HEADER ONCOPROTEIN 30-JAN-20 6VO7 TITLE CRYSTAL STRUCTURE OF PI3K-ALPHA RAS BINDING DOMAIN (RBD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE 3-KINASE CATALYTIC COMPND 3 SUBUNIT ALPHA ISOFORM; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RAS BINDING DOMAIN (RBD); COMPND 6 SYNONYM: PTDINS-3-KINASE SUBUNIT ALPHA,PHOSPHATIDYLINOSITOL 4,5- COMPND 7 BISPHOSPHATE 3-KINASE 110 KDA CATALYTIC SUBUNIT ALPHA,P110ALPHA, COMPND 8 PHOSPHOINOSITIDE-3-KINASE CATALYTIC ALPHA POLYPEPTIDE, COMPND 9 SERINE/THREONINE PROTEIN KINASE PIK3CA; COMPND 10 EC: 2.7.1.153,2.7.11.1; COMPND 11 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: PIK3CA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAS BINDING DOMAIN, ONCOGENIC SIGNALING, EFFECTOR, ONCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.M.CAREY,N.G.MARTINEZ,S.CAMPBELL REVDAT 4 11-OCT-23 6VO7 1 REMARK REVDAT 3 10-MAR-21 6VO7 1 JRNL REVDAT 2 17-FEB-21 6VO7 1 JRNL REVDAT 1 03-FEB-21 6VO7 0 JRNL AUTH N.G.MARTINEZ,D.F.THIEKER,L.M.CAREY,J.A.RASQUINHA, JRNL AUTH 2 S.K.KISTLER,B.A.KUHLMAN,S.L.CAMPBELL JRNL TITL BIOPHYSICAL AND STRUCTURAL CHARACTERIZATION OF NOVEL JRNL TITL 2 RAS-BINDING DOMAINS (RBDS) OF PI3K ALPHA AND PI3K GAMMA. JRNL REF J.MOL.BIOL. V. 433 66838 2021 JRNL REFN ESSN 1089-8638 JRNL PMID 33539876 JRNL DOI 10.1016/J.JMB.2021.166838 REMARK 2 REMARK 2 RESOLUTION. 2.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 8554 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 855 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 35.0900 - 4.2000 0.98 1347 150 0.1697 0.2162 REMARK 3 2 4.2000 - 3.3300 0.98 1300 144 0.1862 0.2321 REMARK 3 3 3.3300 - 2.9100 1.00 1276 143 0.2153 0.3049 REMARK 3 4 2.9100 - 2.6500 1.00 1299 143 0.2288 0.3179 REMARK 3 5 2.6500 - 2.4600 0.99 1289 143 0.2628 0.3058 REMARK 3 6 2.4600 - 2.3100 0.93 1188 132 0.2565 0.3484 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.333 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.74 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 : 0.011 1134 REMARK 3 ANGLE : 0.950 1538 REMARK 3 CHIRALITY : 0.067 174 REMARK 3 PLANARITY : 0.006 192 REMARK 3 DIHEDRAL : 19.182 430 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 6VO7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8574 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.310 REMARK 200 RESOLUTION RANGE LOW (A) : 35.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.17100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.83200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 5XGH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 0.7 M NA CITRATE, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.99400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.99400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.77400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.95700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.77400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.95700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.99400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.77400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.95700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 31.99400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.77400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.95700 REMARK 290 SMTRY3 8 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: 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 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 199 REMARK 465 PRO A 200 REMARK 465 ASN A 201 REMARK 465 ASN A 202 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 SER A 173 OG REMARK 470 ILE A 197 CG1 CG2 CD1 REMARK 470 VAL A 198 CG1 CG2 REMARK 470 ASP A 203 CG OD1 OD2 REMARK 470 LYS A 204 CG CD CE NZ REMARK 470 LYS A 206 CE NZ REMARK 470 GLU A 218 OE1 OE2 REMARK 470 SER A 231 OG REMARK 470 SER A 236 OG REMARK 470 GLU A 237 CG CD OE1 OE2 REMARK 470 LYS A 240 CE NZ REMARK 470 LYS A 249 CG CD CE NZ REMARK 470 GLU A 263 CG CD OE1 OE2 REMARK 470 LYS A 264 CD CE NZ REMARK 470 GLU A 291 CG CD OE1 OE2 REMARK 470 MET A 299 CG SD CE 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 258 52.71 -92.82 REMARK 500 PHE A 261 71.45 -105.61 REMARK 500 LYS A 264 36.53 -81.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 6VO7 A 157 300 UNP P42336 PK3CA_HUMAN 157 300 SEQRES 1 A 144 ASN SER PRO HIS SER ARG ALA MET TYR VAL TYR PRO PRO SEQRES 2 A 144 ASN VAL GLU SER SER PRO GLU LEU PRO LYS HIS ILE TYR SEQRES 3 A 144 ASN LYS LEU ASP LYS GLY GLN ILE ILE VAL VAL ILE TRP SEQRES 4 A 144 VAL ILE VAL SER PRO ASN ASN ASP LYS GLN LYS TYR THR SEQRES 5 A 144 LEU LYS ILE ASN HIS ASP CYS VAL PRO GLU GLN VAL ILE SEQRES 6 A 144 ALA GLU ALA ILE ARG LYS LYS THR ARG SER MET LEU LEU SEQRES 7 A 144 SER SER GLU GLN LEU LYS LEU CYS VAL LEU GLU TYR GLN SEQRES 8 A 144 GLY LYS TYR ILE LEU LYS VAL CYS GLY CYS ASP GLU TYR SEQRES 9 A 144 PHE LEU GLU LYS TYR PRO LEU SER GLN TYR LYS TYR ILE SEQRES 10 A 144 ARG SER CYS ILE MET LEU GLY ARG MET PRO ASN LEU MET SEQRES 11 A 144 LEU MET ALA LYS GLU SER LEU TYR SER GLN LEU PRO MET SEQRES 12 A 144 ASP FORMUL 2 HOH *26(H2 O) HELIX 1 AA1 SER A 158 TYR A 167 1 10 HELIX 2 AA2 PRO A 178 ASN A 183 1 6 HELIX 3 AA3 VAL A 216 ARG A 230 1 15 HELIX 4 AA4 SER A 235 LYS A 249 1 15 HELIX 5 AA5 PRO A 266 GLN A 269 5 4 HELIX 6 AA6 TYR A 270 GLY A 280 1 11 HELIX 7 AA7 LYS A 290 GLN A 296 1 7 SHEET 1 AA1 4 GLN A 205 ASN A 212 0 SHEET 2 AA1 4 GLN A 189 VAL A 196 -1 N ILE A 194 O TYR A 207 SHEET 3 AA1 4 ASN A 284 ALA A 289 1 O LEU A 285 N TRP A 195 SHEET 4 AA1 4 TYR A 250 VAL A 254 -1 N LYS A 253 O MET A 286 CRYST1 71.548 83.914 63.988 90.00 90.00 90.00 C 2 2 21 8 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 0.013977 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011917 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015628 0.00000