HEADER APOPTOSIS 17-MAR-08 2ROD TITLE SOLUTION STRUCTURE OF MCL-1 COMPLEXED WITH NOXAA COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL-1 COMPND 3 HOMOLOG; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 152-308; COMPND 6 SYNONYM: BCL-2-RELATED PROTEIN EAT/MCL1, MCL-1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NOXA; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 17-42; COMPND 12 SYNONYM: NOXAA; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 GENE: MCL-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX6P-3; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 11 ORGANISM_COMMON: MOUSE; SOURCE 12 GENE: NOXA; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 15 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET-31B KEYWDS MCL-1, NOXAA, APOPTOSIS, BH3-ONLY, BCL-2, CYTOPLASM, DEVELOPMENTAL KEYWDS 2 PROTEIN, DIFFERENTIATION, MEMBRANE, MITOCHONDRION, NUCLEUS, KEYWDS 3 PHOSPHOPROTEIN, TRANSMEMBRANE, UBL CONJUGATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.L.DAY,C.SMITS,F.C.FAN,E.F.LEE,W.D.FAIRLIE,M.G.HINDS REVDAT 3 16-MAR-22 2ROD 1 REMARK SEQADV REVDAT 2 24-FEB-09 2ROD 1 VERSN REVDAT 1 08-JUL-08 2ROD 0 JRNL AUTH C.L.DAY,C.SMITS,F.C.FAN,E.F.LEE,W.D.FAIRLIE,M.G.HINDS JRNL TITL STRUCTURE OF THE BH3 DOMAINS FROM THE P53-INDUCIBLE BH3-ONLY JRNL TITL 2 PROTEINS NOXA AND PUMA IN COMPLEX WITH MCL-1 JRNL REF J.MOL.BIOL. V. 380 958 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18589438 JRNL DOI 10.1016/J.JMB.2008.05.071 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE CALCULATED BASED ON REMARK 3 A TOTAL OF 3355 CONSTRAINTS. 2662 ARE NOE DERIVED AND 184 OF REMARK 3 THESE ARE INTERMOLECULAR. A TOTAL OF 325 DIHEDRAL ANGLE REMARK 3 CONSTRAINTS WERE USED AND 184 HYDROGEN BONDS. REMARK 4 REMARK 4 2ROD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000150091. 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 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM [U-100% 13C; U-100% 15N] REMARK 210 MCL-1; 0.5MM NOXAA; 95% H2O/5% REMARK 210 D2O; 0.5MM MCL-1; 0.5MM [U-100% REMARK 210 13C; U-100% 15N] NOXAA; 95% H2O/ REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, XEASY 1.3, 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 : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: STANDARD 3D HETERONUCLEAR NMR METHODS WERE USED FOR REMARK 210 RESONANCE ASSIGNMENT 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 H3 GLY A 147 OD1 ASP A 154 1.47 REMARK 500 HZ2 LYS A 215 OE2 GLU B 22 1.48 REMARK 500 OD2 ASP A 176 HZ1 LYS A 178 1.48 REMARK 500 OE2 GLU A 192 HH12 ARG A 195 1.49 REMARK 500 HD1 HIS