HEADER APOPTOSIS 19-FEB-13 2M5B TITLE THE NMR STRUCTURE OF THE BID-BAK COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APOPTOSIS REGULATOR BAK, BCL-2-LIKE PROTEIN 7, BCL2-L-7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HUMAN_BID_BH3_SAHB; COMPND 8 CHAIN: B; COMPND 9 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: BAK, BAK1, BCL2L7, CDN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: AMP RESISTANT PET VARIANT; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS BCL-2 FAMILY EFFECTOR BAK, BH3-ONLY PROTEIN BID, EFFECTOR DIRECT KEYWDS 2 ACTIVATION, NMR SOLUTION STRUCTURE OF BID-BAK COMPLEX, MITOCHONDRIAL KEYWDS 3 OUTER MEMBRANE PREMEABILIZATION, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.MOLDOVEANU,C.R.GRACE,R.W.KRIWACKI,D.R.GREEN REVDAT 4 14-JUN-23 2M5B 1 REMARK LINK REVDAT 3 22-MAY-13 2M5B 1 JRNL REVDAT 2 08-MAY-13 2M5B 1 JRNL REVDAT 1 17-APR-13 2M5B 0 JRNL AUTH T.MOLDOVEANU,C.R.GRACE,F.LLAMBI,A.NOURSE,P.FITZGERALD, JRNL AUTH 2 K.GEHRING,R.W.KRIWACKI,D.R.GREEN JRNL TITL BID-INDUCED STRUCTURAL CHANGES IN BAK PROMOTE APOPTOSIS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 20 589 2013 JRNL REFN ISSN 1545-9993 JRNL PMID 23604079 JRNL DOI 10.1038/NSMB.2563 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, CYANA REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M5B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000103227. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : ~0.5 MM [U-98% 13C; U-98% 15N] REMARK 210 HUMAN CBAK, ~0.5 MM HUMAN BID REMARK 210 BH3 SAHB, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 2D 1H-1H REMARK 210 TOCSY; 2D 1H-1H COSY; 3D CBCA(CO) REMARK 210 NH; 3D HNCA; 3D HNCACB; 3D REMARK 210 HBHA(CBCACO)NH; 3D 1H HCCH-TOCSY; REMARK 210 3D 13C-DETECTED HCC-TOCSY; 2D REMARK 210 1H-15N TROSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 3D 1H-13C NOESY; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D REMARK 210 1H-13C NOESY AROMATIC; 2D 13C-1H REMARK 210 TROSY; 3D 13C/15N HALF-FILTERED REMARK 210 15N-EDITED NOESY; 3D 13C/15N REMARK 210 HALF-FILTERED 13C-EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: 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 21 160.93 63.31 REMARK 500 1 ALA A 22 148.08 -178.31 REMARK 500 1 PRO A 55 -169.94 -69.80 REMARK 500 1 ALA A 56 42.20 -90.90 REMARK 500 1 ASP A 57 157.90 62.94 REMARK 500 1 PRO A 58 86.98 -69.78 REMARK 500 1 THR A 62 -170.89 -57.78 REMARK 500 1 PRO A 64 83.57 -69.78 REMARK 500 1 GLN A 66 77.23 -112.53 REMARK 500 1 GLN A 101 62.82 63.85 REMARK 500 1 PRO A 102 -174.88 -69.73 REMARK 500 1 LEU A 183 -162.34 -105.44 REMARK 500 1 LEU B 90 41.00 -86.15 REMARK 500 1 MK8 B 92 -25.29 -167.52 REMARK 