HEADER APOPTOSIS 29-JAN-22 7TRM TITLE CRYSTAL STRUCTURE OF HUMAN BIRC2 BIR3 DOMAIN IN COMPLEX WITH INHIBITOR TITLE 2 LCL-161 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BIR3 DOMAIN; COMPND 5 SYNONYM: CELLULAR INHIBITOR OF APOPTOSIS 1,C-IAP1,IAP HOMOLOG B, COMPND 6 INHIBITOR OF APOPTOSIS PROTEIN 2,HIAP-2,HIAP2,RING FINGER PROTEIN 48, COMPND 7 RING-TYPE E3 UBIQUITIN TRANSFERASE BIRC2,TNFR2-TRAF-SIGNALING COMPLEX COMPND 8 PROTEIN 2; COMPND 9 EC: 2.3.2.27; COMPND 10 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: BIRC2, API1, MIHB, RNF48; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEAR PROTEIN, INHIBITOR, HISTONE H3, DNA BINDING, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.H.TENCER,B.J.KLEIN,T.G.KUTATELADZE REVDAT 3 20-SEP-23 7TRM 1 COMPND JRNL HETNAM HETSYN REVDAT 2 16-AUG-23 7TRM 1 JRNL REVDAT 1 02-AUG-23 7TRM 0 JRNL AUTH A.H.TENCER,Y.YU,S.Z.CAUSSE,G.R.CAMPBELL,B.J.KLEIN,H.XUAN, JRNL AUTH 2 J.CARTIER,M.A.MILES,N.GAURAV,A.ZADOROZNYJ,T.A.HOLT,H.WEN, JRNL AUTH 3 C.J.HAWKINS,S.A.SPECTOR,L.DUBREZ,X.SHI,T.G.KUTATELADZE JRNL TITL MOLECULAR BASIS FOR NUCLEAR ACCUMULATION AND TARGETING OF JRNL TITL 2 THE INHIBITOR OF APOPTOSIS BIRC2. JRNL REF NAT.STRUCT.MOL.BIOL. V. 30 1265 2023 JRNL REFN ESSN 1545-9985 JRNL PMID 37524969 JRNL DOI 10.1038/S41594-023-01044-1 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3855 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 6846 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.880 REMARK 3 FREE R VALUE TEST SET COUNT : 1286 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 27.1300 - 4.9800 1.00 1322 145 0.1586 0.1955 REMARK 3 2 4.9800 - 3.9600 0.99 1277 144 0.1386 0.1690 REMARK 3 3 3.9600 - 3.4600 1.00 1295 146 0.1726 0.2024 REMARK 3 4 3.4600 - 3.1400 1.00 1331 144 0.1676 0.2440 REMARK 3 5 3.1400 - 2.9200 1.00 1281 144 0.2174 0.3232 REMARK 3 6 2.9200 - 2.7500 1.00 1284 143 0.2055 0.2324 REMARK 3 7 2.7500 - 2.6100 1.00 1322 140 0.1957 0.2897 REMARK 3 8 2.6100 - 2.5000 1.00 1315 139 0.2052 0.2902 REMARK 3 9 2.4900 - 2.4000 1.00 1297 141 0.2199 0.2883 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.283 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.965 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.007 785 REMARK 3 ANGLE : 0.843 1057 REMARK 3 CHIRALITY : 0.049 99 REMARK 3 PLANARITY : 0.005 137 REMARK 3 DIHEDRAL : 16.516 298 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 7TRM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1000260016. