HEADER OXIDOREDUCTASE 18-MAY-22 8CVN TITLE CRYO-EM STRUCTURE OF HUMAN 15-PGDH IN COMPLEX WITH SMALL MOLECULE TITLE 2 SW209415 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 15-HYDROXYPROSTAGLANDIN DEHYDROGENASE [NAD(+)]; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 15-PGDH,EICOSANOID/DOCOSANOID DEHYDROGENASE [NAD(+)], COMPND 5 PROSTAGLANDIN DEHYDROGENASE 1,SHORT CHAIN DEHYDROGENASE/REDUCTASE COMPND 6 FAMILY 36C MEMBER 1; COMPND 7 EC: 1.1.1.141,1.1.1.-,1.1.1.232; COMPND 8 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: HPGD, PGDH1, SDR36C1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 7 PPPARG4; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1182032 KEYWDS DEHYDROGENASE, INHIBITOR, OXIDOREDUCTASE, OXIDOREDUCTASE-INHIBITOR KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR W.HUANG,D.J.TAYLOR REVDAT 2 29-MAR-23 8CVN 1 REMARK REVDAT 1 01-MAR-23 8CVN 0 JRNL AUTH W.HUANG,H.LI,J.KISELAR,S.P.FINK,S.REGMI,A.DAY,Y.YUAN, JRNL AUTH 2 M.CHANCE,J.M.READY,S.D.MARKOWITZ,D.J.TAYLOR JRNL TITL SMALL MOLECULE INHIBITORS OF 15-PGDH EXPLOIT A PHYSIOLOGIC JRNL TITL 2 INDUCED-FIT CLOSING SYSTEM. JRNL REF NAT COMMUN V. 14 784 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36774348 JRNL DOI 10.1038/S41467-023-36463-7 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.400 REMARK 3 NUMBER OF PARTICLES : 776110 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8CVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265503. 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; POINT REMARK 245 NAME OF SAMPLE : HUMAN 15-PGDH IN COMPLEX WITH REMARK 245 INHIBITOR 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) : 250.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 108.00 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, B 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 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 LYS A 57 0.67 -62.58 REMARK 500 ASN A 99 71.14 -100.34 REMARK 500 SER A 137 -166.13 -125.16 REMARK 500 ALA A 237 31.45 -95.66 REMARK 500 ASN B 99 71.53 -100.35 REMARK 500 SER B 137 -166.16 -125.20 REMARK 500 ALA B 237 31.48 -95.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SWL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SWL B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27010 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN 15-PGDH IN COMPLEX WITH SMALL MOLECULE REMARK 900 SW209415 DBREF 8CVN A 3 256 UNP P15428 PGDH_HUMAN 3 256 DBREF 8CVN B 3 256 UNP P15428 PGDH_HUMAN 3 256 SEQADV 8CVN HIS A 1 UNP P15428 EXPRESSION TAG SEQADV 8CVN MET A 2 UNP P15428 EXPRESSION TAG SEQADV 8CVN HIS B 1 UNP P15428 EXPRESSION TAG SEQADV 8CVN MET B 2 UNP P15428 EXPRESSION TAG SEQRES 1 A 256 HIS MET VAL ASN GLY LYS VAL ALA LEU VAL THR GLY ALA SEQRES 2 A 256 ALA GLN GLY ILE GLY ARG ALA PHE ALA GLU ALA