HEADER SIGNALING PROTEIN 11-JUN-23 8JPF TITLE FOCUSED REFIMENT STRUCTURE OF NTSR1 IN NTSR1-GRK2-GALPHA(Q) COMPLEXES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NTS; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NEUROTENSIN RECEPTOR TYPE 1; COMPND 7 CHAIN: R; COMPND 8 SYNONYM: NT-R-1,NTR1,HIGH-AFFINITY LEVOCABASTINE-INSENSITIVE COMPND 9 NEUROTENSIN RECEPTOR,NTRH; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 GENE: NTSR1, NTRR; SOURCE 10 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS BIASED SIGNALING, SIGNALING PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.DUAN,H.LIU,F.ZHAO,Q.YUAN,Y.JI,H.E.XU REVDAT 3 30-AUG-23 8JPF 1 JRNL REVDAT 2 16-AUG-23 8JPF 1 JRNL REVDAT 1 09-AUG-23 8JPF 0 JRNL AUTH J.DUAN,H.LIU,F.ZHAO,Q.YUAN,Y.JI,X.CAI,X.HE,X.LI,J.LI,K.WU, JRNL AUTH 2 T.GAO,S.ZHU,S.LIN,M.W.WANG,X.CHENG,W.YIN,Y.JIANG,D.YANG, JRNL AUTH 3 H.E.XU JRNL TITL GPCR ACTIVATION AND GRK2 ASSEMBLY BY A BIASED INTRACELLULAR JRNL TITL 2 AGONIST. JRNL REF NATURE V. 620 676 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 37532940 JRNL DOI 10.1038/S41586-023-06395-9 REMARK 2 REMARK 2 RESOLUTION. 3.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL 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) : 3.020 REMARK 3 NUMBER OF PARTICLES : 474232 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8JPF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038526. 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 : FOCUSED REFIMENT STRUCTURE OF REMARK 245 NTSR1 IN NTSR1-GRK2-GALPHA(Q) REMARK 245 COMPLEXES 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 : 7.40 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 : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : DARK FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, R 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 R 1 REMARK 465 ARG R 2 REMARK 465 LEU R 3 REMARK 465 ASN R 4 REMARK 465 SER R 5 REMARK 465 SER R 6 REMARK 465 ALA R 7 REMARK 465 PRO R 8 REMARK 465 GLY R 9 REMARK 465 THR R 10 REMARK 465 PRO R 11 REMARK 465 GLY R 12 REMARK 465 THR R 13 REMARK 465 PRO R 14 REMARK 465 ALA R 15 REMARK 465 ALA R 16 REMARK 465 ASP R 17 REMARK 465 PRO R 18 REMARK 465 PHE R 19 REMARK 465 GLN R 20 REMARK 465 ARG R 21 REMARK 465 ALA R 22 REMARK 465 GLN R 23 REMARK 465 ALA R 24 REMARK 465 GLY R 25 REMARK 465 LEU R 26 REMARK 465 GLU R 27 REMARK 465 GLU R 28 REMARK 465 ALA R 29 REMARK 465 LEU R 30 REMARK 465 LEU R 31 REMARK 465 ALA R 32 REMARK 465 PRO R 33 REMARK 465 GLY R 34 REMARK 465 PHE R 35 REMARK 465 GLY R 36 REMARK 465 ASN R 37 REMARK 465 ALA R 38 REMARK 465 SER R 39 REMARK 465 GLY R 40 REMARK 465 ASN R 41 REMARK 465 ALA R 42 REMARK 465 SER R 43 REMARK 465 GLU R 44 REMARK 465 ARG R 45 REMARK 465 VAL R 46 REMARK 465 LEU R 47 REMARK 465 ALA R 48 REMARK 465 ALA R 49 REMARK 465 PRO R 50 REMARK 465 ALA R 89 REMARK 465 ARG R 90 REMARK 465 LYS R 91 REMARK 465 LYS R 92 REMARK 465 SER R 93 REMARK 465 LEU R 94 REMARK 465 GLN R 95 REMARK 465 SER R 96 REMARK 465 LEU R 97 REMARK 465 GLN R 98 REMARK 465 SER R 99 REMARK 465 GLU R 272 REMARK 465 GLN R 273 REMARK 465 GLY R 274 REMARK 465 GLN R 275 REMARK 465 VAL R 276 REMARK 465 CYS