HEADER MEMBRANE PROTEIN 03-JAN-25 9MQH TITLE INACTIVE MU-OPIOID RECEPTOR WITH NB6M, NABFAB, AND ISOQUINUCLIDINE TITLE 2 COMPOUND #33 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MU-TYPE OPIOID RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: M-OR-1,MOR-1,MU OPIATE RECEPTOR,MU OPIOID RECEPTOR,MOP,HMOP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: OPRM1, MOR1; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS G-PROTEIN COUPLED RECEPTOR, MU-OPIOID, ISOQUINUCLIDINE, ANTAGONIST, KEYWDS 2 NANOBODIES, FABS, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.Y.KIM,S.F.VIGNERON,C.BILLESBOLLE,A.MANGLIK,B.K.SHOICHET REVDAT 1 12-FEB-25 9MQH 0 JRNL AUTH S.F.VIGNERON,S.OHNO,J.BRAZ,J.Y.KIM,O.S.KWEON,C.WEBB, JRNL AUTH 2 C.BILLESBOLLE,K.BHARDWAJ,J.IRWIN,A.MANGLIK,A.I.BASBAUM, JRNL AUTH 3 J.A.ELLMAN,B.K.SHOICHET JRNL TITL DOCKING 14 MILLION VIRTUAL ISOQUINUCLIDINES AGAINST THE MU JRNL TITL 2 AND KAPPA OPIOID RECEPTORS REVEALS DUAL ANTAGONISTS-INVERSE JRNL TITL 3 AGONISTS WITH REDUCED WITHDRAWAL EFFECTS. JRNL REF BIORXIV 2025 JRNL REFN ISSN 2692-8205 JRNL PMID 39868130 JRNL DOI 10.1101/2025.01.09.632033 REMARK 2 REMARK 2 RESOLUTION. 3.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX 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 : NULL 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) : 3.900 REMARK 3 NUMBER OF PARTICLES : 40722 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9MQH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1000291534. 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 : HUMAN MU-OPIOID RECEPTOR 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 : 7.50 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2100.00 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) : 4580.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 ASP A -10 REMARK 465 TYR A -9 REMARK 465 LYS A -8 REMARK 465 ASP A -7 REMARK 465 ASP A -6 REMARK 465 ASP A -5 REMARK 465 ASP A -4 REMARK 465 ALA A -3 REMARK 465 SER A -2 REMARK 465 ILE A -1 REMARK 465 ASP A 0 REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 THR A 8 REMARK 465 ASN A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 ASN A 12 REMARK 465 CYS A 13 REMARK 465 THR A 14 REMARK 465 ASP A 15 REMARK 465 ALA A 16 REMARK 465 LEU A 17 REMARK 465 ALA A 18 REMARK 465 TYR A 19 REMARK 465 SER A 20 REMARK 465 SER A 21 REMARK 465 CYS A 22 REMARK 465 SER A 23 REMARK 465 PRO A 24 REMARK 465 ALA A 25 REMARK 465 PRO A 26 REMARK 465 SER A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 SER A 30 REMARK 465 TRP A 31 REMARK 465 VAL A 32 REMARK 465 ASN A 33 REMARK 465 LEU A 34 REMARK 465 SER A 35 REMARK 465 HIS A 36 REMARK 465 LEU A 37 REMARK 465 ASP A 38 REMARK 465 GLY A 39 REMARK 465 ASN A 40 REMARK 465 LEU A 41 REMARK 465 SER A 42 REMARK 465 ASP A 43 REMARK 465 PRO A 44 REMARK 465 CYS A 45 REMARK 465 GLY A 46 REMARK 465 PRO A 47 REMARK 465 ASN A 48 REMARK 465 ARG A 49 REMARK 465 THR A 50 REMARK 465 ASP A 51 REMARK 465 LEU A 52 REMARK 465 GLY A 53 REMARK 465 GLY A 54 REMARK 465 ARG A 55 REMARK 465 ASP A 56 REMARK 465 SER A 57 REMARK 465 LEU A 58 REMARK 465 CYS A 59 REMARK 465 PRO A 60 REMARK 465 PRO A 61 REMARK 465 THR A 62 REMARK 465 GLY A 63 REMARK 465 SER A 64 REMARK 465 PRO A 65 REMARK 465 SER A 66 REMARK 465 MET A 67 REMARK 465 ILE A 68 REMARK 465 THR A 69 REMARK 465 ALA