10 20 30 40 50 60 70 80 2AMK - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SIGNALING PROTEIN 09-AUG-05 2AMK
TITLE THEORETICAL MODEL OF RAT M3 MUSCARINIC ACETYLCHOLINE TITLE 2 RECEPTOR
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUSCARINIC ACETYLCHOLINE RECEPTOR M3; COMPND 3 CHAIN: A
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT
KEYWDS GPCR, TRANSMEMBRANE PROTEIN
EXPDTA THEORETICAL MODEL
AUTHOR B.LI,N.M.NOWAK,S.K.KIM,K.A.JACOBSON,A.BAGHERI,C.SCHMIDT, AUTHOR 2 J.WESS
REVDAT 1 25-OCT-05 2AMK 0
JRNL AUTH B.LI,N.M.NOWAK,S.K.KIM,K.A.JACOBSON,A.BAGHERI, JRNL AUTH 2 C.SCHMIDT,J.WESS JRNL TITL RANDOM MUTAGENESIS OF THE M3 MUSCARINIC JRNL TITL 2 ACETYLCHOLINE RECEPTOR EXPRESSED IN YEAST JRNL REF J.BIOL.CHEM. V. 280 5664 2005 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.J.HAN,F.F.HAMDAN,S.K.KIM,K.A.JACOBSON,L.BRICHTA, REMARK 1 AUTH 2 L.M.BLOODWORTH,J.H.LI,J.WESS REMARK 1 TITL PRONOUNCED CONFORMATIONAL CHANGES FOLLOWING REMARK 1 TITL 2 AGONIST ACTIVATION OF THE M(3) MUSCARINIC REMARK 1 TITL 3 ACETYLCHOLINE RECEPTOR. REMARK 1 REF J.BIOL.CHEM. V. 280 24870 2005 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SYBYL 7.0 REMARK 3 AUTHORS : TRIPOS COMPANY REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A RAT M3 RECEPTOR MODEL WAS BUILT REMARK 3 USING HOMOLOGY MODELING FROM THE X-RAY STRUCTURE OF BOVINE REMARK 3 RHODOPSIN WITH 2.8 RESOLUTION. MULTIPLE-SEQUENCE ALIGNMENT REMARK 3 DATA OF SELECTED G PROTEIN-COUPLED RECEPTORS WERE USED FOR THE REMARK 3 CONSTRUCTION OF RAT M3 RECEPTOR TM DOMAINS. FOR THE MODEL OF REMARK 3 THE SECOND EXTRACELLULAR LOOP, EL2, TWO BETA-SHEET DOMAINS IN REMARK 3 RHODOPSIN WERE FIRST ALIGNED INCLUDING THE DISULFIDE BOND REMARK 3 BETWEEN CYS140 AND CYS220 AND THEN OTHER PARTS WERE ADDED OR REMARK 3 DELETED. TO CONSTRUCT THE N-TERMINAL REGION, INTRA AND REMARK 3 EXTRACELLULAR LOOPS, EACH ALIGNMENT WAS MANUALLY ADJUSTED REMARK 3 PRESERVING THE OVERALL SHAPE OF LOOP. N-ACETYL AND N-METHYL REMARK 3 AMIDE GROUPS BLOCKED THE N-TERMINAL AND C-TERMINAL REGION, REMARK 3 RESPECTIVELY. ALL HELICES WITH BACKBONE CONSTRAINTS AND LOOPS REMARK 3 WERE MINIMIZED SEPARATELY. AFTER COMBINING TOGETHER, ALL REMARK 3 STRUCTURES WERE RE-MINIMIZED INITIALLY WITH BACKBONE REMARK 3 CONSTRAINTS IN THE SECONDARY STRUCTURE AND THEN WITHOUT ANY REMARK 3 CONSTRAINTS. THE AMBER ALL-ATOM FORCE FIELD AND THE CONJUGATE REMARK 3 GRADIENT