R 277 REMARK 465 THR R 278 REMARK 465 VAL R 279 REMARK 465 GLY R 280 REMARK 465 GLY R 281 REMARK 465 GLU R 282 REMARK 465 HIS R 283 REMARK 465 SER R 284 REMARK 465 THR R 285 REMARK 465 PHE R 286 REMARK 465 SER R 287 REMARK 465 MET R 288 REMARK 465 ALA R 289 REMARK 465 ILE R 290 REMARK 465 LEU R 379 REMARK 465 ALA R 380 REMARK 465 CYS R 381 REMARK 465 LEU R 382 REMARK 465 CYS R 383 REMARK 465 PRO R 384 REMARK 465 VAL R 385 REMARK 465 TRP R 386 REMARK 465 ARG R 387 REMARK 465 ARG R 388 REMARK 465 ARG R 389 REMARK 465 ARG R 390 REMARK 465 LYS R 391 REMARK 465 ARG R 392 REMARK 465 PRO R 393 REMARK 465 ALA R 394 REMARK 465 PHE R 395 REMARK 465 SER R 396 REMARK 465 ARG R 397 REMARK 465 LYS R 398 REMARK 465 ALA R 399 REMARK 465 ASP R 400 REMARK 465 SER R 401 REMARK 465 VAL R 402 REMARK 465 SER R 403 REMARK 465 SER R 404 REMARK 465 ASN R 405 REMARK 465 HIS R 406 REMARK 465 THR R 407 REMARK 465 LEU R 408 REMARK 465 SER R 409 REMARK 465 SER R 410 REMARK 465 ASN R 411 REMARK 465 ALA R 412 REMARK 465 THR R 413 REMARK 465 ARG R 414 REMARK 465 GLU R 415 REMARK 465 THR R 416 REMARK 465 LEU R 417 REMARK 465 TYR R 418 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 R 60 CG1 CG2 CD1 REMARK 470 TYR R 61 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU R 71 CG CD1 CD2 REMARK 470 THR R 78 OG1 CG2 REMARK 470 VAL R 79 CG1 CG2 REMARK 470 THR R 82 OG1 CG2 REMARK 470 PHE R 86 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU R 88 CG CD1 CD2 REMARK 470 TYR R 103 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU R 110 CG CD1 CD2 REMARK 470 MET R 120 CG SD CE REMARK 470 TYR R 125 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN R 126 CG OD1 ND2 REMARK 470 PHE R 127 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE R 128 CG1 CG2 CD1 REMARK 470 TRP R 129 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP R 129 CZ3 CH2 REMARK 470 VAL R 130 CG1 CG2 REMARK 470 HIS R 131 CG ND1 CD2 CE1 NE2 REMARK 470 PHE R 136 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP R 149 CG OD1 OD2 REMARK 470 GLU R 165 CG CD OE1 OE2 REMARK 470 LYS R 177 CG CD CE NZ REMARK 470 THR R 178 OG1 CG2 REMARK 470 LEU R 179 CG CD1 CD2 REMARK 470 MET R 180 CG SD CE REMARK 470 ARG R 182 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 184 CG CD NE CZ NH1 NH2 REMARK 470 LYS R 186 CG CD CE NZ REMARK 470 LYS R 187 CG CD CE NZ REMARK 470 LEU R 198 CG CD1 CD2 REMARK 470 MET R 203 CG SD CE REMARK 470 GLU R 209 CG CD OE1 OE2 REMARK 470 ASN R 211 CG OD1 ND2 REMARK 470 ASP R 215 CG OD1 OD2 REMARK 470 GLN R 217 CG CD OE1 NE2 REMARK 470 HIS R 218 CG ND1 CD2 CE1 NE2 REMARK 470 LEU R 222 CG CD1 CD2 REMARK 470 PHE R 242 CG CD1 CD2 CE1 CE2 CZ REMARK 470 MET R 243 CG SD CE REMARK 470 ARG R 268 CG CD NE CZ NH1 NH2 REMARK 470 ARG R 299 CG CD NE CZ NH1 NH2 REMARK 470 GLU R 332 CG CD OE1 OE2 REMARK 470 PHE R 337 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU R 338 CG CD1 CD2 REMARK 470 HIS R 373 CG ND1 CD2 CE1 NE2 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 TRP R 129 -169.17 -167.95 REMARK 500 GLN R 217 30.97 -141.