HEADER NUCLEAR PROTEIN 25-MAR-24 8YTC TITLE PML-RBCC DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN PML; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: E3 SUMO-PROTEIN LIGASE PML,PROMYELOCYTIC LEUKEMIA PROTEIN, COMPND 5 RING FINGER PROTEIN 71,RING-TYPE E3 SUMO TRANSFERASE PML,TRIPARTITE COMPND 6 MOTIF-CONTAINING PROTEIN 19,TRIM19; COMPND 7 EC: 2.3.2.-; COMPND 8 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: PML, MYL, PP8675, RNF71, TRIM19; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PML NUCLEAR BODY, RBCC DIMER, NUCLEAR PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR Y.TAN,J.LI,S.ZHANG,Y.ZHANG,Y.CONG,G.MENG REVDAT 2 02-JUL-25 8YTC 1 REMARK REVDAT 1 26-FEB-25 8YTC 0 JRNL AUTH Y.TAN,J.LI,S.ZHANG,Y.ZHANG,Z.ZHUO,X.MA,Y.YIN,Y.JIANG,Y.CONG, JRNL AUTH 2 G.MENG JRNL TITL CRYO-EM STRUCTURE OF PML RBCC DIMER REVEALS CC-MEDIATED JRNL TITL 2 OCTOPUS-LIKE NUCLEAR BODY ASSEMBLY MECHANISM. JRNL REF CELL DISCOV V. 10 118 2024 JRNL REFN ESSN 2056-5968 JRNL PMID 39587079 JRNL DOI 10.1038/S41421-024-00735-3 REMARK 2 REMARK 2 RESOLUTION. 5.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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) : 5.300 REMARK 3 NUMBER OF PARTICLES : 307216 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 8YTC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300046018. 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 : PROMYELOCYTIC LEUKEMIA PROTEIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI POLARA 300 REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 3000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL 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: 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 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 ASN A 191 REMARK 465 PRO A 192 REMARK 465 ASN A 193 REMARK 465 HIS A 194 REMARK 465 ARG A 195 REMARK 465 THR A 196 REMARK 465 PRO A 197 REMARK 465 THR A 198 REMARK 465 LEU A 199 REMARK 465 THR A 200 REMARK 465 HIS A 222 REMARK 465 SER A 223 REMARK 465 GLU A 224 REMARK 465 LEU A 225 REMARK 465 LYS A 226 REMARK 465 CYS A 227 REMARK 465 ASP A 228 REMARK 465 ILE A 229 REMARK 465 SER A 230 REMARK 465 ALA A 231 REMARK 465 GLU A 232 REMARK 465 ILE A 233 REMARK 465 GLN A 234 REMARK 465 GLN A 235 REMARK 465 ARG A 236 REMARK 465 GLN A 237 REMARK 465 GLU A 238 REMARK 465 GLU A 239 REMARK 465 LEU A 240 REMARK 465 ASP A 241 REMARK 465 ALA A 242 REMARK 465 MET A 243 REMARK 465 THR A 244 REMARK 465 GLN A 245 REMARK 465 ALA A 246 REMARK 465 LEU A 247 REMARK 465 GLN A 248 REMARK 465 GLU A 249 REMARK 465 GLN A 250 REMARK 465 ASP A 251 REMARK 465 SER A 252 REMARK 465 ALA A 253 REMARK 465 PHE A 254 REMARK 465 GLY A 255 REMARK 465 ALA A 256 REMARK 465 ASN B 191 REMARK 465 PRO B 192 REMARK 465 ASN B 193 REMARK 465 HIS B 194 REMARK 465 ARG B 195 REMARK 465 THR B 196 REMARK 465 PRO B 197 REMARK 465 THR B 198 REMARK 465 LEU B 199 REMARK 465 THR B 200 REMARK 465 HIS B 222 REMARK 465 SER B 223 REMARK 465 GLU B 224 REMARK 465 LEU B 225 REMARK 465 LYS B 226 REMARK 465 CYS B 227 REMARK 465 ASP B 228 REMARK 465 ILE B 229 REMARK 465 SER B 230 REMARK 465 ALA B 231 REMARK 465 GLU B 232 REMARK 465 ILE B 233 REMARK 465 GLN B 234 REMARK 465 GLN B 235 REMARK 465 ARG B 236 REMARK 465 GLN B 237 REMARK 465 GLU B 238 REMARK 465 GLU B 239 REMARK 465 LEU B 240 REMARK 465 ASP B 241 REMARK 465 ALA B 242 REMARK 465 MET B 243 REMARK 465 THR B 244 REMARK 465 GLN B 245 REMARK 465 ALA B 246 REMARK 465 LEU B 247 REMARK 465 GLN B 248 REMARK 465 GLU B 249 REMARK 465 GLN B 250 REMARK 465 ASP B 251 REMARK 465 SER B 252 REMARK 465 ALA B 253 REMARK 465 PHE B 254 REMARK 465 GLY B 255 REMARK 465 ALA B 256 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 OE1 GLU A 51 OG1 THR A 130 2.12 REMARK 500 OE1 GLU B 51 OG1 THR B 130 2.12 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 ALA A 149 -9.46 72.45 REMARK 500 ALA B 149 -9.46 72.