METHOD WITH A FIXED DIELECTRIC CONSTANT OF 4.0 WERE REMARK 3 USED FOR ALL CALCULATIONS, TERMINATING WHEN THE GRADIENT REMARK 3 REACHED 0.05 KCAL/MOL/ . FOR THE CONFORMATIONAL REFINEMENT OF REMARK 3 THE RAT M3 RECEPTOR, THE OPTIMIZED STRUCTURES WERE THEN USED REMARK 3 AS THE STARTING POINT FOR SUBSEQUENT 50 PS MOLECULAR DYNAMICS REMARK 3 (MD), DURING WHICH THE PROTEIN BACKBONE ATOMS IN THE SECONDARY REMARK 3 STRUCTURES WERE CONSTRAINED AS IN THE PREVIOUS STEP. THE REMARK 3 OPTIONS OF MD AT 300K WITH 0.2 PS COUPLING CONSTANT WERE A REMARK 3 TIME STEP OF 1FS AND A NON-BONDED UPDATE EVERY 25 FS. THE REMARK 3 LENGTHS OF BONDS WITH HYDROGEN ATOMS WERE CONSTRAINED REMARK 3 ACCORDING TO THE SHAKE ALGORITHM. THE AVERAGE STRUCTURE FROM REMARK 3 THE LAST 10 PS TRAJECTORY OF MD WAS RE-MINIMIZED WITH BACKBONE REMARK 3 CONSTRAINTS IN THE SECONDARY STRUCTURE AND THEN WITHOUT ALL REMARK 3 CONSTRAINTS.
REMARK 4 REMARK 4 2AMK COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-2005. REMARK 100 THE RCSB ID CODE IS RCSB034068.
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL
REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.
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 A 263 REMARK 465 LEU A 264 REMARK 465 ALA A 265 REMARK 465 GLY A 266 REMARK 465 LEU A 267 REMARK 465 GLN A 268 REMARK 465 ALA A 269 REMARK 465 SER A 270 REMARK 465 GLY A 271 REMARK 465 THR A 272 REMARK 465 GLU A 273 REMARK 465 ALA A 274 REMARK 465 GLU A 275 REMARK 465 ALA A 276 REMARK 465 GLU A 277 REMARK 465 ASN A 278 REMARK 465 PHE A 279 REMARK 465 VAL A 280 REMARK 465 HIS A 281 REMARK 465 PRO A 282 REMARK 465 THR A 283 REMARK 465 GLY A 284 REMARK 465 SER A 285 REMARK 465 SER A 286 REMARK 465 ARG A 287 REMARK 465 SER A 288 REMARK 465 CYS A 289 REMARK 465 SER A 290 REMARK 465 SER A 291 REMARK 465 TYR A 292 REMARK 465 GLU A 293 REMARK 465 LEU A 294 REMARK 465 GLN A 295 REMARK 465 GLN A 296 REMARK 465 GLN A 297 REMARK 465 GLY A 298 REMARK 465 VAL A 299 REMARK 465 LYS A 300 REMARK 465 ARG A 301 REMARK 465 SER A 302 REMARK 465 SER A 303 REMARK 465 ARG A 304 REMARK 465 ARG A 305 REMARK 465 LYS A 306 REMARK 465 TYR A 307 REMARK 465 GLY A 308 REMARK 465 ARG A 309 REMARK 465 CYS A 310 REMARK 465 HIS A 311 REMARK 465 PHE A 312 REMARK 465 TRP A 313 REMARK 465 PHE A 314 REMARK 465 THR A 315 REMARK 465 THR A 316 REMARK 465 LYS A 317 REMARK 465 SER A 318 REMARK 465 TRP A 319 REMARK 465 LYS A 320 