HEADER APOPTOSIS 26-MAR-23 8IVB TITLE K113-UBIQUITINATED BAK COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: APOPTOSIS REGULATOR BAK,BCL-2-LIKE PROTEIN 7,BCL2-L-7; COMPND 9 ENGINEERED: YES; COMPND 10 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: RPS27A, UBA80, UBCEP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: BAK1, BAK, BCL2L7, CDN1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PRO-APOPTOTIC BCL-2 PROTEINS, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.DONG,P.CHENG,Y.Z.HOU,Y.K.CHEN,Z.LIU REVDAT 2 15-MAY-24 8IVB 1 REMARK REVDAT 1 31-JAN-24 8IVB 0 JRNL AUTH P.CHENG,Y.HOU,M.BIAN,X.FANG,Y.LIU,Y.RAO,S.CAO,Y.LIU,S.ZHANG, JRNL AUTH 2 Y.CHEN,X.DONG,Z.LIU JRNL TITL PARKIN-MEDIATED UBIQUITINATION INHIBITS BAK APOPTOTIC JRNL TITL 2 ACTIVITY BY BLOCKING ITS CANONICAL HYDROPHOBIC GROOVE. JRNL REF COMMUN BIOL V. 6 1260 2023 JRNL REFN ESSN 2399-3642 JRNL PMID 38087033 JRNL DOI 10.1038/S42003-023-05650-Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CCPNMR ANALYSIS REMARK 3 AUTHORS : CCPN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8IVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036268. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 BAR REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM PHOSPHATE, 0.1 M REMARK 210 SODIUM CHLORIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 240 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: 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 8 TYR B 38 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 12 TYR B 143 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES 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 ASN A 60 32.04 80.34 REMARK 500 1 VAL A 70 -140.50 -94.74 REMARK 500 1 LEU A 71 134.39 -178.12 REMARK 500 1 LEU A 73 162.44 55.88 REMARK 500 1 SER B 21 156.65 73.98 REMARK 500 1 ALA B 56 46.85 -84.53 REMARK 500 1 ASP B 57 157.93 62.42 REMARK 500 1 GLU B 59 -155.04 -148.51 REMARK 500 1 TYR B 89 54.85 -113.22 REMARK 500 1 GLN B 101 64.12 60.42 REMARK 500 1 TYR B 136 -81.67 -102.03 REMARK 500 1 ARG B 137 -38.61 -37.01 REMARK 500 1 ARG B 156 18.99 -65.07 REMARK 500 1 LEU B 183 -149.87 -103.58 REMARK 500 2 ASN A 60 32.72 80.33 REMARK 500 2 VAL A 70 -143.53 -96.18 REMARK 500 2 LEU A 71 134.38 -175.73 REMARK 500 2 LEU A 73 149.37 57.08 REMARK 500 2 SER B 21 156.70 74.07 REMARK 500 2 ALA B 56 46.69 -85.01 REMARK 500 2 ASP B 57 157.53 62.95 REMARK 500 2 GLU B 59 -155.22 -148.30 REMARK 500 2 TYR B 89 53.58 -113.38 REMARK 500 2 TYR B 136 -81.72 -102.56 REMARK 500 2 ARG B 137 -38.51 -37.07 REMARK 500 2 ARG B 156 18.04 -65.97 REMARK 500 2 LEU B 183 -152.32 -102.72 REMARK 500 3 GLU A 34 -47.50 -131.91 REMARK 500 3 ASN A 60 31.42 77.16 REMARK 500 3 VAL A 70 -140.24 -95.82 REMARK 500 3 LEU A 71 