HEADER APOPTOSIS 25-JAN-24 8Y1Z TITLE CRYSTAL STRUCTURE OF THE MCL-1 IN COMPLEX WITH A SHORT BH3 PEPTIDE OF TITLE 2 BAK COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 171-327; COMPND 6 SYNONYM: BCL-2-LIKE PROTEIN 3,BCL2-L-3,BCL-2-RELATED PROTEIN COMPND 7 EAT/MCL1,MCL1/EAT; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: SHORT BH3 PEPTIDE FROM BCL-2 HOMOLOGOUS ANTAGONIST/KILLER; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: APOPTOSIS REGULATOR BAK,BCL-2-LIKE PROTEIN 7,BCL2-L-7; COMPND 13 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: MCL1, BCL2L3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS MCL-1, BAK, BH3, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,M.GUO,H.WEI,Y.CHEN REVDAT 2 19-FEB-25 8Y1Z 1 JRNL REVDAT 1 29-JAN-25 8Y1Z 0 JRNL AUTH H.WEI,H.WANG,S.XIANG,J.WANG,L.QU,X.CHEN,M.GUO,X.LU,Y.CHEN JRNL TITL DECIPHERING MOLECULAR SPECIFICITY IN MCL-1/BAK INTERACTION JRNL TITL 2 AND ITS IMPLICATIONS FOR DESIGNING POTENT MCL-1 INHIBITORS. JRNL REF CELL DEATH DIFFER. 2025 JRNL REFN ISSN 1350-9047 JRNL PMID 39901037 JRNL DOI 10.1038/S41418-025-01454-2 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.CHEN,H.WEI,H.WANG,S.XIANG,J.WANG,L.QU,X.CHEN,M.GUO,X.LU REMARK 1 TITL DECIPHERING MOLECULAR SPECIFICITY IN MCL-1/BAK INTERACTION REMARK 1 TITL 2 AND ITS IMPLICATIONS FOR DESIGNING POTENT MCL-1 INHIBITORS REMARK 1 REF RES SQ 2024 REMARK 1 REFN ESSN 2693-5015 REMARK 1 DOI 10.21203/RS.3.RS-4708498/V1 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15.2_3472: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 11581 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1163 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 22.5700 - 3.8244 0.99 1408 164 0.1746 0.1862 REMARK 3 2 3.8244 - 3.0374 1.00 1341 145 0.1663 0.2297 REMARK 3 3 3.0374 - 2.6540 1.00 1317 148 0.2051 0.2854 REMARK 3 4 2.6540 - 2.4116 0.99 1310 147 0.2157 0.2651 REMARK 3 5 2.4116 - 2.2389 0.99 1316 145 0.2092 0.2449 REMARK 3 6 2.2389 - 2.1070 0.99 1287 138 0.2086 0.2453 REMARK 3 7 2.1070 - 2.0015 0.96 1256 136 0.2129 0.2595 REMARK 3 8 2.0015 - 1.9144 0.92 1183 140 0.2268 0.3099 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.32 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 : 0.011 1382 REMARK 3 ANGLE : 1.054 1857 REMARK 3 CHIRALITY : 0.052 207 REMARK 3 PLANARITY : 0.005 241 REMARK 3 DIHEDRAL : 25.403 523 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 8Y1Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1300044673. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-21 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 : BL17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11590 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.914 REMARK 200 RESOLUTION RANGE LOW (A) : 22.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.08474 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.00 REMARK 200 R MERGE FOR SHELL (I) : 0.38960 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.960 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM ACETATE, 18-25% REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.14900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.76350 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.14900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.76350 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: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 481 LIES ON A SPECIAL POSITION. 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 GLU A 325 REMARK 465 GLY A 326 REMARK 465 GLY A 327 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 GLU A 171 CG CD OE1 OE2 REMARK 470 ASP A 172 CG OD1 OD2 REMARK 470 THR A 196 OG1 CG2 REMARK 470 ASP A 236 CG OD1 OD2 DBREF 8Y1Z A 171 327 UNP Q07820 MCL1_HUMAN 171 327 DBREF 8Y1Z B 72 87 UNP Q16611 BAK_HUMAN 72 87 SEQRES 1 A 157 GLU ASP GLU LEU TYR ARG GLN SER LEU GLU ILE ILE SER SEQRES 2 A 157 ARG TYR LEU ARG GLU GLN ALA THR GLY ALA LYS ASP THR SEQRES 3 A 157 LYS PRO MET GLY ARG SER GLY ALA THR SER ARG LYS ALA SEQRES 4 A 157 LEU GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN ARG SEQRES 5 A 157 ASN HIS GLU THR ALA PHE GLN GLY MET LEU ARG LYS LEU SEQRES 6 A 157 ASP ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER ARG SEQRES 7 A 157 VAL MET ILE HIS VAL PHE SER ASP GLY VAL THR ASN TRP SEQRES 8 A 157 GLY ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE VAL SEQRES 9 A 157 ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS ILE SEQRES 10 A 157 GLU PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL ARG SEQRES 11 A 157 THR LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP ASP SEQRES 12 A 157 GLY PHE VAL GLU PHE PHE HIS VAL GLU ASP LEU GLU GLY SEQRES 13 A 157 GLY SEQRES 1 B 16 GLY GLN VAL GLY ARG GLN LEU ALA ILE ILE GLY ASP ASP SEQRES 2 B 16 ILE ASN ARG FORMUL 3 HOH *124(H2 O) HELIX 1 AA1 ASP A 172 GLY A 192 1 21 HELIX 2 AA2 SER A 202 HIS A 224 1 23 HELIX 3 AA3 HIS A 224 ASP A 236 1 13 HELIX 4 AA4 ASN A 239 SER A 255 1 17 HELIX 5 AA5 ASN A 260 THR A 280 1 21 HELIX 6 AA6 ILE A 281 ASN A 282 5 2 HELIX 7 AA7 GLN A 283 SER A 285 5 3 HELIX 8 AA8 CYS A 286 GLN A 309 1 24 HELIX 9 AA9 ARG A 310 HIS A 320 1 11 HELIX 10 AB1 GLN B 73 ASN B 86 1 14 CRYST1 47.742 48.298 63.527 90.00 90.00 90.00 P 2 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 0.020946 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020705 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015741 0.00000