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6853 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 3D9T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE, 0.2 M SODIUM REMARK 280 CITRATE, AND 20% PEG3350, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 253 REMARK 465 PRO A 254 REMARK 465 LEU A 255 REMARK 465 GLY A 256 REMARK 465 SER A 257 REMARK 465 PRO A 258 REMARK 465 ASP A 346 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 PRO A 284 34.84 -84.68 REMARK 500 ASN A 301 -131.58 53.99 REMARK 500 CYS A 308 -63.67 -91.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 306 SG REMARK 620 2 CYS A 309 SG 110.1 REMARK 620 3 HIS A 326 NE2 103.6 115.4 REMARK 620 4 CYS A 333 SG 111.0 111.2 105.3 REMARK 620 N 1 2 3 DBREF 7TRM A 261 346 UNP Q13490 BIRC2_HUMAN 261 346 SEQADV 7TRM GLY A 253 UNP Q13490 EXPRESSION TAG SEQADV 7TRM PRO A 254 UNP Q13490 EXPRESSION TAG SEQADV 7TRM LEU A 255 UNP Q13490 EXPRESSION TAG SEQADV 7TRM GLY A 256 UNP Q13490 EXPRESSION TAG SEQADV 7TRM SER A 257 UNP Q13490 EXPRESSION TAG SEQADV 7TRM PRO A 258 UNP Q13490 EXPRESSION TAG SEQADV 7TRM GLU A 259 UNP Q13490 EXPRESSION TAG SEQADV 7TRM PHE A 260 UNP Q13490 EXPRESSION TAG SEQRES 1 A 94 GLY PRO LEU GLY SER PRO GLU PHE ILE SER ASN LEU SER SEQRES 2 A 94 MET GLN THR HIS ALA ALA ARG MET ARG THR PHE MET TYR SEQRES 3 A 94 TRP PRO SER SER VAL PRO VAL GLN PRO GLU GLN LEU ALA SEQRES 4 A 94 SER ALA GLY PHE TYR TYR VAL GLY ARG ASN ASP ASP VAL SEQRES 5 A 94 LYS CYS PHE CYS CYS ASP GLY GLY LEU ARG CYS TRP GLU SEQRES 6 A 94 SER GLY ASP ASP PRO TRP VAL GLU HIS ALA LYS TRP PHE SEQRES 7 A 94 PRO ARG CYS GLU PHE LEU ILE ARG MET LYS GLY GLN GLU SEQRES 8 A 94 PHE VAL ASP HET ZN A 401 1 HET EDO A 402 4 HET EDO A 403 4 HET EDO A 404 4 HET IUN A 405 35 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETNAM IUN LCL-161 HETSYN EDO ETHYLENE GLYCOL HETSYN IUN N-[(1S)-1-CYCLOHEXYL-2-{(2S)-2-[4-(4-FLUOROBENZOYL)-1, HETSYN 2 IUN 3-THIAZOL-2-YL]PYRROLIDIN-1-YL}-2-OXOETHYL]-N~2~- HETSYN 3 IUN METHYL-L-ALANINAMIDE FORMUL 2 ZN ZN 2+ FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 IUN C26 H33 F N4 O3 S FORMUL 7 HOH *45(H2 O) HELIX 1 AA1 ASN A 263 GLN A 267 5 5 HELIX 2 AA2 THR A 268 THR A 275 1 8 HELIX 3 AA3 PHE A 276 TRP A 279 5 4 HELIX 4 AA4 GLN A 286 ALA A 293 1 8 HELIX 5 AA5 ASP A 321 PHE A 330 1 10 HELIX 6 AA6 CYS A 333 VAL A 345 1 13 SHEET 1 AA1 3 PHE A 295 TYR A 297 0 SHEET 2 AA1 3 VAL A 304 CYS A 306 -1 O LYS A 305 N TYR A 296 SHEET 3 AA1 3 GLY A 312 LEU A 313 -1 O LEU A 313 N VAL A 304 LINK SG CYS A 306 ZN ZN A 401 1555 1555 2.36 LINK SG CYS A 309 ZN ZN A 401 1555 1555 2.33 LINK NE2 HIS A 326 ZN ZN A 401 1555 1555 2.08 LINK SG CYS A 333 ZN ZN A 401 1555 1555 2.35 CRYST1 104.710 104.710 27.132 90.00 90.00 120.00 P 3 2 1 6 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 0.009550 0.005514 0.000000 0.00000 SCALE2 0.000000 0.011028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036857 0.00000