HEADER OXIDOREDUCTASE 09-MAR-23 8GHB TITLE THE STRUCTURE OF H12-LOX IN MONOMERIC FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUNSATURATED FATTY ACID LIPOXYGENASE ALOX12; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ARACHIDONATE (12S)-LIPOXYGENASE,12S-LOX,12S-LIPOXYGENASE, COMPND 5 ARACHIDONATE (15S)-LIPOXYGENASE,LINOLEATE (13S)-LIPOXYGENASE,LIPOXIN COMPND 6 SYNTHASE 12-LO,PLATELET-TYPE LIPOXYGENASE 12; COMPND 7 EC: 1.13.11.-,1.13.11.31,1.13.11.33,3.3.2.-; 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: ALOX12, 12LO, LOG12; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: EXPI293 CELLS KEYWDS LIPOXYGENASE, PLATELETS, LIPID-MODIFYING ENZYME, LIPID OXIDATION, KEYWDS 2 OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR K.A.BLACK,J.I.MOBBS,H.VENUGOPAL,D.M.THAL,A.GLUKHOVA REVDAT 3 01-MAY-24 8GHB 1 REMARK REVDAT 2 11-OCT-23 8GHB 1 JRNL REVDAT 1 09-AUG-23 8GHB 0 JRNL AUTH J.I.MOBBS,K.A.BLACK,M.TRAN,W.A.C.BURGER,H.VENUGOPAL, JRNL AUTH 2 T.R.HOLMAN,M.HOLINSTAT,D.M.THAL,A.GLUKHOVA JRNL TITL CRYO-EM STRUCTURES OF HUMAN ARACHIDONATE 12S-LIPOXYGENASE JRNL TITL 2 BOUND TO ENDOGENOUS AND EXOGENOUS INHIBITORS. JRNL REF BLOOD V. 142 1233 2023 JRNL REFN ESSN 1528-0020 JRNL PMID 37506345 JRNL DOI 10.1182/BLOOD.2023020441 REMARK 2 REMARK 2 RESOLUTION. 2.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : GCTF, UCSF CHIMERA, CRYOSPARC, PHENIX 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 : FLEXIBLE 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) : 2.760 REMARK 3 NUMBER OF PARTICLES : 35994 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 8GHB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1000272841. 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 : MONOMERIC HUMAN 12-LIPOXYGENASE REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : 15MA REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 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 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : 105000 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 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 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 ALA A 42 REMARK 465 ARG A 43 REMARK 465 GLY A 44 REMARK 465 GLU A 45 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 ASP A 79 -65.63 -100.46 REMARK 500 PHE A 278 35.90 -99.27 REMARK 500 LEU A 407 -61.35 -94.34 REMARK 500 ALA A 417 -33.47 -136.79 REMARK 500 GLN A 509 64.04 62.11 REMARK 500 ALA A 510 30.42 -89.91 REMARK 500 SER A 598 -15.77 -152.66 REMARK 500 ASP A 603 31.84 -96.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 901 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 360 NE2 REMARK 620 2 HIS A 365 NE2 96.0 REMARK 620 3 ASN A 544 OD1 78.2 164.7 REMARK 620 4 ILE A 663 O 139.4 103.9 89.4 REMARK 620 5 ILE A 663 OXT 167.8 83.0 99.8 52.0 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-40039 RELATED DB: EMDB REMARK 900 THE STRUCTURE OF H12-LOX IN MONOMERIC FORM DBREF 8GHB A 2 663 UNP P18054 LOX12_HUMAN 2 663 SEQADV 