HEADER MEMBRANE PROTEIN 05-JUN-24 8ZRT TITLE CRYO-EM STRUCTURE FOCUSED ON THE RECEPTOR OF THE ET-1 BOUND ETBR-DNGI TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOTHELIN RECEPTOR TYPE B; COMPND 3 CHAIN: R; COMPND 4 SYNONYM: ET-B,ET-BR,ENDOTHELIN RECEPTOR NON-SELECTIVE TYPE; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ENDOTHELIN-1; COMPND 8 CHAIN: L; COMPND 9 SYNONYM: PREPROENDOTHELIN-1,PPET1; COMPND 10 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: EDNRB, ETRB; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: EDN1; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS ENDOTHELIN, RECEPTOR, GI, COMPLEX, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.TANI,S.MAKI-YONEKURA,R.KANNO,T.NEGAMI,T.HAMAGUCHI,M.HALL, AUTHOR 2 A.MIZOGUCHI,B.M.HUMBEL,T.TERADA,K.YONEKURA,T.DOI REVDAT 2 30-OCT-24 8ZRT 1 JRNL REVDAT 1 02-OCT-24 8ZRT 0 JRNL AUTH K.TANI,S.MAKI-YONEKURA,R.KANNO,T.NEGAMI,T.HAMAGUCHI,M.HALL, JRNL AUTH 2 A.MIZOGUCHI,B.M.HUMBEL,T.TERADA,K.YONEKURA,T.DOI JRNL TITL STRUCTURE OF ENDOTHELIN ET B RECEPTOR-G I COMPLEX IN A JRNL TITL 2 CONFORMATION STABILIZED BY UNIQUE NPXXL MOTIF. JRNL REF COMMUN BIOL V. 7 1303 2024 JRNL REFN ESSN 2399-3642 JRNL PMID 39414992 JRNL DOI 10.1038/S42003-024-06905-Z REMARK 2 REMARK 2 RESOLUTION. 3.62 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 : RIGID BODY FIT 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) : 3.620 REMARK 3 NUMBER OF PARTICLES : 401671 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 8ZRT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1300048436. 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 : ET-1 BOUND ETBR COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 4.00 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 : JEOL CRYO ARM 300 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3500.00 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) : 340.00 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: R, L 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 PRO R 62 REMARK 465 GLY R 63 REMARK 465 GLY R 64 REMARK 465 GLY R 65 REMARK 465 LEU R 66 REMARK 465 ALA R 67 REMARK 465 PRO R 68 REMARK 465 ALA R 69 REMARK 465 GLU R 70 REMARK 465 VAL R 71 REMARK 465 PRO R 72 REMARK 465 LYS R 73 REMARK 465 GLY R 74 REMARK 465 ASP R 75 REMARK 465 ARG R 76 REMARK 465 THR R 77 REMARK 465 ALA R 78 REMARK 465 GLY R 79 REMARK 465 SER R 80 REMARK 465 PRO R 81 REMARK 465 PRO R 82 REMARK 465 ARG R 83 REMARK 465 THR R 84 REMARK 465 ILE R 85 REMARK 465 SER R 86 REMARK 465 PRO R 87 REMARK 465 PRO R 88 REMARK 465 PRO R 89 REMARK 465 ASN R 129 REMARK 465 LYS R 130 REMARK 465 CYS R 131 