HEADER CELL CYCLE 14-NOV-23 8X3S TITLE CRYSTAL STRUCTURE OF HUMAN WDR5 IN COMPLEX WITH PTEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: WD REPEAT-CONTAINING PROTEIN 5; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PHOSPHATIDYLINOSITOL 3,4,5-TRISPHOSPHATE 3-PHOSPHATASE AND COMPND 7 DUAL-SPECIFICITY PROTEIN PHOSPHATASE PTEN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: MUTATED IN MULTIPLE ADVANCED CANCERS 1,PHOSPHATASE AND COMPND 10 TENSIN HOMOLOG; COMPND 11 EC: 3.1.3.16,3.1.3.48,3.1.3.67; COMPND 12 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: WDR5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: PTEN, MMAC1, TEP1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, CELL PROLIFERATION, CANCER, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,X.HUANG,X.SHANG REVDAT 1 29-MAY-24 8X3S 0 JRNL AUTH X.HUANG,C.ZHANG,X.SHANG,Y.CHEN,Q.XIAO,Z.WEI,G.WANG,X.ZHEN, JRNL AUTH 2 G.XU,J.MIN,S.SHEN,Y.LIU JRNL TITL THE NTE DOMAIN OF PTEN ALPHA / BETA PROMOTES CANCER JRNL TITL 2 PROGRESSION BY INTERACTING WITH WDR5 VIA ITS SSSRRSS MOTIF. JRNL REF CELL DEATH DIS V. 15 335 2024 JRNL REFN ISSN 2041-4889 JRNL PMID 38744853 JRNL DOI 10.1038/S41419-024-06714-6 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 22670 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 I_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 8X3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300041597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-SEP-22 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 : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22670 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 29.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 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: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M HEPES AT PH 7.5, 25% W/V POLYETHYLENE GLYCOL 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 23.23000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.42000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.87500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.42000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.23000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.87500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 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 SER A -6 REMARK 465 SER A -5 REMARK 465 ALA A -4 REMARK 465 THR A -3 REMARK 465 GLN A -2 REMARK 465 SER A -1 REMARK 465 LYS A 0 REMARK 465 HIS B 8 REMARK 465 TYR B 9 REMARK 465 PRO B 10 REMARK 465 ALA B 11 REMARK 465 ALA B 12 REMARK 465 VAL B 13 REMARK 465 GLN B 14 REMARK 465 SER B 15 REMARK 465 GLN B 16 REMARK 465 ALA B 17 REMARK 465 ALA B 18 REMARK 465 ALA B 19 REMARK 465 GLU B 20 REMARK 465 ARG B 21 REMARK 465 GLY B 22 REMARK 465 ALA B 23 REMARK 465 SER B 24 REMARK 465 ALA B 25 REMARK 465 THR B 26 REMARK 465 ALA B 27 REMARK 465 LYS B 28 REMARK 465 SER B 29 REMARK 465 ARG B 30 REMARK 465 ALA B 31 REMARK 465 ILE B 32 REMARK 465 SER B 33 REMARK 465 ILE B 34 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 GLU A 124 6.77 80.94 REMARK 500 ASP A 185 -140.87 50.72 REMARK 500 ASN A 187 75.56 51.48 REMARK 500 ASP A 208 33.02 -143.88 REMARK 500 ASP A 297 -65.01 -121.48 REMARK 500 REMARK 500 REMARK: NULL DBREF 8X3S A -6 307 UNP P61964 WDR5_HUMAN 21 334 DBREF 8X3S B 1 34 UNP P60484 PTEN_HUMAN 115 148 SEQRES 1 A 314 SER SER ALA THR GLN SER LYS PRO THR PRO VAL LYS PRO SEQRES 2 A 314 ASN TYR ALA