8GHB HIS A -4 UNP P18054 EXPRESSION TAG SEQADV 8GHB HIS A -3 UNP P18054 EXPRESSION TAG SEQADV 8GHB HIS A -2 UNP P18054 EXPRESSION TAG SEQADV 8GHB HIS A -1 UNP P18054 EXPRESSION TAG SEQADV 8GHB HIS A 0 UNP P18054 EXPRESSION TAG SEQADV 8GHB HIS A 1 UNP P18054 EXPRESSION TAG SEQADV 8GHB SER A 322 UNP P18054 ASN 322 VARIANT SEQRES 1 A 668 HIS HIS HIS HIS HIS HIS GLY ARG TYR ARG ILE ARG VAL SEQRES 2 A 668 ALA THR GLY ALA TRP LEU PHE SER GLY SER TYR ASN ARG SEQRES 3 A 668 VAL GLN LEU TRP LEU VAL GLY THR ARG GLY GLU ALA GLU SEQRES 4 A 668 LEU GLU LEU GLN LEU ARG PRO ALA ARG GLY GLU GLU GLU SEQRES 5 A 668 GLU PHE ASP HIS ASP VAL ALA GLU ASP LEU GLY LEU LEU SEQRES 6 A 668 GLN PHE VAL ARG LEU ARG LYS HIS HIS TRP LEU VAL ASP SEQRES 7 A 668 ASP ALA TRP PHE CYS ASP ARG ILE THR VAL GLN GLY PRO SEQRES 8 A 668 GLY ALA CYS ALA GLU VAL ALA PHE PRO CYS TYR ARG TRP SEQRES 9 A 668 VAL GLN GLY GLU ASP ILE LEU SER LEU PRO GLU GLY THR SEQRES 10 A 668 ALA ARG LEU PRO GLY ASP ASN ALA LEU ASP MET PHE GLN SEQRES 11 A 668 LYS HIS ARG GLU LYS GLU LEU LYS ASP ARG GLN GLN ILE SEQRES 12 A 668 TYR CYS TRP ALA THR TRP LYS GLU GLY LEU PRO LEU THR SEQRES 13 A 668 ILE ALA ALA ASP ARG LYS ASP ASP LEU PRO PRO ASN MET SEQRES 14 A 668 ARG PHE HIS GLU GLU LYS ARG LEU ASP PHE GLU TRP THR SEQRES 15 A 668 LEU LYS ALA GLY ALA LEU GLU MET ALA LEU LYS ARG VAL SEQRES 16 A 668 TYR THR LEU LEU SER SER TRP ASN CYS LEU GLU ASP PHE SEQRES 17 A 668 ASP GLN ILE PHE TRP GLY GLN LYS SER ALA LEU ALA GLU SEQRES 18 A 668 LYS VAL ARG GLN CYS TRP GLN ASP ASP GLU LEU PHE SER SEQRES 19 A 668 TYR GLN PHE LEU ASN GLY ALA ASN PRO MET LEU LEU ARG SEQRES 20 A 668 ARG SER THR SER LEU PRO SER ARG LEU VAL LEU PRO SER SEQRES 21 A 668 GLY MET GLU GLU LEU GLN ALA GLN LEU GLU LYS GLU LEU SEQRES 22 A 668 GLN ASN GLY SER LEU PHE GLU ALA ASP PHE ILE LEU LEU SEQRES 23 A 668 ASP GLY ILE PRO ALA ASN VAL ILE ARG GLY GLU LYS GLN SEQRES 24 A 668 TYR LEU ALA ALA PRO LEU VAL MET LEU LYS MET GLU PRO SEQRES 25 A 668 ASN GLY LYS LEU GLN PRO MET VAL ILE GLN ILE GLN PRO SEQRES 26 A 668 PRO SER PRO SER SER PRO THR PRO THR LEU PHE LEU PRO SEQRES 27 A 668 SER ASP PRO PRO LEU ALA TRP LEU LEU ALA LYS SER TRP SEQRES 28 A 668 VAL ARG ASN SER ASP PHE GLN LEU HIS GLU ILE GLN TYR SEQRES 29 A 668 HIS LEU LEU ASN THR HIS LEU VAL ALA GLU VAL ILE ALA SEQRES 30 A 668 VAL ALA THR MET ARG CYS LEU PRO GLY LEU HIS PRO ILE SEQRES 31 A 668 PHE LYS PHE LEU ILE PRO HIS ILE ARG TYR THR MET GLU SEQRES 32 A 668 ILE ASN THR ARG ALA ARG THR GLN LEU ILE SER ASP GLY SEQRES 33 A 668 GLY ILE PHE ASP LYS ALA VAL SER THR GLY GLY GLY GLY SEQRES 34 A 668 HIS VAL GLN LEU LEU ARG ARG ALA ALA ALA GLN LEU THR SEQRES 35 A 668 TYR CYS SER LEU CYS PRO PRO ASP ASP LEU ALA ASP ARG SEQRES 36 A 668 GLY LEU LEU GLY LEU PRO GLY ALA LEU TYR ALA HIS ASP SEQRES 37 A 668 ALA LEU ARG LEU TRP GLU ILE ILE ALA ARG TYR VAL GLU SEQRES 38 A 668 GLY ILE VAL HIS LEU PHE TYR GLN ARG ASP ASP ILE VAL SEQRES 39 A 668 LYS GLY ASP PRO GLU LEU GLN ALA TRP CYS ARG GLU ILE SEQRES 40 A 668 THR GLU VAL GLY LEU CYS