REMARK 465 MET R 132 REMARK 465 SER R 207 REMARK 465 ARG R 208 REMARK 465 ILE R 209 REMARK 465 LYS R 210 REMARK 465 GLY R 211 REMARK 465 ILE R 212 REMARK 465 GLY R 213 REMARK 465 VAL R 214 REMARK 465 ARG R 302 REMARK 465 LYS R 303 REMARK 465 LYS R 304 REMARK 465 SER R 305 REMARK 465 GLY R 306 REMARK 465 MET R 307 REMARK 465 GLN R 308 REMARK 465 ILE R 309 REMARK 465 ALA R 310 REMARK 465 LEU R 311 REMARK 465 ASN R 312 REMARK 465 ASP R 313 REMARK 465 HIS R 314 REMARK 465 LEU R 315 REMARK 465 LYS R 316 REMARK 465 GLN R 317 REMARK 465 ALA R 400 REMARK 465 LEU R 401 REMARK 465 CYS R 402 REMARK 465 CYS R 403 REMARK 465 TRP R 404 REMARK 465 ALA R 405 REMARK 465 GLN R 406 REMARK 465 SER R 407 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 GLN R 91 CG CD OE1 NE2 REMARK 470 GLU R 98 CG CD OE1 OE2 REMARK 470 TYR R 102 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 THR R 105 OG1 CG2 REMARK 470 VAL R 106 CG1 CG2 REMARK 470 TYR R 124 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR R 127 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS R 128 CG CD CE NZ REMARK 470 LYS R 216 CG CD CE NZ REMARK 470 TRP R 217 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP R 217 CZ3 CH2 REMARK 470 GLU R 221 CG CD OE1 OE2 REMARK 470 MET R 245 CG SD CE REMARK 470 LYS R 248 CG CD CE NZ REMARK 470 ARG R 253 CG CD NE CZ NH1 NH2 REMARK 470 LYS R 262 CG CD CE NZ REMARK 470 ARG R 319 CG CD NE CZ NH1 NH2 REMARK 470 GLU R 320 CG CD OE1 OE2 REMARK 470 LYS R 346 CG CD CE NZ REMARK 470 ASP R 354 CG OD1 OD2 REMARK 470 ASN R 356 CG OD1 ND2 REMARK 470 GLU R 359 CG CD OE1 OE2 REMARK 470 LYS R 391 CG CD CE NZ REMARK 470 LYS R 398 CG CD CE NZ REMARK 470 LEU L 6 CG CD1 CD2 REMARK 470 LYS L 9 CG CD CE NZ 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 PRO R 93 56.58 -64.09 REMARK 500 TRP R 167 72.39 53.27 REMARK 500 PHE R 282 -54.29 -120.44 REMARK 500 VAL R 389 -56.96 -124.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-60404 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE FOCUSED ON THE RECEPTOR OF THE ET-1 BOUND ETBR- REMARK 900 DNGI COMPLEX DBREF 8ZRT R 66 407 UNP P24530 EDNRB_HUMAN 66 407 DBREF 8ZRT L 1 21 UNP P05305 EDN1_HUMAN 53 73 SEQADV 8ZRT PRO R 62 UNP P24530 EXPRESSION TAG SEQADV 8ZRT GLY R 63 UNP P24530 EXPRESSION TAG SEQADV 8ZRT GLY R 64 UNP P24530 EXPRESSION TAG SEQADV 8ZRT GLY R 65 UNP P24530 EXPRESSION TAG SEQADV 8ZRT TYR R 124 UNP P24530 ARG 124 CONFLICT SEQADV 8ZRT ALA R 396 UNP P24530 CYS 396 CONFLICT SEQADV 8ZRT ALA R 400 UNP P24530 CYS 400 CONFLICT SEQADV 8ZRT ALA R 405 UNP P24530 CYS 405 CONFLICT SEQRES 1 R 346 PRO GLY GLY GLY LEU ALA PRO ALA GLU VAL PRO LYS