A 301 OE1 GLU A 306 1.49 REMARK 500 HH21 ARG A 165 OE1 GLU A 169 1.51 REMARK 500 HH21 ARG A 168 OE2 GLU A 269 1.52 REMARK 500 HH22 ARG A 291 OE2 GLU A 298 1.52 REMARK 500 OD1 ASP A 237 HH12 ARG A 244 1.53 REMARK 500 HH21 ARG A 203 OE2 GLU A 206 1.53 REMARK 500 HH11 ARG A 157 OE2 GLU A 182 1.53 REMARK 500 HG SER A 151 OE1 GLU A 152 1.53 REMARK 500 HH12 ARG A 291 OE1 GLU A 298 1.53 REMARK 500 HH21 ARG B 28 OD2 ASP B 32 1.53 REMARK 500 OD2 ASP A 217 H3 ALA B 17 1.53 REMARK 500 OE1 GLU A 169 HZ3 LYS A 178 1.54 REMARK 500 HH21 ARG A 189 OE2 GLU A 306 1.54 REMARK 500 HE21 GLN A 303 OD1 ASP B 42 1.54 REMARK 500 OE1 GLU A 192 HH22 ARG A 195 1.55 REMARK 500 HH21 ARG A 291 OD2 ASP A 294 1.55 REMARK 500 HH TYR A 156 OD1 ASP A 277 1.55 REMARK 500 HE ARG A 244 OD1 ASP B 32 1.55 REMARK 500 O LEU A 155 HG SER A 159 1.56 REMARK 500 OD1 ASP A 285 HZ3 LYS A 289 1.57 REMARK 500 OD2 ASP A 237 HH22 ARG A 244 1.57 REMARK 500 HE ARG A 203 OE1 GLU A 206 1.58 REMARK 500 O PRO B 20 H GLU B 22 1.58 REMARK 500 HE ARG A 168 OE1 GLU A 269 1.59 REMARK 500 HE21 GLN A 158 OE1 GLU A 182 1.59 REMARK 500 OE1 GLU A 161 H ALA A 183 1.59 REMARK 500 OE1 GLU A 152 HH11 ARG A 284 1.59 REMARK 500 O LEU A 279 HZ1 LYS A 283 1.59 REMARK 500 HE22 GLN A 170 OD1 ASP A 199 1.59 REMARK 500 O GLY A 243 HG1 THR A 247 1.59 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 SER A 151 -70.92 -149.53 REMARK 500 1 HIS A 205 32.75 -96.59 REMARK 500 1 LYS A 219 -16.76 -150.41 REMARK 500 1 LYS A 283 40.76 -141.02 REMARK 500 1 ASP A 304 61.47 -170.83 REMARK 500 1 LEU A 305 -57.85 -141.53 REMARK 500 1 GLU A 306 46.02 -151.26 REMARK 500 1 PRO B 21 45.21 -63.94 REMARK 500 2 GLU A 152 103.07 -33.16 REMARK 500 2 LYS A 219 4.69 -161.27 REMARK 500 2 PHE A 300 30.73 -90.87 REMARK 500 2 HIS A 301 58.68 -110.06 REMARK 500 2 VAL A 302 -84.69 -98.48 REMARK 500 2 GLN A 303 119.08 -170.65 REMARK 500 2 ASP A 304 -82.22 -145.96 REMARK 500 2 PRO B 21 8.91 -67.57 REMARK 500 3 SER A 174 -168.61 -102.43 REMARK 500 3 LYS A 219 -43.57 -134.33 REMARK 500 3 PRO B 21 6.38 -64.32 REMARK 500 4 THR A 172 33.41 -147.14 REMARK 500 4 LYS A 175 17.42 -142.83 REMARK 500 4 ASP A 176 -159.07 -129.48 REMARK 500 4 ASP A 217 32.07 -83.25 REMARK 500 4 LYS A 219 -24.45 -140.92 REMARK 500 4 PHE A 300 33.23 -80.36 REMARK 500 4 VAL A 302 74.10 -66.74 REMARK 500 5 GLU A 152 -63.67 -142.90 REMARK 500 5 LYS A 175 -68.11 -166.76 REMARK 500 5 PRO A 179 -169.16 -68.87 REMARK 500 5 ILE A 218 106.93 -55.33 REMARK 500 5 LYS A 219 -42.19 -143.48 REMARK 500 5 GLN A 264 39.00 -87.83 REMARK 500 5 ARG A 291 13.91 59.09 REMARK 500 5 GLN A 303 -80.37 -87.99 REMARK 500 5 