500 2 SER A 21 162.14 63.03 REMARK 500 2 ALA A 22 144.96 -177.93 REMARK 500 2 ALA A 56 81.87 -178.68 REMARK 500 2 ASP A 57 70.88 -175.72 REMARK 500 2 PRO A 58 78.24 -69.74 REMARK 500 2 THR A 62 -169.94 51.21 REMARK 500 2 PRO A 64 89.39 -69.82 REMARK 500 2 ASP A 83 -74.91 -61.95 REMARK 500 2 GLN A 101 63.07 64.42 REMARK 500 2 PRO A 102 -172.32 -69.68 REMARK 500 2 SER A 121 -63.27 -95.48 REMARK 500 2 THR A 148 -166.56 44.27 REMARK 500 2 ASP B 81 -38.30 77.56 REMARK 500 2 LEU B 90 35.95 -87.73 REMARK 500 2 MK8 B 92 -17.76 -166.92 REMARK 500 3 ALA A 53 40.74 177.57 REMARK 500 3 ALA A 56 101.58 -55.25 REMARK 500 3 ASP A 57 75.37 -174.18 REMARK 500 3 THR A 62 -74.26 70.21 REMARK 500 3 PRO A 64 83.52 -69.87 REMARK 500 3 GLN A 66 76.62 -112.48 REMARK 500 3 ASP A 83 -74.67 -65.88 REMARK 500 3 PRO A 102 -179.76 -69.77 REMARK 500 3 HIS A 165 179.44 -56.33 REMARK 500 3 CYS A 166 34.16 -93.49 REMARK 500 3 ASN A 182 32.17 -95.64 REMARK 500 3 LEU B 90 36.77 -87.46 REMARK 500 3 MK8 B 92 -19.07 -169.58 REMARK 500 4 SER A 21 164.24 62.74 REMARK 500 4 ASP A 57 85.03 -179.62 REMARK 500 4 GLU A 59 32.96 -162.69 REMARK 500 4 THR A 62 174.04 56.14 REMARK 500 4 PRO A 64 84.79 -69.81 REMARK 500 4 GLN A 66 67.69 -115.91 REMARK 500 4 ASP A 83 -75.17 -65.87 REMARK 500 4 GLN A 101 62.19 65.02 REMARK 500 REMARK 500 THIS ENTRY HAS 279 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA B 91 MK8 B 92 1 -131.17 REMARK 500 ASP B 95 MK8 B 96 1 -131.21 REMARK 500 ALA B 91 MK8 B 92 2 -131.20 REMARK 500 ASP B 95 MK8 B 96 2 -131.21 REMARK 500 ALA B 91 MK8 B 92 3 -131.19 REMARK 500 ASP B 95 MK8 B 96 3 -131.17 REMARK 500 ALA B 91 MK8 B 92 4 -131.21 REMARK 500 ASP B 95 MK8 B 96 4 -131.11 REMARK 500 ALA B 91 MK8 B 92 5 -131.24 REMARK 500 ASP B 95 MK8 B 96 5 -131.16 REMARK 500 ALA B 91 MK8 B 92 6 -131.11 REMARK 500 ASP B 95 MK8 B 96 6 -131.14 REMARK 500 ALA B 91 MK8 B 92 7 -131.20 REMARK 500 ASP B 95 MK8 B 96 7 -131.14 REMARK 500 ALA B 91 MK8 B 92 8 -131.25 REMARK 500 ASP B 95 MK8 B 96 8 -131.18 REMARK 500 ALA B 91 MK8 B 92 9 -131.19 REMARK 500 ASP B 95 MK8 B 96 9 -131.16 REMARK 500 ALA B 91 MK8 B 92 10 -131.18 REMARK 500 ASP B 95 MK8 B 96 10 -131.18 REMARK 500 ALA B 91 MK8 B 92 11 -131.12 REMARK 500 ASP B 95 MK8 B 96 11 -131.13 REMARK 500 ALA B 91 MK8 B 92 12 -131.20 REMARK 500 ASP B 95 MK8 B 96 12 -131.15 REMARK 500 ALA B 91 MK8 B 92 13 -131.21 REMARK 500 ASP B 95 MK8 B 96 13 -131.22 REMARK 500 ALA B 91 MK8 B 92 14 -131.19 REMARK 500 ASP B 95 MK8 B 96 14 -131.16 REMARK 500 ALA B 91 MK8 B 92 15 -131.23 REMARK 500 ASP B 95 MK8 B 96 15 -131.17 REMARK 500 ALA B 91 MK8 B 92 16 -131.18 REMARK 500 ASP B 95 MK8 B 96 16 -131.17 REMARK 500 ALA B 91 MK8 B 92 17 -131.17 REMARK 500 ASP B 95 MK8 B 96 17 -131.13 REMARK 500 ALA B 91 MK8 B 92 18 -131.24 REMARK 500 ASP B 95 MK8 B 96 18 -131.17 REMARK 500 ALA B 91 MK8 B 92 19 -131.15 REMARK 500 ASP B 95 MK8 B 96 19 -131.27 REMARK 500 ALA B 91 MK8 B 92 20 -131.20 REMARK 500 ASP B 95 MK8 B 96 20 -131.