LEU LEU SEQRES 3 A 256 LEU LYS GLY ALA LYS VAL ALA LEU VAL ASP TRP ASN LEU SEQRES 4 A 256 GLU ALA GLY VAL GLN CYS LYS ALA ALA LEU ASP GLU GLN SEQRES 5 A 256 PHE GLU PRO GLN LYS THR LEU PHE ILE GLN CYS ASP VAL SEQRES 6 A 256 ALA ASP GLN GLN GLN LEU ARG ASP THR PHE ARG LYS VAL SEQRES 7 A 256 VAL ASP HIS PHE GLY ARG LEU ASP ILE LEU VAL ASN ASN SEQRES 8 A 256 ALA GLY VAL ASN ASN GLU LYS ASN TRP GLU LYS THR LEU SEQRES 9 A 256 GLN ILE ASN LEU VAL SER VAL ILE SER GLY THR TYR LEU SEQRES 10 A 256 GLY LEU ASP TYR MET SER LYS GLN ASN GLY GLY GLU GLY SEQRES 11 A 256 GLY ILE ILE ILE ASN MET SER SER LEU ALA GLY LEU MET SEQRES 12 A 256 PRO VAL ALA GLN GLN PRO VAL TYR CYS ALA SER LYS HIS SEQRES 13 A 256 GLY ILE VAL GLY PHE THR ARG SER ALA ALA LEU ALA ALA SEQRES 14 A 256 ASN LEU MET ASN SER GLY VAL ARG LEU ASN ALA ILE CYS SEQRES 15 A 256 PRO GLY PHE VAL ASN THR ALA ILE LEU GLU SER ILE GLU SEQRES 16 A 256 LYS GLU GLU ASN MET GLY GLN TYR ILE GLU TYR LYS ASP SEQRES 17 A 256 HIS ILE LYS ASP MET ILE LYS TYR TYR GLY ILE LEU ASP SEQRES 18 A 256 PRO PRO LEU ILE ALA ASN GLY LEU ILE THR LEU ILE GLU SEQRES 19 A 256 ASP ASP ALA LEU ASN GLY ALA ILE MET LYS ILE THR THR SEQRES 20 A 256 SER LYS GLY ILE HIS PHE GLN ASP TYR SEQRES 1 B 256 HIS MET VAL ASN GLY LYS VAL ALA LEU VAL THR GLY ALA SEQRES 2 B 256 ALA GLN GLY ILE GLY ARG ALA PHE ALA GLU ALA LEU LEU SEQRES 3 B 256 LEU LYS GLY ALA LYS VAL ALA LEU VAL ASP TRP ASN LEU SEQRES 4 B 256 GLU ALA GLY VAL GLN CYS LYS ALA ALA LEU ASP GLU GLN SEQRES 5 B 256 PHE GLU PRO GLN LYS THR LEU PHE ILE GLN CYS ASP VAL SEQRES 6 B 256 ALA ASP GLN GLN GLN LEU ARG ASP THR PHE ARG LYS VAL SEQRES 7 B 256 VAL ASP HIS PHE GLY ARG LEU ASP ILE LEU VAL ASN ASN SEQRES 8 B 256 ALA GLY VAL ASN ASN GLU LYS ASN TRP GLU LYS THR LEU SEQRES 9 B 256 GLN ILE ASN LEU VAL SER VAL ILE SER GLY THR TYR LEU SEQRES 10 B 256 GLY LEU ASP TYR MET SER LYS GLN ASN GLY GLY GLU GLY SEQRES 11 B 256 GLY ILE ILE ILE ASN MET SER SER LEU ALA GLY LEU MET SEQRES 12 B 256 PRO VAL ALA GLN GLN PRO VAL TYR CYS ALA SER LYS HIS SEQRES 13 B 256 GLY ILE VAL GLY PHE THR ARG SER ALA ALA LEU ALA ALA SEQRES 14 B 256 ASN LEU MET ASN SER GLY VAL ARG LEU ASN ALA ILE CYS SEQRES 15 B 256 PRO GLY PHE VAL ASN THR ALA ILE LEU GLU SER ILE GLU SEQRES 16 B 256 LYS GLU GLU ASN MET GLY GLN TYR ILE GLU TYR LYS ASP SEQRES 17 B 256 HIS ILE LYS ASP MET ILE LYS TYR TYR GLY ILE LEU ASP SEQRES 18 B 256 PRO PRO LEU ILE ALA ASN GLY LEU ILE THR LEU ILE GLU SEQRES 19 B 256 ASP ASP ALA LEU ASN GLY ALA ILE MET LYS ILE THR THR SEQRES 20 B 256 SER LYS GLY ILE HIS PHE GLN ASP TYR HET NAI A 301 44 HET SWL A 302 28 HET NAI B 301 44 HET SWL B 302 28 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM SWL 2-[BUTYL(OXIDANYL)-$L^{3}-SULFANYL]-4-(2,3- HETNAM 2 SWL DIMETHYLIMIDAZOL-4-YL)-6-(1,3-THIAZOL-2-YL)THIENO[2,3- HETNAM 3 SWL B]PYRIDIN-3-AMINE