HEADER LIGASE 15-AUG-22 8E2J TITLE CRYO-EM STRUCTURE OF BIRC6/SMAC (FROM LOCAL REFINEMENT 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIABLO IAP-BINDING MITOCHONDRIAL PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DIABLO HOMOLOG,MITOCHONDRIAL,DIRECT IAP-BINDING PROTEIN WITH COMPND 5 LOW PI,SECOND MITOCHONDRIA-DERIVED ACTIVATOR OF CASPASE,SMAC; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 6; COMPND 9 CHAIN: C, D; COMPND 10 EC: 6.-.-.-; COMPND 11 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: DIABLO, SMAC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: LOBSTR; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: EXPI293 KEYWDS UBIQUITIN, E3 LIGASE, APOPTOSIS, AUTOPHAGY, IAP, LIGASE EXPDTA ELECTRON MICROSCOPY AUTHOR M.HUNKELER,E.S.FISCHER REVDAT 3 29-MAR-23 8E2J 1 JRNL REVDAT 2 22-FEB-23 8E2J 1 JRNL REVDAT 1 15-FEB-23 8E2J 0 JRNL AUTH M.HUNKELER,C.Y.JIN,E.S.FISCHER JRNL TITL STRUCTURES OF BIRC6-CLIENT COMPLEXES PROVIDE A MECHANISM OF JRNL TITL 2 SMAC-MEDIATED RELEASE OF CASPASES. JRNL REF SCIENCE V. 379 1105 2023 JRNL REFN ESSN 1095-9203 JRNL PMID 36758104 JRNL DOI 10.1126/SCIENCE.ADE5750 REMARK 2 REMARK 2 RESOLUTION. 3.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, SERIALEM, CRYOSPARC, COOT, COOT, REMARK 3 PHENIX, ISOLDE, UCSF CHIMERAX, UCSF REMARK 3 CHIMERA, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : OTHER REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.440 REMARK 3 NUMBER OF PARTICLES : 192025 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8E2J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267622. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : BACULOVIRAL IAP REPEAT REMARK 245 -CONTAINING PROTEIN 6 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.40 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 14574 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5637.90 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 105000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : DATA COLLECTION IN COUNTING REMARK 245 MODE, USING MULTI-SHOT SCHEME (9 HOLES PER STAGE POSITION, 3 REMARK 245 MOVIES PER HOLE) REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 MET A 0 REMARK 465 ALA A 1 REMARK 465 VAL A 2 REMARK 465 PRO A 3 REMARK 465 ILE A 4 REMARK 465 ALA A 5 REMARK 465 GLN A 6 REMARK 465 LYS A 7 REMARK 465 SER A 8 REMARK 465 GLU A 9 REMARK 465 PRO A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 REMARK 465 MET B 0 REMARK 465 ALA B 1 REMARK 465 VAL B 2 REMARK 465 PRO B 3 REMARK 465 ILE B 4 REMARK 465 ALA B 5 REMARK 465 GLN B 6 REMARK 465 LYS B 7 REMARK 465 SER B 8 REMARK 465 GLU B 9 REMARK 465 PRO B 10 REMARK 465 HIS B 11 REMARK 465 HIS B 185 REMARK 465 HIS B 186 REMARK 465 HIS B 187 REMARK 465 HIS B 188 REMARK 465 HIS B 189 REMARK 465 HIS B 190 REMARK 465 HIS B 191 REMARK 465 HIS B 192 REMARK 465 HIS B 193 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O ARG A 21 HG SER A 24 1.46 REMARK 500 O GLN B 61 HG SER B 64 1.56 REMARK 500 O ASN B 70 H GLU B 74 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 ASN A 70 107.99 -53.60 REMARK 500 GLU A 73 -62.14 -98.92 REMARK 500 GLU A 183 -29.14 62.38 REMARK 500 ASN B 70 74.32 -151.85 REMARK 500 GLU B 183 -29.22 62.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-27832 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF BIRC6 (CONSENSUS) REMARK 900 RELATED ID: EMD-27833 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HELICAL ARCH OF BIRC6 (FROM LOCAL REFINEMENT 1) REMARK 900 RELATED ID: EMD-27834 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF N-TERMINAL ARM OF BIRC6 (FROM LOCAL REFINEMENT REMARK 900 2) REMARK 900 RELATED ID: EMD-27836 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF C-TERMINAL ARM OF BIRC6 (FROM LOCAL REFINEMENT REMARK 900 4) REMARK 900 RELATED ID: EMD-27835 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF N-TERMINAL ARM (AA68-966) OF BIRC6 (FROM LOCAL REMARK 900 REFINEMENT 3) REMARK 900 RELATED ID: EMD-27837 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF BIRC6/SMAC REMARK 900 RELATED ID: EMD-27839 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY OF BIRC6/CASP-3 (CLUSTERS) REMARK 900 RELATED ID: EMD-27840 RELATED DB: EMDB REMARK 900 CRYO-EM DENSITY OF BIRC6/CASP-7 (CLUSTERS) REMARK 900 RELATED ID: EMD-27838 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF BIRC6/SMAC (FROM LOCAL REFINEMENT 1) REMARK 900 RELATED ID: EMD-27841 