A 70 REMARK 465 ILE A 71 REMARK 465 HIS A 225 REMARK 465 PRO A 226 REMARK 465 PRO A 355 REMARK 465 THR A 356 REMARK 465 SER A 357 REMARK 465 SER A 358 REMARK 465 ASN A 359 REMARK 465 ILE A 360 REMARK 465 GLU A 361 REMARK 465 GLN A 362 REMARK 465 GLN A 363 REMARK 465 ASN A 364 REMARK 465 SER A 365 REMARK 465 THR A 366 REMARK 465 ARG A 367 REMARK 465 ILE A 368 REMARK 465 ARG A 369 REMARK 465 GLN A 370 REMARK 465 ASN A 371 REMARK 465 THR A 372 REMARK 465 ARG A 373 REMARK 465 ASP A 374 REMARK 465 HIS A 375 REMARK 465 PRO A 376 REMARK 465 SER A 377 REMARK 465 THR A 378 REMARK 465 ALA A 379 REMARK 465 ASN A 380 REMARK 465 THR A 381 REMARK 465 VAL A 382 REMARK 465 ASP A 383 REMARK 465 ARG A 384 REMARK 465 THR A 385 REMARK 465 ASN A 386 REMARK 465 HIS A 387 REMARK 465 GLN A 388 REMARK 465 LEU A 389 REMARK 465 GLU A 390 REMARK 465 ASN A 391 REMARK 465 LEU A 392 REMARK 465 GLU A 393 REMARK 465 ALA A 394 REMARK 465 GLU A 395 REMARK 465 THR A 396 REMARK 465 ALA A 397 REMARK 465 PRO A 398 REMARK 465 LEU A 399 REMARK 465 PRO A 400 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 ILE A 79 CG1 CG2 CD1 REMARK 470 PHE A 86 CG CD1 CD2 CE1 CE2 CZ REMARK 470 MET A 92 CG SD CE REMARK 470 VAL A 96 CG1 CG2 REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 98 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 THR A 99 OG1 CG2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 VAL A 128 CG1 CG2 REMARK 470 LEU A 131 CG CD1 CD2 REMARK 470 VAL A 175 CG1 CG2 REMARK 470 LYS A 176 CG CD CE NZ REMARK 470 LEU A 178 CG CD1 CD2 REMARK 470 ASP A 179 CG OD1 OD2 REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 200 CG1 CG2 CD1 REMARK 470 LYS A 211 CG CD CE NZ REMARK 470 TYR A 212 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 213 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 214 CG CD OE1 NE2 REMARK 470 SER A 216 OG REMARK 470 ASP A 218 CG OD1 OD2 REMARK 470 THR A 222 OG1 CG2 REMARK 470 SER A 224 OG REMARK 470 THR A 227 OG1 CG2 REMARK 470 TRP A 228 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 228 CZ3 CH2 REMARK 470 GLU A 231 CG CD OE1 OE2 REMARK 470 MET A 245 CG SD CE REMARK 470 ARG A 260 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 262 CG CD CE NZ REMARK 470 SER A 263 OG REMARK 470 SER A 268 OG REMARK 470 SER A 270 OG REMARK 470 GLU A 272 CG CD OE1 OE2 REMARK 470 LYS A 273 CG CD CE NZ REMARK 470 ARG A 275 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 279 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 301 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 THR A 309 OG1 CG2 REMARK 470 GLU A 312 CG CD OE1 OE2 REMARK 470 THR A 313 OG1 CG2 REMARK 470 THR A 314 OG1 CG2 REMARK 470 THR A 317 OG1 CG2 REMARK 470 LEU A 337 CG CD1 CD2 REMARK 470 GLU A 343 CG CD OE1 OE2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 ARG A 347 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 350 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 351 CG CD OE1 OE2 REMARK 470 CYS A 353 SG REMARK 470 ILE A 354 CG1 CG2 CD1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-48524 RELATED DB: EMDB REMARK 900 INACTIVE MU-OPIOID RECEPTOR WITH NB6M, NABFAB, AND ISOQUINUCLIDINE REMARK 900 COMPOUND #33 DBREF 9MQH A 1 400 UNP P35372 OPRM_HUMAN 1 400 SEQADV 9MQH ASP A -10 UNP P35372 EXPRESSION TAG SEQADV 9MQH TYR A -9 UNP P35372 EXPRESSION TAG SEQADV 9MQH LYS