GLN ALA GLN ASP ARG GLY PHE SEQRES 41 A 668 PRO VAL SER PHE GLN SER GLN SER GLN LEU CYS HIS PHE SEQRES 42 A 668 LEU THR MET CYS VAL PHE THR CYS THR ALA GLN HIS ALA SEQRES 43 A 668 ALA ILE ASN GLN GLY GLN LEU ASP TRP TYR ALA TRP VAL SEQRES 44 A 668 PRO ASN ALA PRO CYS THR MET ARG MET PRO PRO PRO THR SEQRES 45 A 668 THR LYS GLU ASP VAL THR MET ALA THR VAL MET GLY SER SEQRES 46 A 668 LEU PRO ASP VAL ARG GLN ALA CYS LEU GLN MET ALA ILE SEQRES 47 A 668 SER TRP HIS LEU SER ARG ARG GLN PRO ASP MET VAL PRO SEQRES 48 A 668 LEU GLY HIS HIS LYS GLU LYS TYR PHE SER GLY PRO LYS SEQRES 49 A 668 PRO LYS ALA VAL LEU ASN GLN PHE ARG THR ASP LEU GLU SEQRES 50 A 668 LYS LEU GLU LYS GLU ILE THR ALA ARG ASN GLU GLN LEU SEQRES 51 A 668 ASP TRP PRO TYR GLU TYR LEU LYS PRO SER CYS ILE GLU SEQRES 52 A 668 ASN SER VAL THR ILE HET FE2 A 901 1 HETNAM FE2 FE (II) ION FORMUL 2 FE2 FE 2+ HELIX 1 AA1 ASP A 122 TYR A 139 1 18 HELIX 2 AA2 ARG A 156 LEU A 160 5 5 HELIX 3 AA3 PRO A 161 ARG A 165 5 5 HELIX 4 AA4 HIS A 167 THR A 192 1 26 HELIX 5 AA5 CYS A 199 ILE A 206 5 8 HELIX 6 AA6 SER A 212 TRP A 222 1 11 HELIX 7 AA7 ASP A 224 GLY A 235 1 12 HELIX 8 AA8 MET A 257 GLY A 271 1 15 HELIX 9 AA9 ILE A 279 ASP A 282 5 4 HELIX 10 AB1 PRO A 336 ILE A 357 1 22 HELIX 11 AB2 THR A 364 LEU A 379 1 16 HELIX 12 AB3 HIS A 383 ILE A 390 1 8 HELIX 13 AB4 TYR A 395 LEU A 407 1 13 HELIX 14 AB5 GLY A 412 VAL A 418 1 7 HELIX 15 AB6 GLY A 423 LEU A 436 1 14 HELIX 16 AB7 CYS A 442 ARG A 450 1 9 HELIX 17 AB8 ALA A 458 TYR A 483 1 26 HELIX 18 AB9 ARG A 485 GLY A 491 1 7 HELIX 19 AC1 ASP A 492 GLU A 504 1 13 HELIX 20 AC2 SER A 521 THR A 537 1 17 HELIX 21 AC3 THR A 537 GLN A 545 1 9 HELIX 22 AC4 GLN A 545 ALA A 552 1 8 HELIX 23 AC5 TRP A 553 ALA A 557 5 5 HELIX 24 AC6 THR A 573 LEU A 581 1 9 HELIX 25 AC7 ASP A 583 LEU A 597 1 15 HELIX 26 AC8 GLY A 617 GLU A 643 1 27 SHEET 1 AA1 4 GLU A 47 ASP A 52 0 SHEET 2 AA1 4 ARG A 3 LEU A 14 -1 N TYR A 4 O HIS A 51 SHEET 3 AA1 4 ALA A 75 GLN A 84 -1 O ASP A 79 N ALA A 9 SHEET 4 AA1 4 GLU A 91 TRP A 99 -1 O VAL A 92 N VAL A 83 SHEET 1 AA2 4 GLU A 32 LEU A 39 0 SHEET 2 AA2 4 ASN A 20 GLY A 28 -1 N ASN A 20 O LEU A 39 SHEET 3 AA2 4 LEU A 60 LYS A 67 -1 O PHE A 62 N VAL A 27 SHEET 4 AA2 4 LEU A 106 PRO A 109 -1 O LEU A 108 N VAL A 63 SHEET 1 AA3 2 TRP A 141 ALA A 142 0 SHEET 2 AA3 2 THR A 151 ILE A 152 -1 O THR A 151 N ALA A 142 SHEET 1 AA4 5 ARG A 242 ARG A 243 0 SHEET 2 AA4 5 LEU A 273 ASP A 277 -1 O GLU A 275 N ARG A 242 SHEET 3 AA4 5 LEU A 300 MET A 305 -1 O LEU A 303 N PHE A 274 SHEET 4 AA4 5 LEU A 311 GLN A 317 -1 O GLN A 312 N LYS A 304 SHEET 5 AA4 5 LEU A 330 PHE A 331 -1 O PHE A 331 N ILE A 316 SHEET 1 AA5 2 VAL A 288 ILE A 289 0 SHEET 2 AA5 2 GLU A 292 LYS A 293 -1 O GLU A 292 N ILE A 289 LINK NE2 HIS A 360 FE FE2 A 901 1555 1555 2.15 LINK NE2 HIS A 365 FE FE2 A 901 1555 1555 2.22 LINK OD1 ASN A 544 FE FE2 A 901 1555 1555 2.72 LINK O ILE A 663 FE FE2 A 901 1555 1555 2.60 LINK OXT ILE A 663 FE FE2 A 901 1555 1555 2.07 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