HEADER OXIDOREDUCTASE 27-FEB-24 8S6B TITLE CRYOEM STRUCTURE OF APO FORM OF CATALYTIC DOMAIN OF HUMAN HMG-COA TITLE 2 REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HMG-COA REDUCTASE; COMPND 5 EC: 1.1.1.34; COMPND 6 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: HMGCR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS REDUCTASE, CHOLESTEROL BIOSYNTHESIS, LIPITOR, ATORVASTATIN, STATINS, KEYWDS 2 OXIDOREDUCTASE EXPDTA ELECTRON MICROSCOPY AUTHOR K.MANIKANDAN,J.VAN ROOYEN REVDAT 3 12-MAR-25 8S6B 1 JRNL REVDAT 2 05-MAR-25 8S6B 1 JRNL REVDAT 1 26-FEB-25 8S6B 0 JRNL AUTH M.KARUPPASAMY,J.VAN ROOYEN JRNL TITL CRYO-EM STRUCTURES OF APO AND ATORVASTATIN-BOUND HUMAN JRNL TITL 2 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 81 118 2025 JRNL REFN ESSN 2053-230X JRNL PMID 39976191 JRNL DOI 10.1107/S2053230X25001098 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.S.ISTVAN,J.DEISENHOFER REMARK 1 TITL STRUCTURAL MECHANISM FOR STATIN INHIBITION OF HMG-COA REMARK 1 TITL 2 REDUCTASE. REMARK 1 REF SCIENCE 2001 REMARK 1 REFN ESSN 1095-9203 REMARK 1 PMID 11349148 REMARK 1 DOI 10.1126/SCIENCE.1059344 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, EPU, RELION, COOT, RELION, REMARK 3 RELION, RELION, RELION, REFMAC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 1HWK REMARK 3 REFINEMENT SPACE : REAL 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) : 2.060 REMARK 3 NUMBER OF PARTICLES : 106670 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 8S6B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136895. 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 : HUMAN HMGCOA CATALYTIC DOMAIN REMARK 245 REDUCTASE 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 : 13644 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 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 : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5480.00 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 222.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 222.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 222.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 222.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 222.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 222.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 443 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 440 -166.14 -174.74 REMARK 500 LYS A 460 -24.36 113.80 REMARK 500 ALA A 525 -45.32 -132.01 REMARK 500 CYS A 561 -8.25 83.12 REMARK 500 SER A 651 34.37 -142.49 REMARK 500 LEU A 737 -62.98 -97.47 REMARK 500 TYR A 749 58.16 -95.17 REMARK 500 HIS A 752 43.74 -152.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 440 0.08 SIDE CHAIN REMARK 500 ARG A 443 0.23 SIDE CHAIN REMARK 500 ARG A 590 0.17 SIDE CHAIN REMARK 500 ARG A 595 0.19 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-17748 RELATED DB: EMDB REMARK 900 THE SAME ENZYME WITH LIGAND REMARK 900 RELATED ID: 8PKN RELATED DB: PDB REMARK 900 CONTAINS THE MODEL OF THE SAME ENZYME WITH LIGAND DERIVED FROM EMDB- REMARK 900 17748 REMARK 900 RELATED ID: EMD-19757 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF CATALYTIC DOMAIN OF HUMAN HMG-COA REDUCTASE DBREF 8S6B A 439 861 UNP P04035 HMDH_HUMAN 439 861 SEQRES 1 A 423 PRO ARG GLU PRO ARG PRO ASN GLU GLU CYS LEU GLN ILE SEQRES 2 A 423 LEU GLY ASN ALA GLU LYS GLY ALA LYS PHE LEU SER ASP SEQRES 3 A 423 ALA GLU ILE ILE GLN LEU VAL ASN ALA LYS HIS ILE PRO SEQRES 4 A 423 ALA TYR LYS LEU GLU THR LEU MET GLU THR HIS GLU ARG SEQRES 5 A 423 GLY VAL SER ILE ARG ARG GLN LEU LEU SER LYS LYS LEU SEQRES 6 A 423 SER GLU PRO SER SER LEU GLN TYR LEU PRO TYR ARG ASP SEQRES 7 A 423 TYR ASN TYR SER LEU VAL MET GLY ALA CYS CYS GLU ASN SEQRES 8 A 423 VAL ILE GLY TYR MET PRO ILE PRO VAL GLY VAL ALA GLY