HEADER APOPTOSIS 16-AUG-24 9J6L TITLE SOLUTION STRUCTURE OF HUMAN GLUTATHIONE PEROXIDASE 4 (SEC73CYS) WITH TITLE 2 EIGHT MUTATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE GPX4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHGPX,GLUTATHIONE PEROXIDASE 4,GPX-4,GSHPX-4; COMPND 5 EC: 1.11.1.12,1.11.1.9; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GPX4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FERROPTOSIS, CANCER, ENZYME, PEROXIDASE, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.FURUITA,T.SUGIKI,K.INOMATA,Y.MIYANOIRI,N.KOBAYASHI,T.FUJIWARA, AUTHOR 2 C.KOJIMA REVDAT 1 20-AUG-25 9J6L 0 JRNL AUTH K.INOMATA,K.FURUITA,T.SUGIKI,K.NAKADA,T.S.KODAMA, JRNL AUTH 2 Y.MIYANOIRI,N.KOBAYASHI,T.FUJIWARA,C.KOJIMA JRNL TITL GLUTATHIONE DISULFIDE ACTS AS A FEEDBACK INHIBITOR OF GPX4 JRNL TITL 2 REDOX REACTION THROUGH ALLOSTERIC REGULATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 20 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9J6L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300050402. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 50 MM POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 1 MM DTT, REMARK 210 0.4 MM [U-15N] PHOSPHOLIPID REMARK 210 HYDROPEROXIDE GLUTATHIONE REMARK 210 PEROXIDASE GPX4, 95% H2O/5% D2O; REMARK 210 50 MM POTASSIUM PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 1 MM DTT, REMARK 210 0.4 MM [U-13C; U-15N] REMARK 210 PHOSPHOLIPID HYDROPEROXIDE REMARK 210 GLUTATHIONE PEROXIDASE GPX4, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-1H NOESY; 3D REMARK 210 HNCO; 3D HNCACO; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, HMSIST, MAGRO-NMRVIEW, REMARK 210 CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 2 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 32 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 8 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 89 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.0 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 1 ASP A 34 -157.84 -152.99 REMARK 500 1 ALA A 70 137.31 -171.33 REMARK 500 1 LEU A 157 -109.74 -107.11 REMARK 500 1 ASN A 159 -154.61 68.67 REMARK 500 1 ALA A 160 136.01 83.03 REMARK 500 2 LEU A 157 -112.46 -108.14 REMARK 500 2 ASN A 159 79.67 -109.70 REMARK 500 2 PHE A 165 32.76 74.68 REMARK 500 3 HIS A 27 140.87 85.82 REMARK 500 3 SER A 29 34.56 -84.13 REMARK 500 3 ASP A 34 -112.98 59.53 REMARK 500 3 ALA A 70 134.20 -170.75 REMARK 500 3 PHE A 165 31.93 74.69 REMARK 500 4 HIS A 27 -176.51 66.94 REMARK 500 5 HIS A 27 -151.03 60.06 REMARK 500 5 ARG A 32 -132.70 52.88 REMARK 500 6 ARG A 32 58.73 -102.54 REMARK 500 6 GLU A 109 85.44 -152.88 REMARK 500 6 HIS A 141 115.52 -39.97 REMARK 500 7 HIS A 27 -30.06 73.66 REMARK 500 7 ARG A 32 -128.16 53.79 REMARK 500 7 GLU A 109 79.06 -151.00 REMARK 500 8 ASP A 34 -126.02 59.08 REMARK 500 9 SER A 31 -31.32 72.16 REMARK 500 10 HIS A 27 -54.39 76.19 REMARK 500 10 ASP A 33 -121.92 -100.07 REMARK 500 10 ASP A 34 -121.48 -86.83 REMARK 500 10 LYS A 107 44.37 -84.