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-39571 RELATED DB: EMDB REMARK 900 PML-RBCC DIMER DBREF 8YTC A 46 256 UNP P29590 PML_HUMAN 46 256 DBREF 8YTC B 46 256 UNP P29590 PML_HUMAN 46 256 SEQRES 1 A 211 PRO ALA SER GLU GLU GLU PHE GLN PHE LEU ARG CYS GLN SEQRES 2 A 211 GLN CYS GLN ALA GLU ALA LYS CYS PRO LYS LEU LEU PRO SEQRES 3 A 211 CYS LEU HIS THR LEU CYS SER GLY CYS LEU GLU ALA SER SEQRES 4 A 211 GLY MET GLN CYS PRO ILE CYS GLN ALA PRO TRP PRO LEU SEQRES 5 A 211 GLY ALA ASP THR PRO ALA LEU ASP ASN VAL PHE PHE GLU SEQRES 6 A 211 SER LEU GLN ARG ARG LEU SER VAL TYR ARG GLN ILE VAL SEQRES 7 A 211 ASP ALA GLN ALA VAL CYS THR ARG CYS LYS GLU SER ALA SEQRES 8 A 211 ASP PHE TRP CYS PHE GLU CYS GLU GLN LEU LEU CYS ALA SEQRES 9 A 211 LYS CYS PHE GLU ALA HIS GLN TRP PHE LEU LYS HIS GLU SEQRES 10 A 211 ALA ARG PRO LEU ALA GLU LEU ARG ASN GLN SER VAL ARG SEQRES 11 A 211 GLU PHE LEU ASP GLY THR ARG LYS THR ASN ASN ILE PHE SEQRES 12 A 211 CYS SER ASN PRO ASN HIS ARG THR PRO THR LEU THR SER SEQRES 13 A 211 ILE TYR CYS ARG GLY CYS SER LYS PRO LEU CYS CYS SER SEQRES 14 A 211 CYS ALA LEU LEU ASP SER SER HIS SER GLU LEU LYS CYS SEQRES 15 A 211 ASP ILE SER ALA GLU ILE GLN GLN ARG GLN GLU GLU LEU SEQRES 16 A 211 ASP ALA MET THR GLN ALA LEU GLN GLU GLN ASP SER ALA SEQRES 17 A 211 PHE GLY ALA SEQRES 1 B 211 PRO ALA SER GLU GLU GLU PHE GLN PHE LEU ARG CYS GLN SEQRES 2 B 211 GLN CYS GLN ALA GLU ALA LYS CYS PRO LYS LEU LEU PRO SEQRES 3 B 211 CYS LEU HIS THR LEU CYS SER GLY CYS LEU GLU ALA SER SEQRES 4 B 211 GLY MET GLN CYS PRO ILE CYS GLN ALA PRO TRP PRO LEU SEQRES 5 B 211 GLY ALA ASP THR PRO ALA LEU ASP ASN VAL PHE PHE GLU SEQRES 6 B 211 SER LEU GLN ARG ARG LEU SER VAL TYR ARG GLN ILE VAL SEQRES 7 B 211 ASP ALA GLN ALA VAL CYS THR ARG CYS LYS GLU SER ALA SEQRES 8 B 211 ASP PHE TRP CYS PHE GLU CYS GLU GLN LEU LEU CYS ALA SEQRES 9 B 211 LYS CYS PHE GLU ALA HIS GLN TRP PHE LEU LYS HIS GLU SEQRES 10 B 211 ALA ARG PRO LEU ALA GLU LEU ARG ASN GLN SER VAL ARG SEQRES 11 B 211 GLU PHE LEU ASP GLY THR ARG LYS THR ASN ASN ILE PHE SEQRES 12 B 211 CYS SER ASN PRO ASN HIS ARG THR PRO THR LEU THR SER SEQRES 13 B 211 ILE TYR CYS ARG GLY CYS SER LYS PRO LEU CYS CYS SER SEQRES 14 B 211 CYS ALA LEU LEU ASP SER SER HIS SER GLU LEU LYS CYS SEQRES 15 B 211 ASP ILE SER ALA GLU ILE GLN GLN ARG GLN GLU GLU LEU SEQRES 16 B 211 ASP ALA MET THR GLN ALA LEU GLN GLU GLN ASP SER ALA SEQRES 17 B 211 PHE GLY ALA HELIX 1 AA1 GLU A 49 PHE A 54 1 6 HELIX 2 AA2 GLY A 79 SER A 84 1 6 HELIX 3 AA3 PHE A 109 VAL A 123 1 15 HELIX 4 AA4 GLN A 126 ARG A 131 1 6 HELIX 5 AA5 CYS A 132 PHE A 138 5 7 HELIX 6 AA6 ALA A 149 PHE A 158 1 10 HELIX 7 AA7 PRO A 165 ARG A 170 1 6 HELIX 8 AA8 VAL A 174 LYS A 183 1 10 HELIX 9 AA9 CYS A 213 LEU A 217 5 5 HELIX 10 AB1 GLU B 49 PHE B 54 1 6 HELIX 11 AB2 GLY B 79 SER B 84 1 6 HELIX 12 AB3 PHE B 109 VAL B 123 1 15 HELIX 13 AB4 GLN B 126 ARG B 131 1 6 HELIX 14 AB5 CYS B 132 PHE B 138 5 7 HELIX 15 AB6 ALA B 149 PHE B 158 1 10 HELIX 16 AB7 PRO B 165 ARG B 170 1 6 HELIX 17 AB8 VAL B 174 LYS B 183 1 10 HELIX 18 AB9 CYS B 213 LEU B 217 5 5 SHEET 1 AA1 2 TYR A 203 CYS A 204 0 SHEET 2 AA1 2 LYS A 209 PRO A 210 -1 N LYS A 209 O CYS A 204 SHEET 1 AA2 2 TYR B 203 CYS B 204 0 SHEET 2 AA2 2 LYS B 209 PRO B 210 -1 N LYS B 209 O CYS B 204 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 TER 1303 SER A 221 TER 2606 SER B 221 MASTER 224 0 0 18 4 0 0 6 2604 2 0 34 END