REMARK 465 PRO A 321 REMARK 465 SER A 322 REMARK 465 ALA A 323 REMARK 465 GLU A 324 REMARK 465 GLN A 325 REMARK 465 MET A 326 REMARK 465 ASP A 327 REMARK 465 GLN A 328 REMARK 465 ASP A 329 REMARK 465 HIS A 330 REMARK 465 SER A 331 REMARK 465 SER A 332 REMARK 465 SER A 333 REMARK 465 ASP A 334 REMARK 465 SER A 335 REMARK 465 TRP A 336 REMARK 465 ASN A 337 REMARK 465 ASN A 338 REMARK 465 ASN A 339 REMARK 465 ASP A 340 REMARK 465 ALA A 341 REMARK 465 ALA A 342 REMARK 465 ALA A 343 REMARK 465 SER A 344 REMARK 465 LEU A 345 REMARK 465 GLU A 346 REMARK 465 ASN A 347 REMARK 465 SER A 348 REMARK 465 ALA A 349 REMARK 465 SER A 350 REMARK 465 SER A 351 REMARK 465 ASP A 352 REMARK 465 GLU A 353 REMARK 465 GLU A 354 REMARK 465 ASP A 355 REMARK 465 ILE A 356 REMARK 465 GLY A 357 REMARK 465 SER A 358 REMARK 465 GLU A 359 REMARK 465 THR A 360 REMARK 465 ARG A 361 REMARK 465 ALA A 362 REMARK 465 ILE A 363 REMARK 465 TYR A 364 REMARK 465 SER A 365 REMARK 465 ILE A 366 REMARK 465 VAL A 367 REMARK 465 LEU A 368 REMARK 465 LYS A 369 REMARK 465 LEU A 370 REMARK 465 PRO A 371 REMARK 465 GLY A 372 REMARK 465 HIS A 373 REMARK 465 SER A 374 REMARK 465 SER A 375 REMARK 465 ILE A 376 REMARK 465 LEU A 377 REMARK 465 ASN A 378 REMARK 465 SER A 379 REMARK 465 THR A 380 REMARK 465 LYS A 381 REMARK 465 LEU A 382 REMARK 465 PRO A 383 REMARK 465 SER A 384 REMARK 465 SER A 385 REMARK 465 ASP A 386 REMARK 465 ASN A 387 REMARK 465 LEU A 388 REMARK 465 GLN A 389 REMARK 465 VAL A 390 REMARK 465 SER A 391 REMARK 465 ASN A 392 REMARK 465 GLU A 393 REMARK 465 ASP A 394 REMARK 465 LEU A 395 REMARK 465 GLY A 396 REMARK 465 THR A 397 REMARK 465 VAL A 398 REMARK 465 ASP A 399 REMARK 465 VAL A 400 REMARK 465 GLU A 401 REMARK 465 ARG A 402 REMARK 465 ASN A 403 REMARK 465 ALA A 404 REMARK 465 HIS A 405 REMARK 465 LYS A 406 REMARK 465 LEU A 407 REMARK 465 GLN A 408 REMARK 465 ALA A 409 REMARK 465 GLN A 410 REMARK 465 LYS A 411 REMARK 465 SER A 412 REMARK 465 MET A 413 REMARK 465 GLY A 414 REMARK 465 ASP A 415 REMARK 465 GLY A 416 REMARK 465 ASP A 417 REMARK 465 ASN A 418 REMARK 465 CYS A 419 REMARK 465 GLN A 420 REMARK 465 LYS A 421 REMARK 465 ASP A 422 REMARK 465 PHE A 423 REMARK 465 THR A 424 REMARK 465 LYS A 425 REMARK 465 LEU A 426 REMARK 465 PRO A 427 REMARK 465 ILE A 428 REMARK 465 GLN A 429 REMARK 465 LEU A 430 REMARK 465 GLU A 431 REMARK 465 SER A 432 REMARK 465 ALA A 433 REMARK 465 VAL A 434 REMARK 