HEADER APOPTOSIS 02-NOV-09 3KJ0 TITLE MCL-1 IN COMPLEX WITH BIM BH3 MUTANT I2DY 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 172-326); COMPND 6 SYNONYM: BCL-2-RELATED PROTEIN EAT/MCL1, MCL1/EAT, BCL-2-LIKE PROTEIN COMPND 7 3, BCL2-L-3; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: BCL-2-LIKE PROTEIN 11; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: BH3 REGION OF BIM (UNP 1-23); COMPND 13 SYNONYM: BCL2-L-11, BCL2-INTERACTING MEDIATOR OF CELL DEATH; COMPND 14 ENGINEERED: YES; COMPND 15 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: BCL2L3, MCL-1, MCL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSV282; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: BCL2L11, BIM; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PSV282 KEYWDS BCL-2, BH3, APOPTOSIS, PROTEIN-PEPTIDE COMPLEX, ALTERNATIVE SPLICING, KEYWDS 2 CYTOPLASM, DEVELOPMENTAL PROTEIN, DIFFERENTIATION, ISOPEPTIDE BOND, KEYWDS 3 MEMBRANE, MITOCHONDRION, NUCLEUS, PHOSPHOPROTEIN, POLYMORPHISM, KEYWDS 4 TRANSMEMBRANE, UBL CONJUGATION EXPDTA X-RAY DIFFRACTION AUTHOR E.FIRE,R.A.GRANT,A.E.KEATING REVDAT 4 21-FEB-24 3KJ0 1 REMARK REVDAT 3 13-OCT-21 3KJ0 1 REMARK SEQADV REVDAT 2 23-MAR-10 3KJ0 1 JRNL REVDAT 1 16-FEB-10 3KJ0 0 JRNL AUTH E.FIRE,S.V.GULLA,R.A.GRANT,A.E.KEATING JRNL TITL MCL-1-BIM COMPLEXES ACCOMMODATE SURPRISING POINT MUTATIONS JRNL TITL 2 VIA MINOR STRUCTURAL CHANGES. JRNL REF PROTEIN SCI. V. 19 507 2010 JRNL REFN ISSN 0961-8368 JRNL PMID 20066663 JRNL DOI 10.1002/PRO.329 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.4_129 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 16317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 777 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 29.1424 - 3.0887 1.00 2811 149 0.1796 0.1977 REMARK 3 2 3.0887 - 2.4520 1.00 2741 113 0.1813 0.2363 REMARK 3 3 2.4520 - 2.1422 1.00 2640 142 0.1799 0.2517 REMARK 3 4 2.1422 - 1.9464 1.00 2656 139 0.1814 0.2297 REMARK 3 5 1.9464 - 1.8069 0.99 2628 127 0.1965 0.2381 REMARK 3 6 1.8069 - 1.7004 0.79 2064 107 0.2229 0.2686 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 : 0.34 REMARK 3 B_SOL : 44.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.51 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.05400 REMARK 3 B22 (A**2) : 3.04700 REMARK 3 B33 (A**2) : 0.00700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.003 1521 REMARK 3 ANGLE : 0.643 2047 REMARK 3 CHIRALITY : 0.048 217 REMARK 3 PLANARITY : 0.003 266 REMARK 3 DIHEDRAL : 13.305 572 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 3KJ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : CRYSTAL MONOCHRONOMATER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16362 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 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 (%): 30.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 45% MPD, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 20.19050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.68650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.47150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.68650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.19050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.47150 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: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 GLY A 327 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 GLY B -1 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 325 CG CD OE1 OE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS B 7359 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KJ1 RELATED DB: PDB REMARK 900 MCL-1 IN COMPLEX WITH BIM BH3 MUTANT I2DA REMARK 900 RELATED ID: 3KJ2 RELATED DB: PDB REMARK 900 MCL-1 IN COMPLEX WITH BIM BH3 MUTANT F4AE REMARK 900 RELATED ID: 2PQK RELATED DB: PDB REMARK 900 HUMAN MCL-1 IN COMPLEX WITH WILD-TYPE BIM BH3 DBREF 3KJ0 A 172 327 UNP Q07820 MCL1_HUMAN 172 327 DBREF 3KJ0 B 1 23 UNP O43521 B2L11_HUMAN 143 165 SEQADV 3KJ0 GLY A 170 UNP Q07820 EXPRESSION TAG SEQADV 3KJ0 SER A 171 UNP Q07820 EXPRESSION TAG SEQADV 3KJ0 GLY B -3 UNP O43521 EXPRESSION TAG SEQADV 3KJ0 SER B -2 UNP O43521 EXPRESSION TAG SEQADV 3KJ0 GLY B -1 UNP O43521 EXPRESSION TAG SEQADV 3KJ0 GLY B 0 UNP O43521 EXPRESSION TAG SEQADV 3KJ0 TYR B 6 UNP O43521 ILE 148 ENGINEERED MUTATION SEQRES 1 A 158 GLY SER ASP GLU LEU TYR ARG GLN SER LEU GLU ILE ILE SEQRES 2 A 158 SER ARG TYR LEU ARG GLU GLN ALA THR GLY ALA LYS ASP SEQRES 3 A 158 THR LYS PRO MET GLY ARG SER GLY ALA THR SER ARG LYS SEQRES 4 A 158 ALA LEU GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN SEQRES 5 A 158 ARG ASN HIS GLU THR ALA PHE GLN GLY MET LEU ARG LYS SEQRES 6 A 158 LEU ASP ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER SEQRES 7 A 158 ARG VAL MET ILE HIS VAL PHE SER ASP GLY VAL THR ASN SEQRES 8 A 158 TRP GLY ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE SEQRES 9 A 158 VAL ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS SEQRES 10 A 158 ILE GLU PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL SEQRES 11 A 158 ARG THR LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP SEQRES 12 A 158 ASP GLY PHE VAL GLU PHE PHE HIS VAL GLU ASP LEU GLU SEQRES 13 A 158 GLY GLY SEQRES 1 B 27 GLY SER GLY GLY ARG PRO GLU ILE TRP TYR ALA GLN GLU SEQRES 2 B 27 LEU ARG ARG ILE GLY ASP GLU PHE ASN ALA TYR TYR ALA SEQRES 3 B 27 ARG HET TRS B7359 8 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 HOH *139(H2 O) HELIX 1 1 ASP A 172 GLY A 192 1 21 HELIX 2 2 SER A 202 HIS A 224 1 23 HELIX 3 3 HIS A 224 ASP A 236 1 13 HELIX 4 4 ASN A 239 PHE A 254 1 16 HELIX 5 5 ASN A 260 ILE A 281 1 22 HELIX 6 6 GLN A 283 SER A 285 5 3 HELIX 7 7 CYS A 286 GLN A 309 1 24 HELIX 8 8 ARG A 310 PHE A 319 1 10 HELIX 9 9 ARG B 1 ALA B 22 1 22 SITE 1 AC1 10 HOH A 121 GLU A 173 LEU A 174 GLN A 177 SITE 2 AC1 10 SER A 202 GLU B 16 ALA B 19 TYR B 20 SITE 3 AC1 10 HOH B 37 HOH B 98 CRYST1 40.381 52.943 69.373 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 0.024764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018888 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014415 0.00000