HEADER APOPTOSIS 17-OCT-06 2JM6 TITLE SOLUTION STRUCTURE OF MCL-1 COMPLEXED WITH NOXAB COMPND MOL_ID: 1; COMPND 2 MOLECULE: NOXA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 68-93; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: MYELOID CELL LEUKEMIA-1 PROTEIN MCL-1 HOMOLOG; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: RESIDUES 152-308; COMPND 10 SYNONYM: BCL-2-RELATED PROTEIN EAT/MCL1, INDUCED MYELOID LEUKEMIA COMPND 11 CELL DIFFERENTIATION PROTEIN; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PMAIP1, NOXA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-31B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 GENE: MCL1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21-DE3; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX6P-3 KEYWDS APOPTOSIS, MCL-1, BCL-2, HELICAL BUNDLE, BH3-ONLY EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.E.CZABOTAR,E.F.LEE,M.F.VAN DELFT,C.L.DAY,B.J.SMITH,D.C.S.HUANG, AUTHOR 2 W.D.FAIRLIE,M.G.HINDS,P.M.COLMAN REVDAT 5 20-DEC-23 2JM6 1 REMARK REVDAT 4 09-MAR-22 2JM6 1 REMARK SEQADV REVDAT 3 24-FEB-09 2JM6 1 VERSN REVDAT 2 08-MAY-07 2JM6 1 JRNL REVDAT 1 20-MAR-07 2JM6 0 JRNL AUTH P.E.CZABOTAR,E.F.LEE,M.F.VAN DELFT,C.L.DAY,B.J.SMITH, JRNL AUTH 2 D.C.S.HUANG,W.D.FAIRLIE,M.G.HINDS,P.M.COLMAN JRNL TITL STRUCTURAL INSIGHTS INTO THE DEGRADATION OF MCL-1 INDUCED BY JRNL TITL 2 BH3 DOMAINS JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 6217 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17389404 JRNL DOI 10.1073/PNAS.0701297104 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, X-PLOR NIH 2.14 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JM6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000100006. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C, U-99% 15N] REMARK 210 MCL_1, 0.5 MM NOXAB, 95% H2O, 5% REMARK 210 D2O; 0.5 MM MCL-1, 0.5 MM [U-100% REMARK 210 13C, U-100% 15N] NOXAB, 95% H2O, REMARK 210 5% D2O; 0.5 MM [U-15N] MCL-1, REMARK 210 0.5 MM NOXAB, 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 3D 1H-15N REMARK 210 NOESY; 3D HNHA; 3D HNHB; 3D HNCA; REMARK 210 3D HCCH-TOCSY; 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AV; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, XEASY 1.3.13, CYANA REMARK 210 2.1 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 256 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY, LEAST RESTRAINT REMARK 210 VIOLATIONS, STRUCTURES WITH REMARK 210 ACCEPTABLE COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 3D REMARK 210 HETERONUCLEAR METHODS REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLU B 161 HE ARG B 165 1.56 REMARK 500 HZ1 LYS B 260 OE1 GLU B 265 1.56 REMARK 500 OE2 GLU B 169 HZ1 LYS B 175 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 1 PRO B 179 100.81 -59.26 REMARK 500 1 LYS B 219 -47.21 -165.81 REMARK 500 1 ASN B 241 133.18 -35.23 REMARK 500 2 ALA A 69 50.12 -97.48 REMARK 500 2 LEU B 149 -38.86 -130.73 REMARK 500 2 LYS B 219 -41.42 -135.35 REMARK 500 2 ASN B 241 133.63 -31.90 REMARK 500 2 LYS B 283 40.54 -107.91 REMARK 500 3 ASP B 217 31.88 -84.74 REMARK 500 3 LYS B 219 -41.37 -174.61 REMARK 500 3 ASN B 241 136.92 -36.25 REMARK 500 3 GLN B 303 110.92 -31.90 REMARK 500 3 ASP B 304 