HETSYN NAI NADH FORMUL 3 NAI 2(C21 H29 N7 O14 P2) FORMUL 4 SWL 2(C19 H23 N5 O S3) HELIX 1 AA1 GLY A 16 GLY A 29 1 14 HELIX 2 AA2 ASN A 38 GLU A 51 1 14 HELIX 3 AA3 GLU A 54 GLN A 56 5 3 HELIX 4 AA4 ASP A 67 GLY A 83 1 17 HELIX 5 AA5 ASN A 99 LEU A 108 1 10 HELIX 6 AA6 LEU A 108 SER A 123 1 16 HELIX 7 AA7 LYS A 124 GLY A 127 5 4 HELIX 8 AA8 SER A 138 LEU A 142 5 5 HELIX 9 AA9 GLN A 148 ASN A 173 1 26 HELIX 10 AB1 THR A 188 GLU A 195 5 8 HELIX 11 AB2 LYS A 196 GLY A 201 1 6 HELIX 12 AB3 GLN A 202 GLU A 205 5 4 HELIX 13 AB4 TYR A 206 GLY A 218 1 13 HELIX 14 AB5 ASP A 221 ASP A 235 1 15 HELIX 15 AB6 GLY B 16 GLY B 29 1 14 HELIX 16 AB7 ASN B 38 GLU B 51 1 14 HELIX 17 AB8 GLU B 54 GLN B 56 5 3 HELIX 18 AB9 ASP B 67 GLY B 83 1 17 HELIX 19 AC1 ASN B 99 LEU B 108 1 10 HELIX 20 AC2 LEU B 108 SER B 123 1 16 HELIX 21 AC3 LYS B 124 GLY B 127 5 4 HELIX 22 AC4 SER B 138 LEU B 142 5 5 HELIX 23 AC5 GLN B 148 ASN B 173 1 26 HELIX 24 AC6 THR B 188 GLU B 195 5 8 HELIX 25 AC7 LYS B 196 GLY B 201 1 6 HELIX 26 AC8 GLN B 202 GLU B 205 5 4 HELIX 27 AC9 TYR B 206 GLY B 218 1 13 HELIX 28 AD1 ASP B 221 ASP B 235 1 15 SHEET 1 AA1 8 THR A 58 GLN A 62 0 SHEET 2 AA1 8 LYS A 31 ASP A 36 1 N LEU A 34 O ILE A 61 SHEET 3 AA1 8 VAL A 7 THR A 11 1 N ALA A 8 O LYS A 31 SHEET 4 AA1 8 ILE A 87 ASN A 90 1 O VAL A 89 N LEU A 9 SHEET 5 AA1 8 GLY A 131 MET A 136 1 O MET A 136 N ASN A 90 SHEET 6 AA1 8 VAL A 176 PRO A 183 1 O ARG A 177 N ILE A 133 SHEET 7 AA1 8 ILE A 242 ILE A 245 1 O MET A 243 N CYS A 182 SHEET 8 AA1 8 ILE A 251 PHE A 253 -1 O HIS A 252 N LYS A 244 SHEET 1 AA2 8 THR B 58 GLN B 62 0 SHEET 2 AA2 8 LYS B 31 ASP B 36 1 N LEU B 34 O LEU B 59 SHEET 3 AA2 8 VAL B 7 THR B 11 1 N ALA B 8 O LYS B 31 SHEET 4 AA2 8 ILE B 87 ASN B 90 1 O VAL B 89 N LEU B 9 SHEET 5 AA2 8 GLY B 131 MET B 136 1 O MET B 136 N ASN B 90 SHEET 6 AA2 8 VAL B 176 PRO B 183 1 O ARG B 177 N ILE B 133 SHEET 7 AA2 8 ILE B 242 ILE B 245 1 O MET B 243 N CYS B 182 SHEET 8 AA2 8 ILE B 251 PHE B 253 -1 O HIS B 252 N LYS B 244 SITE 1 AC1 20 GLN A 15 ILE A 17 ASP A 36 TRP A 37 SITE 2 AC1 20 CYS A 63 ASP A 64 VAL A 65 ASN A 91 SITE 3 AC1 20 ALA A 92 GLY A 93 VAL A 94 SER A 137 SITE 4 AC1 20 SER A 138 TYR A 151 LYS A 155 GLY A 184 SITE 5 AC1 20 VAL A 186 THR A 188 ILE A 190 SWL A 302 SITE 1 AC2 9 ASN A 95 SER A 138 PRO A 144 GLN A 148 SITE 2 AC2 9 TYR A 151 PHE A 185 MET A 213 TYR A 217 SITE 3 AC2 9 NAI A 301 SITE 1 AC3 20 GLN B 15 ILE B 17 ASP B 36 TRP B 37 SITE 2 AC3 20 CYS B 63 ASP B 64 VAL B 65 ASN B 91 SITE 3 AC3 20 ALA B 92 GLY B 93 VAL B 94 SER B 137 SITE 4 AC3 20 SER B 138 TYR B 151 LYS B 155 GLY B 184 SITE 5 AC3 20 VAL B 186 THR B 188 ILE B 190 SWL B 302 SITE 1 AC4 9 ASN B 95 SER B 138 PRO B 144 GLN B 148 SITE 2 AC4 9 TYR B 151 PHE B 185 MET B 213 TYR B 217 SITE 3 AC4 9 NAI B 301 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