GLY SEQRES 2 R 346 ASP ARG THR ALA GLY SER PRO PRO ARG THR ILE SER PRO SEQRES 3 R 346 PRO PRO CYS GLN GLY PRO ILE GLU ILE LYS GLU THR PHE SEQRES 4 R 346 LYS TYR ILE ASN THR VAL VAL SER CYS LEU VAL PHE VAL SEQRES 5 R 346 LEU GLY ILE ILE GLY ASN SER THR LEU LEU TYR ILE ILE SEQRES 6 R 346 TYR LYS ASN LYS CYS MET ARG ASN GLY PRO ASN ILE LEU SEQRES 7 R 346 ILE ALA SER LEU ALA LEU GLY ASP LEU LEU HIS ILE VAL SEQRES 8 R 346 ILE ASP ILE PRO ILE ASN VAL TYR LYS LEU LEU ALA GLU SEQRES 9 R 346 ASP TRP PRO PHE GLY ALA GLU MET CYS LYS LEU VAL PRO SEQRES 10 R 346 PHE ILE GLN LYS ALA SER VAL GLY ILE THR VAL LEU SER SEQRES 11 R 346 LEU CYS ALA LEU SER ILE ASP ARG TYR ARG ALA VAL ALA SEQRES 12 R 346 SER TRP SER ARG ILE LYS GLY ILE GLY VAL PRO LYS TRP SEQRES 13 R 346 THR ALA VAL GLU ILE VAL LEU ILE TRP VAL VAL SER VAL SEQRES 14 R 346 VAL LEU ALA VAL PRO GLU ALA ILE GLY PHE ASP ILE ILE SEQRES 15 R 346 THR MET ASP TYR LYS GLY SER TYR LEU ARG ILE CYS LEU SEQRES 16 R 346 LEU HIS PRO VAL GLN LYS THR ALA PHE MET GLN PHE TYR SEQRES 17 R 346 LYS THR ALA LYS ASP TRP TRP LEU PHE SER PHE TYR PHE SEQRES 18 R 346 CYS LEU PRO LEU ALA ILE THR ALA PHE PHE TYR THR LEU SEQRES 19 R 346 MET THR CYS GLU MET LEU ARG LYS LYS SER GLY MET GLN SEQRES 20 R 346 ILE ALA LEU ASN ASP HIS LEU LYS GLN ARG ARG GLU VAL SEQRES 21 R 346 ALA LYS THR VAL PHE CYS LEU VAL LEU VAL PHE ALA LEU SEQRES 22 R 346 CYS TRP LEU PRO LEU HIS LEU SER ARG ILE LEU LYS LEU SEQRES 23 R 346 THR LEU TYR ASN GLN ASN ASP PRO ASN ARG CYS GLU LEU SEQRES 24 R 346 LEU SER PHE LEU LEU VAL LEU ASP TYR ILE GLY ILE ASN SEQRES 25 R 346 MET ALA SER LEU ASN SER CYS ILE ASN PRO ILE ALA LEU SEQRES 26 R 346 TYR LEU VAL SER LYS ARG PHE LYS ASN ALA PHE LYS SER SEQRES 27 R 346 ALA LEU CYS CYS TRP ALA GLN SER SEQRES 1 L 21 CYS SER CYS SER SER LEU MET ASP LYS GLU CYS VAL TYR SEQRES 2 L 21 PHE CYS HIS LEU ASP ILE ILE TRP HELIX 1 AA1 LYS R 97 LYS R 128 1 32 HELIX 2 AA2 ASN R 134 ALA R 164 1 31 HELIX 3 AA3 GLY R 170 SER R 205 1 36 HELIX 4 AA4 LYS R 216 ILE R 238 1 23 HELIX 5 AA5 THR R 263 ALA R 272 1 10 HELIX 6 AA6 ALA R 272 LEU R 301 1 30 HELIX 7 AA7 ARG R 319 LEU R 349 1 31 HELIX 8 AA8 ASN R 356 LEU R 388 1 33 HELIX 9 AA9 SER R 390 SER R 399 1 10 HELIX 10 AB1 GLU L 10 ASP L 18 1 9 SHEET 1 AA1 2 PHE R 240 ILE R 243 0 SHEET 2 AA1 2 ILE R 254 LEU R 257 -1 O ILE R 254 N ILE R 243 SHEET 1 AA2 2 ASP R 246 TYR R 247 0 SHEET 2 AA2 2 SER R 250 TYR R 251 -1 N SER R 250 O TYR R 247 SSBOND 1 CYS R 90 CYS R 358 1555 1555 2.03 SSBOND 2 CYS R 174 CYS R 255 1555 1555 2.03 SSBOND 3 CYS L 1 CYS L 15 1555 1555 2.03 SSBOND 4 CYS L 3 CYS L 11 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