85.14 -66.15 REMARK 500 3 GLU B 306 -71.53 -97.54 REMARK 500 4 SER B 151 -162.23 -163.88 REMARK 500 4 GLU B 152 -150.94 -95.03 REMARK 500 4 SER B 177 41.15 -99.44 REMARK 500 4 ASP B 217 45.52 -81.58 REMARK 500 4 LYS B 219 -37.57 -169.65 REMARK 500 4 VAL B 239 98.94 -61.19 REMARK 500 4 ASN B 241 135.66 -37.14 REMARK 500 5 GLU B 152 33.33 -84.10 REMARK 500 5 ASP B 153 64.03 -101.99 REMARK 500 5 SER B 177 35.39 -143.96 REMARK 500 5 LYS B 219 -41.46 -174.28 REMARK 500 5 ASN B 241 124.74 -24.17 REMARK 500 6 ALA A 69 38.83 -96.81 REMARK 500 6 SER B 151 -163.45 -113.38 REMARK 500 6 SER B 177 50.84 -98.34 REMARK 500 6 LYS B 219 -39.73 -140.28 REMARK 500 6 ASN B 241 124.04 -19.65 REMARK 500 6 LYS B 283 42.44 -96.00 REMARK 500 7 LYS B 219 -50.62 -142.32 REMARK 500 7 VAL B 239 98.06 -69.62 REMARK 500 7 ASN B 241 139.77 -38.81 REMARK 500 7 GLN B 264 46.10 -106.62 REMARK 500 8 LEU A 71 35.32 -84.14 REMARK 500 8 GLU B 152 51.25 -104.57 REMARK 500 8 LYS B 219 -50.82 -136.88 REMARK 500 8 VAL B 239 99.00 -68.20 REMARK 500 8 ASN B 241 132.37 -37.12 REMARK 500 8 GLN B 264 45.64 -102.16 REMARK 500 8 GLN B 303 64.57 -171.50 REMARK 500 9 ALA A 69 38.10 -97.99 REMARK 500 9 LEU B 149 35.87 -97.82 REMARK 500 9 THR B 172 -10.98 -141.35 REMARK 500 9 SER B 174 94.52 -160.26 REMARK 500 9 ASP B 176 49.80 -74.27 REMARK 500 9 PRO B 179 -163.97 -76.83 REMARK 500 9 VAL B 239 98.41 -62.42 REMARK 500 REMARK 500 THIS ENTRY HAS 119 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WSX RELATED DB: PDB REMARK 900 UNLIGANDED MCL-1 DBREF 2JM6 A 68 93 UNP Q9JM54 Q9JM54_MOUSE 68 93 DBREF 2JM6 B 152 308 UNP P97287 MCL1_MOUSE 152 308 SEQADV 2JM6 MET A 94 UNP Q9JM54 EXPRESSION TAG SEQADV 2JM6 GLY B 147 UNP P97287 EXPRESSION TAG SEQADV 2JM6 PRO B 148 UNP P97287 EXPRESSION TAG SEQADV 2JM6 LEU B 149 UNP P97287 EXPRESSION TAG SEQADV 2JM6 GLY B 150 UNP P97287 EXPRESSION TAG SEQADV 2JM6 SER B 151 UNP P97287 EXPRESSION TAG SEQRES 1 A 27 PRO ALA ASP LEU LYS ASP GLU CYS ALA GLN LEU ARG ARG SEQRES 2 A 27 ILE GLY ASP LYS VAL ASN LEU ARG GLN LYS LEU LEU ASN SEQRES 3 A 27 MET SEQRES 1 B 162 GLY PRO LEU GLY SER GLU ASP ASP LEU TYR ARG GLN SER SEQRES 2 B 162 LEU GLU ILE ILE SER ARG TYR LEU ARG GLU GLN ALA THR SEQRES 3 B 162 GLY SER LYS ASP SER LYS PRO LEU GLY GLU ALA GLY ALA SEQRES 4 B 162 ALA GLY ARG ARG ALA LEU GLU THR LEU ARG ARG VAL GLY SEQRES 5 B 162 ASP GLY VAL GLN ARG ASN HIS GLU THR ALA PHE GLN GLY SEQRES 6 B 162 MET LEU ARG LYS LEU ASP ILE LYS ASN GLU GLY ASP VAL SEQRES 7 B 162 LYS SER PHE SER ARG VAL MET VAL HIS VAL PHE LYS ASP SEQRES 8 B 162 GLY VAL THR ASN TRP GLY ARG ILE VAL THR LEU ILE SER SEQRES 9 B 162 PHE GLY ALA PHE VAL ALA LYS HIS LEU LYS SER VAL ASN SEQRES 10 B 162 GLN GLU SER PHE ILE GLU PRO LEU ALA GLU THR ILE THR SEQRES 11 B 162 ASP VAL LEU VAL ARG THR LYS ARG ASP TRP LEU VAL LYS SEQRES 12 B 162 GLN ARG GLY TRP ASP GLY PHE VAL GLU PHE PHE HIS VAL SEQRES 13 B 162 GLN ASP LEU GLU GLY GLY HELIX 1 1 ASP A 70 MET A 94 1 25 HELIX 2 2 GLU B 152 GLY B 173 1 22 HELIX 3 3 GLY B 184 LEU B 216 1 33 HELIX 4 4 GLY B 222 PHE B 235 1 14 HELIX 5 5 ASN B 241 VAL B 262 1 22 HELIX 6 6 GLN B 264 LYS B 283 1 20 HELIX 7 7 LYS B 283 GLN B 290 1 8 HELIX 8 8 GLY B 292 HIS B 301 1 10 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1