HEADER MEMBRANE PROTEIN 28-JUL-22 7YMJ TITLE CRYO-EM STRUCTURE OF ALPHA1AAR-NB6 COMPLEX BOUND TO TAMSULOSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA1A-ADRENERGIC RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NB6; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 8 ORGANISM_TAXID: 9844; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GPCR, NANOBODY, ANTAGONIST, COMPLEX, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.TOYODA,A.ZHU,C.YAN,B.K.KOBILKA,X.LIU REVDAT 1 05-JUL-23 7YMJ 0 JRNL AUTH Y.TOYODA,A.ZHU,F.KONG,S.SHAN,J.ZHAO,N.WANG,X.SUN,L.ZHANG, JRNL AUTH 2 C.YAN,B.K.KOBILKA,X.LIU JRNL TITL STRUCTURAL BASIS OF ALPHA 1A -ADRENERGIC RECEPTOR ACTIVATION JRNL TITL 2 AND RECOGNITION BY AN EXTRACELLULAR NANOBODY. JRNL REF NAT COMMUN V. 14 3655 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37339967 JRNL DOI 10.1038/S41467-023-39310-X REMARK 2 REMARK 2 RESOLUTION. 3.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : 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 : 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) : 3.350 REMARK 3 NUMBER OF PARTICLES : 285000 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 7YMJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031258. 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 : ALPHA1AAR-NB6 COMPLEX; REMARK 245 ALPHA1AAR; NB6 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1300.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1800.00 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) : 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 APPLY THE FOLLOWING TO CHAINS: A, D 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 -23 REMARK 465 LYS A -22 REMARK 465 THR A -21 REMARK 465 ILE A -20 REMARK 465 ILE A -19 REMARK 465 ALA A -18 REMARK 465 LEU A -17 REMARK 465 SER A -16 REMARK 465 TYR A -15 REMARK 465 ILE A -14 REMARK 465 PHE A -13 REMARK 465 CYS A -12 REMARK 465 LEU A -11 REMARK 465 VAL A -10 REMARK 465 PHE A -9 REMARK 465 ALA A -8 REMARK 465 ASP A -7 REMARK 465 TYR A -6 REMARK 465 LYS A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ASP A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 PHE A 3 REMARK 465 LEU A 4 REMARK 465 SER A 5 REMARK 465 GLY A 6 REMARK 465 GLN A 7 REMARK 465 ALA A 8 REMARK 465 SER A 9 REMARK 465 ASP A 10 REMARK 465 SER A 11 REMARK 465 SER A 12 REMARK 465 GLN A 13 REMARK 465 CYS A 14 REMARK 465 THR A 15 REMARK 465 GLN A 16 REMARK 465 PRO A 17 REMARK 465 PRO A 18 REMARK 465 ALA A 19 REMARK 465 PRO A 20 REMARK 465 VAL A 21 REMARK 465 GLN A 22 REMARK 465 ILE A 23 REMARK 465 GLN A 344 REMARK 465 CYS A 345 REMARK 465 LEU A 346 REMARK 465 CYS A 347 REMARK 465 ARG A 348 REMARK 465 LYS A 349 REMARK 465 GLN A 350 REMARK 465 SER A 351 REMARK 465 SER A 352 REMARK 465 LYS A 353 REMARK 465 HIS A 354 REMARK 465 ALA A 355 REMARK 465 LEU A 356 REMARK 465 GLY A 357 REMARK 465 TYR A 358 REMARK 465 THR A 359 REMARK 465 LEU A 360 REMARK 465 HIS A 361 REMARK 465 PRO A 362 REMARK 465 PRO A 363 REMARK 465 SER A 364 REMARK 465 GLN A 365 REMARK 465 ALA A 366 REMARK 465 VAL A 367 REMARK 465 GLU A 368 REMARK 465 GLY A 369 REMARK 465 GLN A 370 REMARK 465 HIS A 371 REMARK 465 HIS