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2IMT RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF HUMAN APO BAK REMARK 900 RELATED ID: 2BID RELATED DB: PDB REMARK 900 NMR STRUCUTURE OF APO HUMAN BID REMARK 900 RELATED ID: 19045 RELATED DB: BMRB DBREF 2M5B A 18 186 UNP Q16611 BAK_HUMAN 18 186 DBREF 2M5B B 80 102 PDB 2M5B 2M5B 80 102 SEQRES 1 A 169 ALA LEU PRO SER ALA SER GLU GLU GLN VAL ALA GLN ASP SEQRES 2 A 169 THR GLU GLU VAL PHE ARG SER TYR VAL PHE TYR ARG HIS SEQRES 3 A 169 GLN GLN GLU GLN GLU ALA GLU GLY VAL ALA ALA PRO ALA SEQRES 4 A 169 ASP PRO GLU MET VAL THR LEU PRO LEU GLN PRO SER SER SEQRES 5 A 169 THR MET GLY GLN VAL GLY ARG GLN LEU ALA ILE ILE GLY SEQRES 6 A 169 ASP ASP ILE ASN ARG ARG TYR ASP SER GLU PHE GLN THR SEQRES 7 A 169 MET LEU GLN HIS LEU GLN PRO THR ALA GLU ASN ALA TYR SEQRES 8 A 169 GLU TYR PHE THR LYS ILE ALA THR SER LEU PHE GLU SER SEQRES 9 A 169 GLY ILE ASN TRP GLY ARG VAL VAL ALA LEU LEU GLY PHE SEQRES 10 A 169 GLY TYR ARG LEU ALA LEU HIS VAL TYR GLN HIS GLY LEU SEQRES 11 A 169 THR GLY PHE LEU GLY GLN VAL THR ARG PHE VAL VAL ASP SEQRES 12 A 169 PHE MET LEU HIS HIS CYS ILE ALA ARG TRP ILE ALA GLN SEQRES 13 A 169 ARG GLY GLY TRP VAL ALA ALA LEU ASN LEU GLY ASN GLY SEQRES 1 B 23 GLU ASP ILE ILE ARG ASN ILE ALA ARG HIS LEU ALA MK8 SEQRES 2 B 23 VAL GLY ASP MK8 NLE ASP ARG SER ILE NH2 MODRES 2M5B MK8 B 92 LEU 2-METHYL-L-NORLEUCINE MODRES 2M5B MK8 B 96 LEU 2-METHYL-L-NORLEUCINE MODRES 2M5B NLE B 97 LEU NORLEUCINE HET MK8 B 92 20 HET MK8 B 96 20 HET NLE B 97 19 HET NH2 B 102 3 HETNAM MK8 2-METHYL-L-NORLEUCINE HETNAM NLE NORLEUCINE HETNAM NH2 AMINO GROUP FORMUL 2 MK8 2(C7 H15 N O2) FORMUL 2 NLE C6 H13 N O2 FORMUL 2 NH2 H2 N HELIX 1 1 SER A 23 GLU A 50 1 28 HELIX 2 2 SER A 69 GLY A 82 1 14 HELIX 3 3 GLY A 82 GLN A 98 1 17 HELIX 4 4 ASN A 106 PHE A 119 1 14 HELIX 5 5 GLU A 120 GLY A 122 5 3 HELIX 6 6 ASN A 124 GLY A 146 1 23 HELIX 7 7 PHE A 150 LEU A 163 1 14 HELIX 8 8 CYS A 166 ARG A 174 1 9 HELIX 9 9 GLY A 176 LEU A 183 5 8 HELIX 10 10 ASP B 81 HIS B 89 1 9 HELIX 11 11 GLY B 94 SER B 100 1 7 LINK C ALA B 91 N MK8 B 92 1555 1555 1.34 LINK C MK8 B 92 N VAL B 93 1555 1555 1.33 LINK CE MK8 B 92 CE MK8 B 96 1555 1555 2.82 LINK C ASP B 95 N MK8 B 96 1555 1555 1.34 LINK C MK8 B 96 N NLE B 97 1555 1555 1.33 LINK C NLE B 97 N ASP B 98 1555 1555 1.33 LINK C ILE B 101 N NH2 B 102 1555 1555 1.32 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20