SEQRES 9 A 423 PRO LEU CYS LEU ASP GLU LYS GLU PHE GLN VAL PRO MET SEQRES 10 A 423 ALA THR THR GLU GLY CYS LEU VAL ALA SER THR ASN ARG SEQRES 11 A 423 GLY CYS ARG ALA ILE GLY LEU GLY GLY GLY ALA SER SER SEQRES 12 A 423 ARG VAL LEU ALA ASP GLY MET THR ARG GLY PRO VAL VAL SEQRES 13 A 423 ARG LEU PRO ARG ALA CYS ASP SER ALA GLU VAL LYS ALA SEQRES 14 A 423 TRP LEU GLU THR SER GLU GLY PHE ALA VAL ILE LYS GLU SEQRES 15 A 423 ALA PHE ASP SER THR SER ARG PHE ALA ARG LEU GLN LYS SEQRES 16 A 423 LEU HIS THR SER ILE ALA GLY ARG ASN LEU TYR ILE ARG SEQRES 17 A 423 PHE GLN SER ARG SER GLY ASP ALA MET GLY MET ASN MET SEQRES 18 A 423 ILE SER LYS GLY THR GLU LYS ALA LEU SER LYS LEU HIS SEQRES 19 A 423 GLU TYR PHE PRO GLU MET GLN ILE LEU ALA VAL SER GLY SEQRES 20 A 423 ASN TYR CYS THR ASP LYS LYS PRO ALA ALA ILE ASN TRP SEQRES 21 A 423 ILE GLU GLY ARG GLY LYS SER VAL VAL CYS GLU ALA VAL SEQRES 22 A 423 ILE PRO ALA LYS VAL VAL ARG GLU VAL LEU LYS THR THR SEQRES 23 A 423 THR GLU ALA MET ILE GLU VAL ASN ILE ASN LYS ASN LEU SEQRES 24 A 423 VAL GLY SER ALA MET ALA GLY SER ILE GLY GLY TYR ASN SEQRES 25 A 423 ALA HIS ALA ALA ASN ILE VAL THR ALA ILE TYR ILE ALA SEQRES 26 A 423 CYS GLY GLN ASP ALA ALA GLN ASN VAL GLY SER SER ASN SEQRES 27 A 423 CYS ILE THR LEU MET GLU ALA SER GLY PRO THR ASN GLU SEQRES 28 A 423 ASP LEU TYR ILE SER CYS THR MET PRO SER ILE GLU ILE SEQRES 29 A 423 GLY THR VAL GLY GLY GLY THR ASN LEU LEU PRO GLN GLN SEQRES 30 A 423 ALA CYS LEU GLN MET LEU GLY VAL GLN GLY ALA CYS LYS SEQRES 31 A 423 ASP ASN PRO GLY GLU ASN ALA ARG GLN LEU ALA ARG ILE SEQRES 32 A 423 VAL CYS GLY THR VAL MET ALA GLY GLU LEU SER LEU MET SEQRES 33 A 423 ALA ALA LEU ALA ALA GLY HIS HELIX 1 AA1 PRO A 444 ASN A 454 1 11 HELIX 2 AA2 SER A 463 ALA A 473 1 11 HELIX 3 AA3 PRO A 477 TYR A 479 5 3 HELIX 4 AA4 LYS A 480 MET A 485 1 6 HELIX 5 AA5 THR A 487 LYS A 502 1 16 HELIX 6 AA6 SER A 507 LEU A 512 5 6 HELIX 7 AA7 CYS A 561 GLY A 576 1 16 HELIX 8 AA8 ARG A 598 THR A 611 1 14 HELIX 9 AA9 THR A 611 SER A 624 1 14 HELIX 10 AB1 GLY A 656 PHE A 675 1 20 HELIX 11 AB2 ALA A 694 GLY A 701 1 8 HELIX 12 AB3 PRO A 713 VAL A 720 1 8 HELIX 13 AB4 THR A 724 LEU A 737 1 14 HELIX 14 AB5 LEU A 737 ALA A 743 1 7 HELIX 15 AB6 HIS A 752 CYS A 764 1 13 HELIX 16 AB7 ASP A 767 ALA A 769 5 3 HELIX 17 AB8 GLN A 770 SER A 775 1 6 HELIX 18 AB9 GLY A 806 ASN A 810 5 5 HELIX 19 AC1 LEU A 811 LEU A 821 1 11 HELIX 20 AC2 GLY A 832 GLY A 860 1 29 SHEET 1 AA1 2 VAL A 538 LEU A 546 0 SHEET 2 AA1 2 LYS A 549 ALA A 556 -1 O MET A 555 N GLY A 539 SHEET 1 AA2 4 ARG A 630 LEU A 631 0 SHEET 2 AA2 4 ASN A 642 ARG A 650 -1 N ARG A 650 O ARG A 630 SHEET 3 AA2 4 VAL A 593 ARG A 595 -1 N VAL A 594 O LEU A 643 SHEET 4 AA2 4 GLN A 679 ALA A 682 -1 O GLN A 679 N ARG A 595 SHEET 1 AA3 7 HIS A 635 ALA A 639 0 SHEET 2 AA3 7 ASN A 642 ARG A 650 -1 O TYR A 644 N SER A 637 SHEET 3 AA3 7 SER A 580 ARG A 590 -1 N ARG A 590 O PHE A 647 SHEET 4 AA3 7 GLY A 703 ILE A 712 -1 O SER A 705 N LEU A 584 SHEET 5 AA3 7 ASP A 790 ILE A 800 -1 O LEU A 791 N ILE A 712 SHEET 6 AA3 7 CYS A 777 SER A 784 -1 N LEU A 780 O SER A 794 SHEET 7 AA3 7 GLY A 748 TYR A 749 1 N TYR A 749 O THR A 779 CISPEP 1 GLY A 542 PRO A 543 0 2.47 CISPEP 2 CYS A 688 THR A 689 0 -1.62 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 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -1.000000 0.000000 0.000000 222.00000 MTRIX2 2 0.000000 -1.000000 0.000000 222.00000 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 MTRIX1 3 1.000000 0.000000 0.000000 0.00000 MTRIX2 3 0.000000 -1.000000 0.000000 222.00000 MTRIX3 3 0.000000 0.000000 -1.000000 222.00000 MTRIX1 4 -1.000000 0.000000 0.000000 222.00000 MTRIX2 4 0.000000 1.000000 0.000000 0.00000 MTRIX3 4 0.000000 0.000000 -1.000000 222.00000 MASTER 187 0 0 20 13 0 0 18 3151 1 0 33 END