A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 REMARK 465 HIS A 375 REMARK 465 HIS A 376 REMARK 465 HIS A 377 REMARK 465 HIS A 378 REMARK 465 MET D -21 REMARK 465 LYS D -20 REMARK 465 TYR D -19 REMARK 465 LEU D -18 REMARK 465 LEU D -17 REMARK 465 PRO D -16 REMARK 465 THR D -15 REMARK 465 ALA D -14 REMARK 465 ALA D -13 REMARK 465 ALA D -12 REMARK 465 GLY D -11 REMARK 465 LEU D -10 REMARK 465 LEU D -9 REMARK 465 LEU D -8 REMARK 465 LEU D -7 REMARK 465 ALA D -6 REMARK 465 ALA D -5 REMARK 465 GLN D -4 REMARK 465 PRO D -3 REMARK 465 ALA D -2 REMARK 465 MET D -1 REMARK 465 ALA D 0 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 VAL D 42 REMARK 465 SER D 43 REMARK 465 GLY D 44 REMARK 465 ASN D 45 REMARK 465 SER D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 HIS D 127 REMARK 465 HIS D 128 REMARK 465 HIS D 129 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 LYS A 25 CG CD CE NZ REMARK 470 ILE A 27 CG1 CG2 CD1 REMARK 470 PHE A 301 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN D 3 CG CD OE1 NE2 REMARK 470 GLN D 5 CG CD OE1 NE2 REMARK 470 GLN D 7 CG CD OE1 NE2 REMARK 470 LEU D 13 CG CD1 CD2 REMARK 470 VAL D 14 CG1 CG2 REMARK 470 GLU D 18 CG CD OE1 OE2 REMARK 470 SER D 27 OG REMARK 470 THR D 29 OG1 CG2 REMARK 470 ARG D 47 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 60 CG CD CE NZ REMARK 470 ASP D 63 CG OD1 OD2 REMARK 470 LYS D 66 CG CD CE NZ REMARK 470 LYS D 77 CG CD CE NZ REMARK 470 LYS D 88 CG CD CE NZ REMARK 470 GLU D 90 CG CD OE1 OE2 REMARK 470 GLN D 115 CG CD OE1 NE2 REMARK 470 SER D 122 OG 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 A 165 40.49 -104.60 REMARK 500 GLU A 173 10.21 57.53 REMARK 500 PHE A 301 32.41 -97.59 REMARK 500 LYS D 66 51.73 -90.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7YM8 RELATED DB: PDB REMARK 900 RELATED ID: 7YMH RELATED DB: PDB REMARK 900 RELATED ID: EMD-33924 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-33928 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-33930 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF ALPHA1AAR-NB6 COMPLEX BOUND TO TAMSULOSIN DBREF 7YMJ A -23 378 PDB 7YMJ 7YMJ -23 378 DBREF 7YMJ D -21 129 PDB 7YMJ 7YMJ -21 129 SEQRES 1 A 362 MET LYS THR ILE ILE ALA LEU SER TYR ILE PHE CYS LEU SEQRES 2 A 362 VAL PHE ALA ASP TYR LYS ASP ASP ASP ASP ALA MET VAL SEQRES 3 A 362 PHE LEU SER GLY GLN ALA SER ASP SER SER GLN CYS THR SEQRES 4 A 362 GLN PRO PRO ALA PRO VAL GLN ILE SER LYS ALA ILE LEU SEQRES 5 A 362 LEU GLY VAL ILE LEU GLY GLY LEU ILE LEU PHE GLY VAL SEQRES 6 A 362 LEU GLY ASN ILE LEU VAL ILE LEU SER VAL ALA CYS HIS SEQRES 7 A 362 ARG HIS LEU HIS SER VAL THR HIS TYR TYR ILE VAL ASN SEQRES 8 A 362 LEU ALA VAL ALA ASP LEU LEU LEU THR SER THR VAL LEU SEQRES 9 A 362 PRO PHE SER ALA ILE PHE GLU VAL LEU GLY TYR TRP ALA SEQRES 10 A 362 PHE GLY ARG VAL PHE CYS ASN ILE TRP ALA ALA VAL ASP SEQRES 11 A 362 VAL LEU CYS CYS THR ALA ARG ILE TRP GLY LEU CYS ILE SEQRES 12 A 362 ILE SER ILE ASP ARG TYR ILE GLY VAL SER TYR PRO LEU SEQRES 13 A 362 ARG TYR PRO THR ILE VAL THR GLN ARG ARG GLY LEU MET SEQRES 14 A 362 ALA LEU LEU CYS VAL TRP ALA LEU SER LEU VAL ILE SER SEQRES 15 A 362 ILE GLY PRO LEU PHE GLY TRP ARG