HEADER STRUCTURAL PROTEIN 04-JUN-25 9RF1 TITLE STRUCTURE OF HUMAN GPX4-U46C-R152K MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPID HYDROPEROXIDE GLUTATHIONE PEROXIDASE GPX4; COMPND 3 CHAIN: A, B; 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, GPX4, XRAY, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.MOURAO,M.SATTLER,G.POPOWICZ REVDAT 2 17-DEC-25 9RF1 1 REMARK REVDAT 1 03-DEC-25 9RF1 0 JRNL AUTH A.MOURAO,M.SATTLER,G.POPOWICZ JRNL TITL CRYSTAL STRUCTURE OF HUMAN GPX4-U46C-R152K JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 25375 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.330 REMARK 3 FREE R VALUE TEST SET COUNT : 1352 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.0000 - 4.1000 0.99 2473 143 0.1761 0.2182 REMARK 3 2 4.0900 - 3.2500 0.99 2461 110 0.1695 0.2732 REMARK 3 3 3.2500 - 2.8400 0.99 2443 130 0.2057 0.2813 REMARK 3 4 2.8400 - 2.5800 0.98 2396 123 0.2321 0.3064 REMARK 3 5 2.5800 - 2.4000 0.98 2366 162 0.2276 0.3000 REMARK 3 6 2.4000 - 2.2500 0.99 2399 124 0.2419 0.3137 REMARK 3 7 2.2500 - 2.1400 0.99 2421 120 0.2534 0.2862 REMARK 3 8 2.1400 - 2.0500 0.99 2404 130 0.2747 0.3055 REMARK 3 9 2.0500 - 1.9700 0.99 2354 140 0.3003 0.3861 REMARK 3 10 1.9700 - 1.9000 0.96 2306 170 0.3261 0.3562 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.347 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.897 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2727 REMARK 3 ANGLE : 0.826 3678 REMARK 3 CHIRALITY : 0.058 376 REMARK 3 PLANARITY : 0.006 478 REMARK 3 DIHEDRAL : 15.407 994 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9RF1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1292148277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8731 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88991 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 37.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE 0.1M BIS-TRIS PH REMARK 280 5.5 25% W/V PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 31.47600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLY B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 CYS B 2 REMARK 465 ALA B 3 REMARK 465 SER B 4 REMARK 465 ARG B 5 REMARK 465 ILE B 129 REMARK 465 LEU B 130 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 ARG A 5 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 125 CG CD CE NZ REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 ARG B 12 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 127 CG CD CE NZ REMARK 470 ASN B 132 CG OD1 ND2 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 6 44.24 -108.71 REMARK 500 ASN A 132 -16.01 70.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 330 DISTANCE = 5.89 ANGSTROMS DBREF 9RF1 A 1 170 UNP P36969 GPX4_HUMAN 28 197 DBREF 9RF1 B 1 170 UNP P36969 GPX4_HUMAN 28 197 SEQADV 9RF1 GLY A -1 UNP P36969 EXPRESSION TAG SEQADV 9RF1 ALA A 0 UNP P36969 EXPRESSION TAG SEQADV 9RF1 CYS A 46 UNP P36969 SEC 73 ENGINEERED MUTATION SEQADV 9RF1 LYS A 152 UNP P36969 ARG 179 ENGINEERED MUTATION SEQADV 9RF1 GLY B -1 UNP P36969 EXPRESSION TAG SEQADV 9RF1 ALA B 0 UNP P36969 EXPRESSION TAG SEQADV 9RF1 CYS B 46 UNP P36969 SEC 73 ENGINEERED MUTATION SEQADV 9RF1 LYS B 152 UNP P36969 ARG 179 ENGINEERED MUTATION SEQRES 1 A 172 GLY ALA MET CYS ALA SER ARG ASP ASP TRP ARG CYS ALA SEQRES 2 A 172 ARG SER MET HIS