136.97 -177.63 REMARK 500 3 LEU A 73 78.11 26.59 REMARK 500 3 SER B 21 155.90 74.80 REMARK 500 3 ALA B 56 47.46 -84.88 REMARK 500 3 ASP B 57 159.94 61.04 REMARK 500 3 GLU B 59 -157.18 -148.61 REMARK 500 3 TYR B 89 52.49 -116.74 REMARK 500 3 TYR B 136 -79.62 -102.21 REMARK 500 3 ARG B 137 -36.21 -37.32 REMARK 500 3 ARG B 156 16.33 -66.58 REMARK 500 3 ASN B 182 30.65 -96.29 REMARK 500 3 LEU B 183 -151.50 -103.97 REMARK 500 4 ASN A 60 32.97 80.21 REMARK 500 4 VAL A 70 -142.53 -95.16 REMARK 500 4 LEU A 71 134.93 -175.18 REMARK 500 4 LEU A 73 153.94 67.54 REMARK 500 4 SER B 21 156.79 73.81 REMARK 500 4 ALA B 56 46.81 -84.21 REMARK 500 4 ASP B 57 157.94 62.59 REMARK 500 4 GLU B 59 -154.98 -148.83 REMARK 500 REMARK 500 THIS ENTRY HAS 288 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19045 RELATED DB: BMRB REMARK 900 RELATED ID: 6457 RELATED DB: BMRB DBREF 8IVB A 1 76 UNP P62979 RS27A_HUMAN 1 76 DBREF 8IVB B 18 186 UNP Q16611 BAK_HUMAN 18 186 SEQADV 8IVB CYS A 76 UNP P62979 GLY 76 CONFLICT SEQADV 8IVB CYS B 113 UNP Q16611 LYS 113 ENGINEERED MUTATION SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY CYS SEQRES 1 B 169 ALA LEU PRO SER ALA SER GLU GLU GLN VAL ALA GLN ASP SEQRES 2 B 169 THR GLU GLU VAL PHE ARG SER TYR VAL PHE TYR ARG HIS SEQRES 3 B 169 GLN GLN GLU GLN GLU ALA GLU GLY VAL ALA ALA PRO ALA SEQRES 4 B 169 ASP PRO GLU MET VAL THR LEU PRO LEU GLN PRO SER SER SEQRES 5 B 169 THR MET GLY GLN VAL GLY ARG GLN LEU ALA ILE ILE GLY SEQRES 6 B 169 ASP ASP ILE ASN ARG ARG TYR ASP SER GLU PHE GLN THR SEQRES 7 B 169 MET LEU GLN HIS LEU GLN PRO THR ALA GLU ASN ALA TYR SEQRES 8 B 169 GLU TYR PHE THR CYS ILE ALA THR SER LEU PHE GLU SER SEQRES 9 B 169 GLY ILE ASN TRP GLY ARG VAL VAL ALA LEU LEU GLY PHE SEQRES 10 B 169 GLY TYR ARG LEU ALA LEU HIS VAL TYR GLN HIS GLY LEU SEQRES 11 B 169 THR GLY PHE LEU GLY GLN VAL THR ARG PHE VAL VAL ASP SEQRES 12 B 169 PHE MET LEU HIS HIS CYS ILE ALA ARG TRP ILE ALA GLN SEQRES 13 B 169 ARG GLY GLY TRP VAL ALA ALA LEU ASN LEU GLY ASN GLY HELIX 1 AA1 THR A 22 GLU A 34 1 13 HELIX 2 AA2 PRO A 37 GLN A 41 5 5 HELIX 3 AA3 THR A 55 ASN A 60 1 6 HELIX 4 AA4 SER B 23 GLU B 50 1 28 HELIX 5 AA5 THR B 70 GLY B 82 1 13 HELIX 6 AA6 ASP B 83 TYR B 89 1 7 HELIX 7 AA7 ASP B 90 GLN B 101 1 12 HELIX 8 AA8 ASN B 106 PHE B 119 1 14 HELIX 9 AA9 ASN B 124 PHE B 134 1 11 HELIX 10 AB1 TYR B 136 GLY B 146 1 11 HELIX 11 AB2 PHE B 150 HIS B 165 1 16 HELIX 12 AB3 CYS B 166 ARG B 174 1 9 HELIX 13 AB4 GLY B 175 LEU B 181 5 7 SHEET 1 AA1 4 THR A 12 GLU A 16 0 SHEET 2 AA1 4 GLN A 2 LYS A 6 -1 N ILE A 3 O LEU A 15 SHEET 3 AA1 4 THR A 66 LEU A 69 1 O LEU A 67 N LYS A 6 SHEET 4 AA1 4 LEU A 43 ILE A 44 -1 N ILE A 44 O HIS A 68 SSBOND 1 CYS A 76 CYS B 113 1555 1555 2.03 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