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 47 ASP A 48 5 149.24 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 1 TYR A 59 0.07 SIDE CHAIN REMARK 500 7 HIS A 141 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 51397 RELATED DB: BMRB DBREF 9J6L A 26 197 UNP P36969 GPX4_HUMAN 26 197 SEQADV 9J6L GLY A 24 UNP P36969 EXPRESSION TAG SEQADV 9J6L PRO A 25 UNP P36969 EXPRESSION TAG SEQADV 9J6L HIS A 27 UNP P36969 THR 27 ENGINEERED MUTATION SEQADV 9J6L SER A 29 UNP P36969 CYS 29 ENGINEERED MUTATION SEQADV 9J6L ALA A 37 UNP P36969 CYS 37 ENGINEERED MUTATION SEQADV 9J6L SER A 64 UNP P36969 CYS 64 ENGINEERED MUTATION SEQADV 9J6L CYS A 73 UNP P36969 SEC 73 ENGINEERED MUTATION SEQADV 9J6L ARG A 93 UNP P36969 CYS 93 ENGINEERED MUTATION SEQADV 9J6L SER A 102 UNP P36969 CYS 102 ENGINEERED MUTATION SEQADV 9J6L GLU A 134 UNP P36969 CYS 134 ENGINEERED MUTATION SEQADV 9J6L VAL A 175 UNP P36969 CYS 175 ENGINEERED MUTATION SEQRES 1 A 174 GLY PRO GLY HIS MET SER ALA SER ARG ASP ASP TRP ARG SEQRES 2 A 174 ALA ALA ARG SER MET HIS GLU PHE SER ALA LYS ASP ILE SEQRES 3 A 174 ASP GLY HIS MET VAL ASN LEU ASP LYS TYR ARG GLY PHE SEQRES 4 A 174 VAL SER ILE VAL THR ASN VAL ALA SER GLN CYS GLY LYS SEQRES 5 A 174 THR GLU VAL ASN TYR THR GLN LEU VAL ASP LEU HIS ALA SEQRES 6 A 174 ARG TYR ALA GLU ARG GLY LEU ARG ILE LEU ALA PHE PRO SEQRES 7 A 174 SER ASN GLN PHE GLY LYS GLN GLU PRO GLY SER ASN GLU SEQRES 8 A 174 GLU ILE LYS GLU PHE ALA ALA GLY TYR ASN VAL LYS PHE SEQRES 9 A 174 ASP MET PHE SER LYS ILE GLU VAL ASN GLY ASP ASP ALA SEQRES 10 A 174 HIS PRO LEU TRP LYS TRP MET LYS ILE GLN PRO LYS GLY SEQRES 11 A 174 LYS GLY ILE LEU GLY ASN ALA ILE LYS TRP ASN PHE THR SEQRES 12 A 174 LYS PHE LEU ILE ASP LYS ASN GLY VAL VAL VAL LYS ARG SEQRES 13 A 174 TYR GLY PRO MET GLU GLU PRO LEU VAL ILE GLU LYS ASP SEQRES 14 A 174 LEU PRO HIS TYR PHE HELIX 1 AA1 ASP A 34 ALA A 38 5 5 HELIX 2 AA2 SER A 40 GLU A 43 5 4 HELIX 3 AA3 ASP A 57 ARG A 60 5 4 HELIX 4 AA4 LYS A 75 ALA A 91 1 17 HELIX 5 AA5 SER A 112 GLY A 122 1 11 HELIX 6 AA6 HIS A 141 GLN A 150 1 10 HELIX 7 AA7 GLU A 185 GLU A 190 1 6 HELIX 8 AA8 ASP A 192 PHE A 197 1 6 SHEET 1 AA1 3 MET A 53 ASN A 55 0 SHEET 2 AA1 3 SER A 45 ASP A 48 -1 N ALA A 46 O VAL A 54 SHEET 3 AA1 3 PHE A 130 SER A 131 -1 O SER A 131 N LYS A 47 SHEET 1 AA2 4 LEU A 95 PRO A 101 0 SHEET 2 AA2 4 VAL A 63 VAL A 69 1 N THR A 67 O PHE A 100 SHEET 3 AA2 4 LYS A 167 ILE A 170 -1 O PHE A 168 N VAL A 66 SHEET 4 AA2 4 VAL A 176 TYR A 180 -1 O LYS A 178 N LEU A 169 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1 TER 2771 PHE A 197 ENDMDL MODEL 2 TER 2771 PHE A 197 ENDMDL MODEL 3 TER 2771 PHE A 197 ENDMDL MODEL 4 TER 2771 PHE A 197 ENDMDL MODEL 5 TER 2771 PHE A 197 ENDMDL MODEL 6 TER 2771 PHE A 197 ENDMDL MODEL 7 TER 2771 PHE A 197 ENDMDL MODEL 8 TER 2771 PHE A 197 ENDMDL MODEL 9 TER 2771 PHE A 197 ENDMDL MODEL 10 TER 2771 PHE A 197 ENDMDL MASTER 209 0 0 8 7 0 0 6 1399 1 0 14 END