GLU PHE SER ALA LYS ASP ILE ASP GLY SEQRES 3 A 172 HIS MET VAL ASN LEU ASP LYS TYR ARG GLY PHE VAL CYS SEQRES 4 A 172 ILE VAL THR ASN VAL ALA SER GLN CYS GLY LYS THR GLU SEQRES 5 A 172 VAL ASN TYR THR GLN LEU VAL ASP LEU HIS ALA ARG TYR SEQRES 6 A 172 ALA GLU CYS GLY LEU ARG ILE LEU ALA PHE PRO CYS ASN SEQRES 7 A 172 GLN PHE GLY LYS GLN GLU PRO GLY SER ASN GLU GLU ILE SEQRES 8 A 172 LYS GLU PHE ALA ALA GLY TYR ASN VAL LYS PHE ASP MET SEQRES 9 A 172 PHE SER LYS ILE CYS VAL ASN GLY ASP ASP ALA HIS PRO SEQRES 10 A 172 LEU TRP LYS TRP MET LYS ILE GLN PRO LYS GLY LYS GLY SEQRES 11 A 172 ILE LEU GLY ASN ALA ILE LYS TRP ASN PHE THR LYS PHE SEQRES 12 A 172 LEU ILE ASP LYS ASN GLY CYS VAL VAL LYS LYS TYR GLY SEQRES 13 A 172 PRO MET GLU GLU PRO LEU VAL ILE GLU LYS ASP LEU PRO SEQRES 14 A 172 HIS TYR PHE SEQRES 1 B 172 GLY ALA MET CYS ALA SER ARG ASP ASP TRP ARG CYS ALA SEQRES 2 B 172 ARG SER MET HIS GLU PHE SER ALA LYS ASP ILE ASP GLY SEQRES 3 B 172 HIS MET VAL ASN LEU ASP LYS TYR ARG GLY PHE VAL CYS SEQRES 4 B 172 ILE VAL THR ASN VAL ALA SER GLN CYS GLY LYS THR GLU SEQRES 5 B 172 VAL ASN TYR THR GLN LEU VAL ASP LEU HIS ALA ARG TYR SEQRES 6 B 172 ALA GLU CYS GLY LEU ARG ILE LEU ALA PHE PRO CYS ASN SEQRES 7 B 172 GLN PHE GLY LYS GLN GLU PRO GLY SER ASN GLU GLU ILE SEQRES 8 B 172 LYS GLU PHE ALA ALA GLY TYR ASN VAL LYS PHE ASP MET SEQRES 9 B 172 PHE SER LYS ILE CYS VAL ASN GLY ASP ASP ALA HIS PRO SEQRES 10 B 172 LEU TRP LYS TRP MET LYS ILE GLN PRO LYS GLY LYS GLY SEQRES 11 B 172 ILE LEU GLY ASN ALA ILE LYS TRP ASN PHE THR LYS PHE SEQRES 12 B 172 LEU ILE ASP LYS ASN GLY CYS VAL VAL LYS LYS TYR GLY SEQRES 13 B 172 PRO MET GLU GLU PRO LEU VAL ILE GLU LYS ASP LEU PRO SEQRES 14 B 172 HIS TYR PHE FORMUL 3 HOH *228(H2 O) HELIX 1 AA1 ASP A 7 ALA A 11 5 5 HELIX 2 AA2 SER A 13 GLU A 16 5 4 HELIX 3 AA3 ASP A 30 ARG A 33 5 4 HELIX 4 AA4 LYS A 48 ALA A 64 1 17 HELIX 5 AA5 SER A 85 TYR A 96 1 12 HELIX 6 AA6 HIS A 114 GLN A 123 1 10 HELIX 7 AA7 GLU A 158 GLU A 163 5 6 HELIX 8 AA8 ASP A 165 TYR A 169 5 5 HELIX 9 AA9 ASP B 6 ALA B 11 5 6 HELIX 10 AB1 SER B 13 GLU B 16 5 4 HELIX 11 AB2 ASP B 30 ARG B 33 5 4 HELIX 12 AB3 LYS B 48 ALA B 64 1 17 HELIX 13 AB4 SER B 85 TYR B 96 1 12 HELIX 14 AB5 HIS B 114 GLN B 123 1 10 HELIX 15 AB6 GLU B 158 TYR B 169 5 12 SHEET 1 AA1 2 SER A 18 LYS A 20 0 SHEET 2 AA1 2 MET A 26 ASN A 28 -1 O VAL A 27 N ALA A 19 SHEET 1 AA2 5 ASP A 101 MET A 102 0 SHEET 2 AA2 5 LEU A 68 PRO A 74 1 N ALA A 72 O ASP A 101 SHEET 3 AA2 5 VAL A 36 VAL A 42 1 N THR A 40 O PHE A 73 SHEET 4 AA2 5 LYS A 140 ILE A 143 -1 O ILE A 143 N CYS A 37 SHEET 5 AA2 5 VAL A 149 TYR A 153 -1 O VAL A 150 N LEU A 142 SHEET 1 AA3 2 SER B 18 LYS B 20 0 SHEET 2 AA3 2 MET B 26 ASN B 28 -1 O VAL B 27 N ALA B 19 SHEET 1 AA4 5 ASP B 101 MET B 102 0 SHEET 2 AA4 5 LEU B 68 PRO B 74 1 N ALA B 72 O ASP B 101 SHEET 3 AA4 5 VAL B 36 VAL B 42 1 N THR B 40 O PHE B 73 SHEET 4 AA4 5 LYS B 140 ILE B 143 -1 O ILE B 143 N CYS B 37 SHEET 5 AA4 5 VAL B 149 TYR B 153 -1 O VAL B 150 N LEU B 142 SSBOND 1 CYS A 2 CYS A 10 1555 1555 2.04 CRYST1 35.392 62.952 75.442 90.00 100.79 90.00 P 1 21 1 4 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 0.028255 0.000000 0.005385 0.00000 SCALE2 0.000000 0.015885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013494 0.00000 CONECT 23 86 CONECT 86 23 MASTER 256 0 0 15 14 0 0 6 2886 2 2 28 END