HEADER APOPTOSIS 10-DEC-22 8HOH TITLE CRYSTAL STRUCTURE OF BCL-2 G101V IN COMPLEX WITH SONROTOCLAX COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPTOSIS REGULATOR BCL-2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR J.LIU,M.XU,Y.FENG,Y.HONG,Y.LIU REVDAT 3 15-MAY-24 8HOH 1 JRNL REVDAT 2 31-JAN-24 8HOH 1 JRNL REVDAT 1 17-JAN-24 8HOH 0 JRNL AUTH J.LIU,S.LI,Q.WANG,Y.FENG,H.XING,X.YANG,Y.GUO,Y.GUO,H.SUN, JRNL AUTH 2 X.LIU,S.YANG,Z.MEI,Y.ZHU,Z.CHENG,S.CHEN,M.XU,W.ZHANG,N.WAN, JRNL AUTH 3 J.WANG,Y.MA,S.ZHANG,X.LUAN,A.XU,L.LI,H.WANG,X.YANG,Y.HONG, JRNL AUTH 4 H.XUE,X.YUAN,N.HU,X.SONG,Z.WANG,X.LIU,L.WANG,Y.LIU JRNL TITL SONROTOCLAX OVERCOMES BCL2 G101V MUTATION-INDUCED VENETOCLAX JRNL TITL 2 RESISTANCE IN PRECLINICAL MODELS OF HEMATOLOGIC MALIGNANCY. JRNL REF BLOOD V. 143 1825 2024 JRNL REFN ESSN 1528-0020 JRNL PMID 38211332 JRNL DOI 10.1182/BLOOD.2023019706 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 43.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 13717 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 650 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 43.7800 - 3.2500 1.00 2737 149 0.2076 0.2192 REMARK 3 2 3.2500 - 2.5800 1.00 2632 128 0.2319 0.2694 REMARK 3 3 2.5800 - 2.2500 1.00 2592 127 0.2405 0.2788 REMARK 3 4 2.2500 - 2.0500 1.00 2556 120 0.2392 0.2952 REMARK 3 5 2.0500 - 1.9000 0.99 2550 126 0.2944 0.3984 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.276 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.472 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.69 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 1256 REMARK 3 ANGLE : 0.883 1710 REMARK 3 CHIRALITY : 0.057 170 REMARK 3 PLANARITY : 0.006 248 REMARK 3 DIHEDRAL : 15.234 486 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 8HOH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ. REMARK 100 THE DEPOSITION ID IS D_1300034033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-19 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 : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13776 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 53.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 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) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 0.66300 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: PHENIX REMARK 200 STARTING MODEL: 5VAU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M REMARK 280 TRIS HYDROCHLORIDE PH 8.5, 30% PEG 4000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.15K 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 16.23950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.20900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.01800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.20900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.23950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.01800 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: 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 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 5 REMARK 465 ARG A 6 REMARK 465 THR A 7 REMARK 465 GLY A 8 REMARK 465 TYR A 9 REMARK 465 GLY A 74 REMARK 465 ASP A 75 REMARK 465 ASP A 76 REMARK 465 VAL A 77 REMARK 465 GLU A 78 REMARK 465 GLU A 79 REMARK 465 ASN A 80 REMARK 465 ARG A 81 REMARK 465 THR A 82 REMARK 465 GLU A 83 REMARK 465 ALA A 84 REMARK 465 PRO A 85 REMARK 465 GLU A 86 REMARK 465 GLY A 87 REMARK 465 THR A 88 REMARK 465 GLU A 89 REMARK 465 SER A 205 REMARK 465 MET A 206 REMARK 465 ARG A 207 DBREF 8HOH A 5 207 PDB 8HOH 8HOH 5 207 SEQRES 1 A 162 SER ARG THR GLY TYR ASP ASN ARG GLU ILE VAL MET LYS SEQRES 2 A 162 TYR ILE HIS TYR LYS LEU SER GLN ARG GLY TYR GLU TRP SEQRES 3 A 162 ASP ALA GLY ASP ASP VAL GLU GLU ASN ARG THR GLU ALA SEQRES 4 A 162 PRO GLU GLY THR GLU SER GLU VAL VAL HIS LEU THR LEU SEQRES 5 A 162 ARG GLN ALA VAL ASP ASP PHE SER ARG ARG TYR ARG ARG SEQRES 6 A 162 ASP PHE ALA GLU MET SER SER GLN LEU HIS LEU THR PRO SEQRES 7 A 162 PHE THR ALA ARG GLY ARG PHE ALA THR VAL VAL GLU GLU SEQRES 8 A 162 LEU PHE ARG ASP GLY VAL ASN TRP GLY ARG ILE VAL ALA SEQRES 9 A 162 PHE PHE GLU PHE GLY GLY VAL MET CYS VAL GLU SER VAL SEQRES 10 A 162 ASN ARG GLU MET SER PRO LEU VAL ASP ASN ILE ALA LEU SEQRES 11 A 162 TRP MET THR GLU TYR LEU ASN ARG HIS LEU HIS THR TRP SEQRES 12 A 162 ILE GLN ASP ASN GLY GLY TRP ASP ALA PHE VAL GLU LEU SEQRES 13 A 162 TYR GLY PRO SER MET ARG HET 98I A 301 64 HETNAM 98I ~{N}-[4-[(4-METHYL-4-OXIDANYL-CYCLOHEXYL)METHYLAMINO]- HETNAM 2 98I 3-NITRO-PHENYL]SULFONYL-4-[2-[(2~{S})-2-(2-PROPAN-2- HETNAM 3 98I YLPHENYL)PYRROLIDIN-1-YL]-7-AZASPIRO[3.5]NONAN-7-YL]- HETNAM 4 98I 2-(1~{H}-PYRROLO[2,3-B]PYRIDIN-5-YLOXY)BENZAMIDE FORMUL 2 98I C49 H59 N7 O7 S FORMUL 3 HOH *67(H2 O) HELIX 1 AA1 ASP A 10 ARG A 26 1 17 HELIX 2 AA2 GLU A 91 TYR A 108 1 18 HELIX 3 AA3 TYR A 108 GLN A 118 1 11 HELIX 4 AA4 THR A 125 PHE A 138 1 14 HELIX 5 AA5 ASN A 143 ARG A 164 1 22 HELIX 6 AA6 PRO A 168 LEU A 185 1 18 HELIX 7 AA7 LEU A 185 ASN A 192 1 8 HELIX 8 AA8 GLY A 194 GLY A 203 1 10 CRYST1 32.479 48.036 106.418 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 0.030789 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020818 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009397 0.00000