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF BIRC6 (CONSENSUS) DBREF 8E2J A 1 184 UNP Q9NR28 DBLOH_HUMAN 56 239 DBREF 8E2J B 1 184 UNP Q9NR28 DBLOH_HUMAN 56 239 DBREF 8E2J C 51 107 PDB 8E2J 8E2J 51 107 DBREF 8E2J D 51 107 PDB 8E2J 8E2J 51 107 SEQADV 8E2J MET A 0 UNP Q9NR28 INITIATING METHIONINE SEQADV 8E2J HIS A 185 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS A 186 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS A 187 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS A 188 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS A 189 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS A 190 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS A 191 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS A 192 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS A 193 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J MET B 0 UNP Q9NR28 INITIATING METHIONINE SEQADV 8E2J HIS B 185 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS B 186 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS B 187 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS B 188 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS B 189 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS B 190 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS B 191 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS B 192 UNP Q9NR28 EXPRESSION TAG SEQADV 8E2J HIS B 193 UNP Q9NR28 EXPRESSION TAG SEQRES 1 A 194 MET ALA VAL PRO ILE ALA GLN LYS SER GLU PRO HIS SER SEQRES 2 A 194 LEU SER SER GLU ALA LEU MET ARG ARG ALA VAL SER LEU SEQRES 3 A 194 VAL THR ASP SER THR SER THR PHE LEU SER GLN THR THR SEQRES 4 A 194 TYR ALA LEU ILE GLU ALA ILE THR GLU TYR THR LYS ALA SEQRES 5 A 194 VAL TYR THR LEU THR SER LEU TYR ARG GLN TYR THR SER SEQRES 6 A 194 LEU LEU GLY LYS MET ASN SER GLU GLU GLU ASP GLU VAL SEQRES 7 A 194 TRP GLN VAL ILE ILE GLY ALA ARG ALA GLU MET THR SER SEQRES 8 A 194 LYS HIS GLN GLU TYR LEU LYS LEU GLU THR THR TRP MET SEQRES 9 A 194 THR ALA VAL GLY LEU SER GLU MET ALA ALA GLU ALA ALA SEQRES 10 A 194 TYR GLN THR GLY ALA ASP GLN ALA SER ILE THR ALA ARG SEQRES 11 A 194 ASN HIS ILE GLN LEU VAL LYS LEU GLN VAL GLU GLU VAL SEQRES 12 A 194 HIS GLN LEU SER ARG LYS ALA GLU THR LYS LEU ALA GLU SEQRES 13 A 194 ALA GLN ILE GLU GLU LEU ARG GLN LYS THR GLN GLU GLU SEQRES 14 A 194 GLY GLU GLU ARG ALA GLU SER GLU GLN GLU ALA TYR LEU SEQRES 15 A 194 ARG GLU ASP HIS HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 B 194 MET ALA VAL PRO ILE ALA GLN LYS SER GLU PRO HIS SER SEQRES 2 B 194 LEU SER SER GLU ALA LEU MET ARG ARG ALA VAL SER LEU SEQRES 3 B 194 VAL THR ASP SER THR SER THR PHE LEU SER GLN THR THR SEQRES 4 B 194 TYR ALA LEU ILE GLU ALA ILE THR GLU TYR THR LYS ALA SEQRES 5 B 194 VAL TYR THR LEU THR SER LEU TYR ARG GLN TYR THR SER SEQRES 6 B 194 LEU LEU GLY LYS MET ASN SER GLU GLU GLU ASP GLU VAL SEQRES 7 B 194 TRP GLN VAL ILE ILE GLY ALA ARG ALA GLU MET THR SER SEQRES 8 B 194 LYS HIS GLN GLU TYR LEU LYS LEU GLU THR THR TRP MET SEQRES 9 B 194 THR ALA VAL GLY LEU SER GLU MET ALA ALA GLU ALA ALA SEQRES 10 B 194 TYR GLN THR GLY ALA ASP GLN ALA SER ILE THR ALA ARG SEQRES 11 B 194 ASN HIS ILE GLN LEU VAL LYS LEU GLN VAL GLU GLU VAL SEQRES 12 B 194 HIS GLN LEU SER ARG LYS ALA GLU THR LYS LEU ALA GLU SEQRES 13 B 194 ALA GLN ILE GLU GLU LEU ARG GLN LYS THR GLN GLU GLU SEQRES 14 B 194 GLY GLU GLU ARG ALA GLU SER GLU GLN GLU ALA TYR LEU SEQRES 15 B 194 ARG GLU ASP HIS HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 C 57 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 2 C 57 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 3 C 57 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 4 C 57 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 5 C 57 UNK UNK UNK UNK UNK SEQRES 1 D 57 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 2 D 57 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 3 D 57 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 4 D 57 UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK UNK SEQRES 5 D 57 UNK UNK UNK UNK UNK HELIX 1 AA1 SER A 12 LEU A 65 1 54 HELIX 2 AA2 GLU A 73 GLY A 120 1 48 HELIX 3 AA3 ALA A 121 TYR A 180 1 60 HELIX 4 AA4 LEU B 13 LEU B 65 1 53 HELIX 5 AA5 LEU B 66 MET B 69 5 4 HELIX 6 AA6 ASN B 70 THR B 119 1 50 HELIX 7 AA7 ALA B 121 TYR B 180 1 60 HELIX 8 AA8 UNK C 52 UNK C 107 1 56 HELIX 9 AA9 UNK D 52 UNK D 107 1 56 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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