465 ASP A 435 REMARK 465 THR A 436 REMARK 465 GLY A 437 REMARK 465 LYS A 438 REMARK 465 THR A 439 REMARK 465 SER A 440 REMARK 465 ASP A 441 REMARK 465 THR A 442 REMARK 465 ASN A 443 REMARK 465 SER A 444 REMARK 465 SER A 445 REMARK 465 ALA A 446 REMARK 465 ASP A 447 REMARK 465 LYS A 448 REMARK 465 THR A 449 REMARK 465 THR A 450 REMARK 465 ALA A 451 REMARK 465 THR A 452 REMARK 465 LEU A 453 REMARK 465 PRO A 454 REMARK 465 LEU A 455 REMARK 465 SER A 456 REMARK 465 PHE A 457 REMARK 465 LYS A 458 REMARK 465 GLU A 459 REMARK 465 ALA A 460 REMARK 465 THR A 461 REMARK 465 LEU A 462 REMARK 465 ALA A 463 REMARK 465 LYS A 464 REMARK 465 ARG A 465 REMARK 465 PHE A 466 REMARK 465 ALA A 467 REMARK 465 LEU A 468 REMARK 465 LYS A 469 REMARK 465 THR A 470 REMARK 465 ARG A 471 REMARK 465 SER A 472 REMARK 465 GLN A 473 REMARK 465 ILE A 474 REMARK 465 THR A 475 REMARK 465 LYS A 476 REMARK 465 ARG A 477 REMARK 465 NME A 561
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 C CYS A 560 N NME A 561 1.34 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 M RES CSSEQI PSI PHI REMARK 500 ASN A 131 -41.37 74.93 REMARK 500 ARG A 171 158.31 63.39 REMARK 500 GLN A 207 150.66 117.70 REMARK 500 LEU A 225 -71.55 148.28
DBREF 2AMK A 56 560 UNP P08483 ACM3_RAT 56 560
SEQADV 2AMK ACE A 55 UNP P08483 INSERTION SEQADV 2AMK NME A 561 UNP P08483 INSERTION
SEQRES 1 A 507 ACE SER ASP PRO LEU GLY GLY HIS THR ILE TRP GLN VAL SEQRES 2 A 507 VAL PHE ILE ALA PHE LEU THR GLY PHE LEU ALA LEU VAL SEQRES 3 A 507 THR ILE ILE GLY ASN ILE LEU VAL ILE VAL ALA PHE LYS SEQRES 4 A 507 VAL ASN LYS GLN LEU LYS THR VAL ASN ASN TYR PHE LEU SEQRES 5 A 507 LEU SER LEU ALA CYS ALA ASP LEU ILE ILE GLY VAL ILE SEQRES 6 A 507 SER MET ASN LEU PHE THR THR TYR ILE ILE MET ASN ARG SEQRES 7 A 507 TRP ALA LEU GLY ASN LEU ALA CYS ASP LEU TRP LEU SER SEQRES 8 A 507 ILE ASP TYR VAL ALA SER ASN ALA SER VAL MET ASN LEU SEQRES 9 A 507 LEU VAL ILE SER PHE ASP ARG TYR PHE SER ILE THR ARG SEQRES 10 A 507 PRO LEU THR TYR ARG ALA LYS ARG THR THR LYS ARG ALA SEQRES 11 A 507 GLY VAL MET ILE GLY LEU ALA TRP VAL ILE SER PHE VAL SEQRES 12 A 507 LEU TRP ALA PRO ALA ILE LEU PHE TRP GLN TYR PHE VAL SEQRES 13 A 507 GLY LYS ARG THR VAL PRO PRO GLY GLU CYS PHE ILE GLN SEQRES 14 A 507 PHE LEU SER GLU PRO THR ILE THR PHE GLY THR ALA ILE SEQRES 15 A 507 ALA ALA PHE TYR MET PRO VAL THR ILE MET THR ILE LEU SEQRES 16 A 507 TYR TRP ARG ILE TYR LYS