILE B 266 -1 N THR B 265 O TYR B 274 SHEET 3 AA8 5 MET B 249 THR B 255 -1 N THR B 255 O ARG B 259 SHEET 4 AA8 5 ALA B 307 ARG B 313 -1 O THR B 312 N TYR B 250 SHEET 5 AA8 5 THR B 328 VAL B 330 -1 O VAL B 330 N ALA B 307 SHEET 1 AA9 4 PRO B 344 LEU B 345 0 SHEET 2 AA9 4 LEU B 359 CYS B 361 -1 O GLY B 360 N LEU B 345 SHEET 3 AA9 4 TYR B 396 VAL B 402 -1 O VAL B 402 N LEU B 359 SHEET 4 AA9 4 VAL B 384 LEU B 391 -1 N HIS B 385 O SER B 401 SHEET 1 AB1 2 THR B 372 TRP B 375 0 SHEET 2 AB1 2 CYS B 416 ALA B 419 -1 O ALA B 419 N THR B 372 SHEET 1 AB2 2 TRP C 125 TYR C 127 0 SHEET 2 AB2 2 ARG C 135 GLU C 137 -1 O GLN C 136 N CYS C 126 SSBOND 1 CYS A 23 CYS A 89 1555 1555 2.04 SSBOND 2 CYS A 135 CYS A 195 1555 1555 2.04 SSBOND 3 CYS B 237 CYS B 311 1555 1555 2.04 SSBOND 4 CYS B 361 CYS B 416 1555 1555 2.03 SSBOND 5 CYS C 65 CYS C 143 1555 1555 2.03 SSBOND 6 CYS C 86 CYS C 126 1555 1555 2.03 SSBOND 7 CYS C 114 CYS C 138 1555 1555 2.03 CISPEP 1 SER A 7 PRO A 8 0 -8.49 CISPEP 2 PHE B 367 PRO B 368 0 0.24 CISPEP 3 GLU B 369 PRO B 370 0 3.21 CISPEP 4 TYR C 93 PRO C 94 0 2.88 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