GLN PRO ALA PRO GLU SEQRES 16 A 362 ASP GLU THR ILE CYS GLN ILE ASN GLU GLU PRO GLY TYR SEQRES 17 A 362 VAL LEU PHE SER ALA LEU GLY SER PHE TYR LEU PRO LEU SEQRES 18 A 362 ALA ILE ILE LEU VAL MET TYR THR LEU MET ILE LEU ARG SEQRES 19 A 362 LEU LYS SER VAL ARG LEU LEU SER GLY SER ARG GLU LYS SEQRES 20 A 362 ASP ARG ASN LEU ARG ARG ILE THR ARG LEU VAL LEU ILE SEQRES 21 A 362 VAL VAL GLY CYS PHE VAL LEU CYS TRP LEU PRO PHE PHE SEQRES 22 A 362 LEU VAL MET PRO ILE GLY SER PHE PHE PRO ASP PHE LYS SEQRES 23 A 362 PRO SER GLU THR VAL PHE LYS ILE VAL PHE TRP LEU GLY SEQRES 24 A 362 TYR LEU ASN SER CYS ILE ASN PRO ILE ILE TYR PRO CYS SEQRES 25 A 362 SER SER GLN GLU PHE LYS LYS ALA PHE GLN ASN VAL LEU SEQRES 26 A 362 ARG ILE GLN CYS LEU CYS ARG LYS GLN SER SER LYS HIS SEQRES 27 A 362 ALA LEU GLY TYR THR LEU HIS PRO PRO SER GLN ALA VAL SEQRES 28 A 362 GLU GLY GLN HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 D 151 MET LYS TYR LEU LEU PRO THR ALA ALA ALA GLY LEU LEU SEQRES 2 D 151 LEU LEU ALA ALA GLN PRO ALA MET ALA MET ALA GLN VAL SEQRES 3 D 151 GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN ALA GLY SEQRES 4 D 151 GLU SER LEU ARG LEU SER CYS ALA ALA SER GLY THR ILE SEQRES 5 D 151 PHE ARG LEU TYR ASP MET GLY TRP TYR ARG ARG VAL SER SEQRES 6 D 151 GLY ASN GLN ARG GLU LEU VAL ALA SER ILE THR SER GLY SEQRES 7 D 151 GLY SER THR LYS TYR GLY ASP SER VAL LYS GLY ARG PHE SEQRES 8 D 151 THR ILE SER ARG ASP ASN ALA LYS ASN THR VAL TYR LEU SEQRES 9 D 151 GLN MET SER SER LEU LYS PRO GLU ASP THR ALA VAL TYR SEQRES 10 D 151 TYR CYS ASN ALA GLU TYR ARG THR GLY ILE TRP GLU GLU SEQRES 11 D 151 LEU LEU ASP GLY TRP GLY GLN GLY THR GLN VAL THR VAL SEQRES 12 D 151 SER SER HIS HIS HIS HIS HIS HIS HET JGX A 401 28 HETNAM JGX TAMSULOSIN FORMUL 3 JGX C20 H28 N2 O5 S HELIX 1 AA1 LYS A 25 HIS A 54 1 30 HELIX 2 AA2 THR A 61 VAL A 79 1 19 HELIX 3 AA3 VAL A 79 GLY A 90 1 12 HELIX 4 AA4 VAL A 97 TYR A 130 1 34 HELIX 5 AA5 ARG A 133 VAL A 138 1 6 HELIX 6 AA6 THR A 139 ILE A 159 1 21 HELIX 7 AA7 GLY A 160 GLY A 164 5 5 HELIX 8 AA8 GLU A 181 PHE A 193 1 13 HELIX 9 AA9 PHE A 193 VAL A 214 1 22 HELIX 10 AB1 SER A 220 PHE A 298 1 39 HELIX 11 AB2 VAL A 307 PHE A 312 1 6 HELIX 12 AB3 TRP A 313 ASN A 322 1 10 HELIX 13 AB4 ILE A 324 SER A 329 1 6 HELIX 14 AB5 GLN A 331 ILE A 343 1 13 SHEET 1 AA1 4 GLN D 5 SER D 9 0 SHEET 2 AA1 4 SER D 19 SER D 27 -1 O SER D 27 N GLN D 5 SHEET 3 AA1 4 THR D 79 SER D 85 -1 O MET D 84 N LEU D 20 SHEET 4 AA1 4 THR D 70 ASP D 74 -1 N SER D 72 O TYR D 81 SHEET 1 AA2 6 GLY D 12 LEU D 13 0 SHEET 2 AA2 6 THR D 117 THR D 120 1 O THR D 120 N GLY D 12 SHEET 3 AA2 6 ALA D 93 ARG D 102 -1 N TYR D 95 O THR D 117 SHEET 4 AA2 6 ARG D 32 TYR D 39 -1 N TYR D 39 O TYR D 96 SHEET 5 AA2 6 LEU D 49 THR D 54 -1 O ALA D 51 N TRP D 38 SHEET 6 AA2 6 LYS D 60 TYR D 61 -1 O LYS D 60 N SER D 52 SHEET 1 AA3 4 GLY D 12 LEU D 13 0 SHEET 2 AA3 4 THR D 117 THR D 120 1 O THR D 120 N GLY D 12 SHEET 3 AA3 4 ALA D 93 ARG D 102 -1 N TYR D 95 O THR D 117 SHEET 4 AA3 4 LEU D 110 TRP D 113 -1 O GLY D 112 N ALA D 99 SSBOND 1 CYS A 99 CYS A 176 1555 1555 2.03 SSBOND 2 CYS D 24 CYS D 97 1555 1555 2.04 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