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-36478 RELATED DB: EMDB REMARK 900 FOCUSED REFIMENT STRUCTURE OF NTSR1 IN NTSR1-GRK2-GALPHA(Q) REMARK 900 COMPLEXES DBREF 8JPF L 8 13 PDB 8JPF 8JPF 8 13 DBREF 8JPF R 1 418 UNP P30989 NTR1_HUMAN 1 418 SEQRES 1 L 6 ARG ARG PRO TYR ILE LEU SEQRES 1 R 418 MET ARG LEU ASN SER SER ALA PRO GLY THR PRO GLY THR SEQRES 2 R 418 PRO ALA ALA ASP PRO PHE GLN ARG ALA GLN ALA GLY LEU SEQRES 3 R 418 GLU GLU ALA LEU LEU ALA PRO GLY PHE GLY ASN ALA SER SEQRES 4 R 418 GLY ASN ALA SER GLU ARG VAL LEU ALA ALA PRO SER SER SEQRES 5 R 418 GLU LEU ASP VAL ASN THR ASP ILE TYR SER LYS VAL LEU SEQRES 6 R 418 VAL THR ALA VAL TYR LEU ALA LEU PHE VAL VAL GLY THR SEQRES 7 R 418 VAL GLY ASN THR VAL THR ALA PHE THR LEU ALA ARG LYS SEQRES 8 R 418 LYS SER LEU GLN SER LEU GLN SER THR VAL HIS TYR HIS SEQRES 9 R 418 LEU GLY SER LEU ALA LEU SER ASP LEU LEU THR LEU LEU SEQRES 10 R 418 LEU ALA MET PRO VAL GLU LEU TYR ASN PHE ILE TRP VAL SEQRES 11 R 418 HIS HIS PRO TRP ALA PHE GLY ASP ALA GLY CYS ARG GLY SEQRES 12 R 418 TYR TYR PHE LEU ARG ASP ALA CYS THR TYR ALA THR ALA SEQRES 13 R 418 LEU ASN VAL ALA SER LEU SER VAL GLU ARG TYR LEU ALA SEQRES 14 R 418 ILE CYS HIS PRO PHE LYS ALA LYS THR LEU MET SER ARG SEQRES 15 R 418 SER ARG THR LYS LYS PHE ILE SER ALA ILE TRP LEU ALA SEQRES 16 R 418 SER ALA LEU LEU ALA VAL PRO MET LEU PHE THR MET GLY SEQRES 17 R 418 GLU GLN ASN ARG SER ALA ASP GLY GLN HIS ALA GLY GLY SEQRES 18 R 418 LEU VAL CYS THR PRO THR ILE HIS THR ALA THR VAL LYS SEQRES 19 R 418 VAL VAL ILE GLN VAL ASN THR PHE MET SER PHE ILE PHE SEQRES 20 R 418 PRO MET VAL VAL ILE SER VAL LEU ASN THR ILE ILE ALA SEQRES 21 R 418 ASN LYS LEU THR VAL MET VAL ARG GLN ALA ALA GLU GLN SEQRES 22 R 418 GLY GLN VAL CYS THR VAL GLY GLY GLU HIS SER THR PHE SEQRES 23 R 418 SER MET ALA ILE GLU PRO GLY ARG VAL GLN ALA LEU ARG SEQRES 24 R 418 HIS GLY VAL ARG VAL LEU ARG ALA VAL VAL ILE ALA PHE SEQRES 25 R 418 VAL VAL CYS TRP LEU PRO TYR HIS VAL ARG ARG LEU MET SEQRES 26 R 418 PHE CYS TYR ILE SER ASP GLU GLN TRP THR PRO PHE LEU SEQRES 27 R 418 TYR ASP PHE TYR HIS TYR PHE TYR MET VAL THR ASN ALA SEQRES 28 R 418 LEU PHE TYR VAL SER SER THR ILE ASN PRO ILE LEU TYR SEQRES 29 R 418 ASN LEU VAL SER ALA ASN PHE ARG HIS ILE PHE LEU ALA SEQRES 30 R 418 THR LEU ALA CYS LEU CYS PRO VAL TRP ARG ARG ARG ARG SEQRES 31 R 418 LYS ARG PRO ALA PHE SER ARG LYS ALA ASP SER VAL SER SEQRES 32 R 418 SER ASN HIS THR LEU SER SER ASN ALA THR ARG GLU THR SEQRES 33 R 418 LEU TYR HET SRW R 501 33 HETNAM SRW 2-[{2-(1-FLUOROCYCLOPROPYL)-4-[4-(2-METHOXYPHENYL) HETNAM 2 SRW PIPERIDIN-1-YL]QUINAZOLIN-6-YL}(METHYL)AMINO]ETHAN-1- HETNAM 3 SRW OL FORMUL 3 SRW C26 H31 F N4 O2 HELIX 1 AA1 SER R 51 ASP R 55 5 5 HELIX 2 AA2 ASP R 59 LEU R 88 1 30 HELIX 3 AA3 VAL R 101 PHE R 127 1 27 HELIX 4 AA4 PHE R 136 HIS R 172 1 37 HELIX 5 AA5 HIS R 172 MET R 180 1 9 HELIX 6 AA6 SER R 181 ALA R 200 1 20 HELIX 7 AA7 PRO R 202 MET R 207 1 6 HELIX 8 AA8 HIS R 229 PHE R 245 1 17 HELIX 9 AA9 PHE R 245 ALA R 271 1 27 HELIX 10 AB1 GLY R 293 ILE R 329 1 37 HELIX 11 AB2 THR R 335 SER R 368 1 34 HELIX 12 AB3 SER R 368 THR R 378 1 11 SHEET 1 AA1 2 GLU R 209 ASN R 211 0 SHEET 2 AA1 2 LEU R 222 CYS R 224 -1 O VAL R 223 N GLN R 210 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