A -8 UNP P35372 EXPRESSION TAG SEQADV 9MQH ASP A -7 UNP P35372 EXPRESSION TAG SEQADV 9MQH ASP A -6 UNP P35372 EXPRESSION TAG SEQADV 9MQH ASP A -5 UNP P35372 EXPRESSION TAG SEQADV 9MQH ASP A -4 UNP P35372 EXPRESSION TAG SEQADV 9MQH ALA A -3 UNP P35372 EXPRESSION TAG SEQADV 9MQH SER A -2 UNP P35372 EXPRESSION TAG SEQADV 9MQH ILE A -1 UNP P35372 EXPRESSION TAG SEQADV 9MQH ASP A 0 UNP P35372 EXPRESSION TAG SEQADV 9MQH LEU A 266 UNP P35372 MET 266 CONFLICT SEQADV 9MQH ARG A 271 UNP P35372 LYS 271 CONFLICT SEQRES 1 A 411 ASP TYR LYS ASP ASP ASP ASP ALA SER ILE ASP MET ASP SEQRES 2 A 411 SER SER ALA ALA PRO THR ASN ALA SER ASN CYS THR ASP SEQRES 3 A 411 ALA LEU ALA TYR SER SER CYS SER PRO ALA PRO SER PRO SEQRES 4 A 411 GLY SER TRP VAL ASN LEU SER HIS LEU ASP GLY ASN LEU SEQRES 5 A 411 SER ASP PRO CYS GLY PRO ASN ARG THR ASP LEU GLY GLY SEQRES 6 A 411 ARG ASP SER LEU CYS PRO PRO THR GLY SER PRO SER MET SEQRES 7 A 411 ILE THR ALA ILE THR ILE MET ALA LEU TYR SER ILE VAL SEQRES 8 A 411 CYS VAL VAL GLY LEU PHE GLY ASN PHE LEU VAL MET TYR SEQRES 9 A 411 VAL ILE VAL ARG TYR THR LYS MET LYS THR ALA THR ASN SEQRES 10 A 411 ILE TYR ILE PHE ASN LEU ALA LEU ALA ASP ALA LEU ALA SEQRES 11 A 411 THR SER THR LEU PRO PHE GLN SER VAL ASN TYR LEU MET SEQRES 12 A 411 GLY THR TRP PRO PHE GLY THR ILE LEU CYS LYS ILE VAL SEQRES 13 A 411 ILE SER ILE ASP TYR TYR ASN MET PHE THR SER ILE PHE SEQRES 14 A 411 THR LEU CYS THR MET SER VAL ASP ARG TYR ILE ALA VAL SEQRES 15 A 411 CYS HIS PRO VAL LYS ALA LEU ASP PHE ARG THR PRO ARG SEQRES 16 A 411 ASN ALA LYS ILE ILE ASN VAL CYS ASN TRP ILE LEU SER SEQRES 17 A 411 SER ALA ILE GLY LEU PRO VAL MET PHE MET ALA THR THR SEQRES 18 A 411 LYS TYR ARG GLN GLY SER ILE ASP CYS THR LEU THR PHE SEQRES 19 A 411 SER HIS PRO THR TRP TYR TRP GLU ASN LEU LEU LYS ILE SEQRES 20 A 411 CYS VAL PHE ILE PHE ALA PHE ILE MET PRO VAL LEU ILE SEQRES 21 A 411 ILE THR VAL CYS TYR GLY LEU MET ILE LEU ARG LEU LYS SEQRES 22 A 411 SER VAL ARG LEU LEU SER GLY SER ARG GLU LYS ASP ARG SEQRES 23 A 411 ASN LEU ARG ARG ILE THR ARG MET VAL LEU VAL VAL VAL SEQRES 24 A 411 ALA VAL PHE ILE VAL CYS TRP THR PRO ILE HIS ILE TYR SEQRES 25 A 411 VAL ILE ILE LYS ALA LEU VAL THR ILE PRO GLU THR THR SEQRES 26 A 411 PHE GLN THR VAL SER TRP HIS PHE CYS ILE ALA LEU GLY SEQRES 27 A 411 TYR THR ASN SER CYS LEU ASN PRO VAL LEU TYR ALA PHE SEQRES 28 A 411 LEU ASP GLU ASN PHE LYS ARG CYS PHE ARG GLU PHE CYS SEQRES 29 A 411 ILE PRO THR SER SER ASN ILE GLU GLN GLN ASN SER THR SEQRES 30 A 411 ARG ILE ARG GLN ASN THR ARG ASP HIS PRO SER THR ALA SEQRES 31 A 411 ASN THR VAL ASP ARG THR ASN HIS GLN LEU GLU ASN LEU SEQRES 32 A 411 GLU ALA GLU THR ALA PRO LEU PRO HELIX 1 AA1 THR A 72 ARG A 97 1 26 HELIX 2 AA2 TYR A 98 LYS A 102 5 5 HELIX 3 AA3 THR A 103 THR A 122 1 20 HELIX 4 AA4 THR A 122 ASN A 129 1 8 HELIX 5 AA5 GLY A 138 HIS A 173 1 36 HELIX 6 AA6 HIS A 173 ARG A 181 1 9 HELIX 7 AA7 THR A 182 LYS A 187 1 6 HELIX 8 AA8 LYS A 187 ALA A 208 1 22 HELIX 9 AA9 TYR A 229 PHE A 243 1 15 HELIX 10 AB1 PHE A 243 LYS A 262 1 20 HELIX 11 AB2 SER A 270 THR A 309 1 40 HELIX 12 AB3 THR A 313 TYR A 338 1 26 HELIX 13 AB4 ASP A 342 ILE A 354 1 13 SHEET 1 AA1 2 LYS A 211 TYR A 212 0 SHEET 2 AA1 2 ILE A 217 ASP A 218 -1 O ASP A 218 N LYS A 211 SSBOND 1 CYS A 142 CYS A 219 1555 1555 2.03 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