LEU LYS PHE THR LEU ALA GLY HIS THR LYS SEQRES 3 A 314 ALA VAL SER SER VAL LYS PHE SER PRO ASN GLY GLU TRP SEQRES 4 A 314 LEU ALA SER SER SER ALA ASP LYS LEU ILE LYS ILE TRP SEQRES 5 A 314 GLY ALA TYR ASP GLY LYS PHE GLU LYS THR ILE SER GLY SEQRES 6 A 314 HIS LYS LEU GLY ILE SER ASP VAL ALA TRP SER SER ASP SEQRES 7 A 314 SER ASN LEU LEU VAL SER ALA SER ASP ASP LYS THR LEU SEQRES 8 A 314 LYS ILE TRP ASP VAL SER SER GLY LYS CYS LEU LYS THR SEQRES 9 A 314 LEU LYS GLY HIS SER ASN TYR VAL PHE CYS CYS ASN PHE SEQRES 10 A 314 ASN PRO GLN SER ASN LEU ILE VAL SER GLY SER PHE ASP SEQRES 11 A 314 GLU SER VAL ARG ILE TRP ASP VAL LYS THR GLY LYS CYS SEQRES 12 A 314 LEU LYS THR LEU PRO ALA HIS SER ASP PRO VAL SER ALA SEQRES 13 A 314 VAL HIS PHE ASN ARG ASP GLY SER LEU ILE VAL SER SER SEQRES 14 A 314 SER TYR ASP GLY LEU CYS ARG ILE TRP ASP THR ALA SER SEQRES 15 A 314 GLY GLN CYS LEU LYS THR LEU ILE ASP ASP ASP ASN PRO SEQRES 16 A 314 PRO VAL SER PHE VAL LYS PHE SER PRO ASN GLY LYS TYR SEQRES 17 A 314 ILE LEU ALA ALA THR LEU ASP ASN THR LEU LYS LEU TRP SEQRES 18 A 314 ASP TYR SER LYS GLY LYS CYS LEU LYS THR TYR THR GLY SEQRES 19 A 314 HIS LYS ASN GLU LYS TYR CYS ILE PHE ALA ASN PHE SER SEQRES 20 A 314 VAL THR GLY GLY LYS TRP ILE VAL SER GLY SER GLU ASP SEQRES 21 A 314 ASN LEU VAL TYR ILE TRP ASN LEU GLN THR LYS GLU ILE SEQRES 22 A 314 VAL GLN LYS LEU GLN GLY HIS THR ASP VAL VAL ILE SER SEQRES 23 A 314 THR ALA CYS HIS PRO THR GLU ASN ILE ILE ALA SER ALA SEQRES 24 A 314 ALA LEU GLU ASN ASP LYS THR ILE LYS LEU TRP LYS SER SEQRES 25 A 314 ASP CYS SEQRES 1 B 34 SER SER SER ARG ARG SER SER HIS TYR PRO ALA ALA VAL SEQRES 2 B 34 GLN SER GLN ALA ALA ALA GLU ARG GLY ALA SER ALA THR SEQRES 3 B 34 ALA LYS SER ARG ALA ILE SER ILE FORMUL 3 HOH *125(H2 O) SHEET 1 AA1 4 ALA A 9 LEU A 14 0 SHEET 2 AA1 4 ILE A 300 LYS A 304 -1 O ILE A 300 N LEU A 14 SHEET 3 AA1 4 ILE A 288 ALA A 293 -1 N ILE A 289 O TRP A 303 SHEET 4 AA1 4 VAL A 277 CYS A 282 -1 N ALA A 281 O ALA A 290 SHEET 1 AA2 4 VAL A 21 PHE A 26 0 SHEET 2 AA2 4 TRP A 32 SER A 37 -1 O ALA A 34 N LYS A 25 SHEET 3 AA2 4 ILE A 42 GLY A 46 -1 O TRP A 45 N LEU A 33 SHEET 4 AA2 4 PHE A 52 ILE A 56 -1 O GLU A 53 N ILE A 44 SHEET 1 AA3 4 ILE A 63 TRP A 68 0 SHEET 2 AA3 4 LEU A 74 SER A 79 -1 O VAL A 76 N ALA A 67 SHEET 3 AA3 4 THR A 83 ASP A 88 -1 O TRP A 87 N LEU A 75 SHEET 4 AA3 4 CYS A 94 LYS A 99 -1 O LEU A 95 N ILE A 86 SHEET 1 AA4 4 VAL A 105 PHE A 110 0 SHEET 2 AA4 4 LEU A 116 SER A 121 -1 O VAL A 118 N ASN A 109 SHEET 3 AA4 4 VAL A 126 ASP A 130 -1 O TRP A 129 N ILE A 117 SHEET 4 AA4 4 CYS A 136 LEU A 140 -1 O LEU A 140 N VAL A 126 SHEET 1 AA5 4 VAL A 147 PHE A 152 0 SHEET 2 AA5 4 LEU A 158 SER A 163 -1 O VAL A 160 N HIS A 151 SHEET 3 AA5 4 CYS A 168 ASP A 172 -1 O TRP A 171 N ILE A 159 SHEET 4 AA5 4 CYS A 178 LEU A 182 -1 O LEU A 182 N CYS A 168 SHEET 1 AA6 4 VAL A 190 PHE A 195 0 SHEET 2 AA6 4 TYR A 201 THR A 206 -1 O LEU A 203 N LYS A 194 SHEET 3 AA6 4 THR A 210 ASP A 215 -1 O TRP A 214 N ILE A 202 SHEET 4 AA6 4 LYS A 220 TYR A 225 -1 O LEU A 222 N LEU A 213 SHEET 1 AA7 4 ALA A 237 SER A 240 0 SHEET 2 AA7 4 TRP A 246 SER A 249 -1 O VAL A 248 N ASN A 238 SHEET 3 AA7 4 VAL A 256 ASN A 260 -1 O TYR A 257 N SER A 249 SHEET 4 AA7 4 ILE A 266 LEU A 270 -1 O VAL A 267 N ILE A 258 CRYST1 46.460 63.750 92.840 90.00 90.00 90.00 P 21 21 21 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 0.021524 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010771 0.00000