GLU THR GLU LYS ARG THR LYS SEQRES 17 A 507 GLU LEU ALA GLY LEU GLN ALA SER GLY THR GLU ALA GLU SEQRES 18 A 507 ALA GLU ASN PHE VAL HIS PRO THR GLY SER SER ARG SER SEQRES 19 A 507 CYS SER SER TYR GLU LEU GLN GLN GLN GLY VAL LYS ARG SEQRES 20 A 507 SER SER ARG ARG LYS TYR GLY ARG CYS HIS PHE TRP PHE SEQRES 21 A 507 THR THR LYS SER TRP LYS PRO SER ALA GLU GLN MET ASP SEQRES 22 A 507 GLN ASP HIS SER SER SER ASP SER TRP ASN ASN ASN ASP SEQRES 23 A 507 ALA ALA ALA SER LEU GLU ASN SER ALA SER SER ASP GLU SEQRES 24 A 507 GLU ASP ILE GLY SER GLU THR ARG ALA ILE TYR SER ILE SEQRES 25 A 507 VAL LEU LYS LEU PRO GLY HIS SER SER ILE LEU ASN SER SEQRES 26 A 507 THR LYS LEU PRO SER SER ASP ASN LEU GLN VAL SER ASN SEQRES 27 A 507 GLU ASP LEU GLY THR VAL ASP VAL GLU ARG ASN ALA HIS SEQRES 28 A 507 LYS LEU GLN ALA GLN LYS SER MET GLY ASP GLY ASP ASN SEQRES 29 A 507 CYS GLN LYS ASP PHE THR LYS LEU PRO ILE GLN LEU GLU SEQRES 30 A 507 SER ALA VAL ASP THR GLY LYS THR SER ASP THR ASN SER SEQRES 31 A 507 SER ALA ASP LYS THR THR ALA THR LEU PRO LEU SER PHE SEQRES 32 A 507 LYS GLU ALA THR LEU ALA LYS ARG PHE ALA LEU LYS THR SEQRES 33 A 507 ARG SER GLN ILE THR LYS ARG LYS ARG MET SER LEU ILE SEQRES 34 A 507 LYS GLU LYS LYS ALA ALA GLN THR LEU SER ALA ILE LEU SEQRES 35 A 507 LEU ALA PHE ILE ILE THR TRP THR PRO TYR ASN ILE MET SEQRES 36 A 507 VAL LEU VAL ASN THR PHE CYS ASP SER CYS ILE PRO LYS SEQRES 37 A 507 THR TYR TRP ASN LEU GLY TYR TRP LEU CYS TYR ILE ASN SEQRES 38 A 507 SER THR VAL ASN PRO VAL CYS TYR ALA LEU CYS ASN LYS SEQRES 39 A 507 THR PHE ARG THR THR PHE LYS THR LEU LEU LEU CYS NME
HET ACE A 55 6 HET NME A 561 6
HETNAM ACE ACETYL GROUP HETNAM NME METHYLAMINE
FORMUL 1 ACE C2 H4 O FORMUL 2 NME C H5 N
HELIX 1 1 THR A 63 ASN A 95 1 33 HELIX 2 2 THR A 100 ILE A 119 1 20 HELIX 3 3 ILE A 119 MET A 130 1 12 HELIX 4 4 ASN A 137 ILE A 169 1 33 HELIX 5 5 THR A 180 VAL A 197 1 18 HELIX 6 6 LEU A 198 LEU A 204 1 7 HELIX 7 7 GLU A 227 PHE A 239 1 13 HELIX 8 8 PHE A 239 TYR A 254 1 16 HELIX 9 9 LEU A 482 THR A 514 1 33 HELIX 10 10 PRO A 521 CYS A 532 1 12 HELIX 11 11 ILE A 534 ASN A 547 1 14 HELIX 12 12 ASN A 547 LEU A 559 1 13
SHEET 1 A 2 PHE A 209 LYS A 212 0 SHEET 2 A 2 GLU A 219 ILE A 222 -1 O GLU A 219 N LYS A 212
SSBOND 1 CYS A 140 CYS A 220
CISPEP 1 PRO A 216 PRO A 217 0 1.40
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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