PRO B 21 35.55 -68.99 REMARK 500 6 LEU A 149 149.64 -170.86 REMARK 500 6 ILE A 218 105.93 -59.33 REMARK 500 6 LYS A 219 -65.64 -159.56 REMARK 500 6 GLN A 264 36.61 -91.54 REMARK 500 6 PRO B 21 47.23 -65.14 REMARK 500 7 GLU A 152 -30.56 -138.93 REMARK 500 7 GLU A 182 75.46 4.46 REMARK 500 7 ALA A 183 72.96 -169.00 REMARK 500 7 LYS A 219 -42.60 -135.08 REMARK 500 7 LYS A 283 41.76 -142.26 REMARK 500 7 GLU B 18 -74.23 -142.94 REMARK 500 7 PRO B 21 27.57 -69.04 REMARK 500 7 PRO B 41 65.33 -69.21 REMARK 500 8 GLU A 152 -72.76 -117.19 REMARK 500 8 LYS A 175 95.90 -165.56 REMARK 500 REMARK 500 THIS ENTRY HAS 159 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 REMARK 900 RELATED ID: 2JM6 RELATED DB: PDB REMARK 900 MCL-1:NOXAB COMPLEX REMARK 900 RELATED ID: 2ROC RELATED DB: PDB REMARK 900 MCL-1:PUMA COMPLEX DBREF 2ROD A 152 308 UNP P97287 MCL1_MOUSE 152 308 DBREF 2ROD B 17 42 UNP Q9JM54 Q9JM54_MOUSE 17 42 SEQADV 2ROD GLY A 147 UNP P97287 EXPRESSION TAG SEQADV 2ROD PRO A 148 UNP P97287 EXPRESSION TAG SEQADV 2ROD LEU A 149 UNP P97287 EXPRESSION TAG SEQADV 2ROD GLY A 150 UNP P97287 EXPRESSION TAG SEQADV 2ROD SER A 151 UNP P97287 EXPRESSION TAG SEQADV 2ROD MET B 43 UNP Q9JM54 EXPRESSION TAG SEQRES 1 A 162 GLY PRO LEU GLY SER GLU ASP ASP LEU TYR ARG GLN SER SEQRES 2 A 162 LEU GLU ILE ILE SER ARG TYR LEU ARG GLU GLN ALA THR SEQRES 3 A 162 GLY SER LYS ASP SER LYS PRO LEU GLY GLU ALA GLY ALA SEQRES 4 A 162 ALA GLY ARG ARG ALA LEU GLU THR LEU ARG ARG VAL GLY SEQRES 5 A 162 ASP GLY VAL GLN ARG ASN HIS GLU THR ALA PHE GLN GLY SEQRES 6 A 162 MET LEU ARG LYS LEU ASP ILE LYS ASN GLU GLY ASP VAL SEQRES 7 A 162 LYS SER PHE SER ARG VAL MET VAL HIS VAL PHE LYS ASP SEQRES 8 A 162 GLY VAL THR ASN TRP GLY ARG ILE VAL THR LEU ILE SER SEQRES 9 A 162 PHE GLY ALA PHE VAL ALA LYS HIS LEU LYS SER VAL ASN SEQRES 10 A 162 GLN GLU SER PHE ILE GLU PRO LEU ALA GLU THR ILE THR SEQRES 11 A 162 ASP VAL LEU VAL ARG THR LYS ARG ASP TRP LEU VAL LYS SEQRES 12 A 162 GLN ARG GLY TRP ASP GLY PHE VAL GLU PHE PHE HIS VAL SEQRES 13 A 162 GLN ASP LEU GLU GLY GLY SEQRES 1 B 27 ALA GLU LEU PRO PRO GLU PHE ALA ALA GLN LEU ARG LYS SEQRES 2 B 27 ILE GLY ASP LYS VAL TYR CYS THR TRP SER ALA PRO ASP SEQRES 3 B 27 MET HELIX 1 1 GLU A 152 THR A 172 1 21 HELIX 2 2 GLY A 184 HIS A 205 1 22 HELIX 3 3 HIS A 205 LEU A 216 1 12 HELIX 4 4 ASN A 220 GLY A 222 5 3 HELIX 5 5 ASP A 223 VAL A 234 1 12 HELIX 6 6 ASN A 241 VAL A 262 1 22 HELIX 7 7 GLN A 264 THR A 282 1 19 HELIX 8 8 LYS A 283 GLN A 290 1 8 HELIX 9 9 GLY A 292 PHE A 300 1 9 HELIX 10 10 PRO B 21 ALA B 40 1 20 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