HEADER TRANSFERASE 21-JAN-26 22RD TITLE HIGH-RESOLUTION CRYO-EM STRUCTURE OF HUMAN POLO-LIKE KINASE 1 IN TITLE 2 COMPLEX WITH ONVANSERTIB COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PLK1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 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: PLK1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS SMALL PROTEIN-LIGAND COMPLEX, TRANSFERASE EXPDTA ELECTRON MICROSCOPY AUTHOR K.PARK,Y.YOO,H.JEON,K.CHOI,E.KWON,H.LIM,D.Y.KIM,K.T.NO REVDAT 1 29-APR-26 22RD 0 JRNL AUTH K.PARK,Y.YOO,H.JEON,K.CHOI,H.KIM,E.KWON,H.H.LIM,D.Y.KIM, JRNL AUTH 2 K.T.NO JRNL TITL HIGH-RESOLUTION CRYO-EM STRUCTURES OF SMALL PROTEIN-LIGAND JRNL TITL 2 COMPLEXES NEAR THE THEORETICAL SIZE LIMIT. JRNL REF NAT COMMUN 2026 JRNL REFN ESSN 2041-1723 JRNL PMID 41980966 JRNL DOI 10.1038/S41467-026-71934-7 REMARK 2 REMARK 2 RESOLUTION. 3.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX, PHENIX, COOT, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 2YAC REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 3.380 REMARK 3 NUMBER OF PARTICLES : 200803 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING ONLY REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 22RD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1300069038. 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 : HIGH-RESOLUTION CRYO-EM REMARK 245 STRUCTURE OF HUMAN POLO-LIKE REMARK 245 KINASE 1 IN COMPLEX WITH REMARK 245 ONVANSERTIB 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 6000.00 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: MONOMERIC 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 ALA A 13 REMARK 465 PRO A 14 REMARK 465 ALA A 15 REMARK 465 ASP A 16 REMARK 465 PRO A 17 REMARK 465 GLY A 18 REMARK 465 LYS A 19 REMARK 465 ALA A 20 REMARK 465 GLY A 21 REMARK 465 VAL A 22 REMARK 465 PRO A 23 REMARK 465 GLY A 24 REMARK 465 VAL A 25 REMARK 465 ALA A 26 REMARK 465 ALA A 27 REMARK 465 PRO A 28 REMARK 465 GLY A 29 REMARK 465 ALA A 30 REMARK 465 PRO A 31 REMARK 465 ALA A 32 REMARK 465 ALA A 33 REMARK 465 ALA A 34 REMARK 465 PRO A 35 REMARK 465 PRO A 36 REMARK 465 ALA A 37 REMARK 465 SER A 307 REMARK 465 GLY A 308 REMARK 465 TYR A 309 REMARK 465 ILE A 310 REMARK 465 PRO A 311 REMARK 465 ALA A 312 REMARK 465 ARG A 313 REMARK 465 LEU A 314 REMARK 465 PRO A 315 REMARK 465 ILE A 316 REMARK 465 THR A 317 REMARK 465 CYS A 318 REMARK 465 LEU A 319 REMARK 465 THR A 320 REMARK 465 ILE A 321 REMARK 465 PRO A 322 REMARK 465 PRO A 323 REMARK 465 ARG A 324 REMARK 465 PHE A 325 REMARK 465 SER A 326 REMARK 465 ILE A 327 REMARK 465 ALA A 328 REMARK 465 PRO A 329 REMARK 465 SER A 330 REMARK 465 SER A 331 REMARK 465 LEU A 332 REMARK 465 ASP A 333 REMARK 465 PRO A 334 REMARK 465 SER A 335 REMARK 465 ASN A 336 REMARK 465 ARG A 337 REMARK 465 LYS A 338 REMARK 465 PRO A 339 REMARK 465 LEU A 340 REMARK 465 THR A 341 REMARK 465 VAL A 342 REMARK 465 LEU A 343 REMARK 465 ASN A 344 REMARK 465 LYS A 345 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 LYS A 76 63.26 63.62 REMARK 500 PHE A 79 -169.05 -126.88 REMARK 500 ARG A 136 -125.11 61.72 REMARK 500 LYS A 146 -131.85 62.59 REMARK 500 LEU A 188 47.74 70.66 REMARK 500 PHE A 195 33.79 -87.54 REMARK 500 SER A 229 -159.13 -151.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-68616 RELATED DB: EMDB REMARK 900 HIGH-RESOLUTION CRYO-EM STRUCTURE OF HUMAN POLO-LIKE KINASE 1 IN REMARK 900 COMPLEX WITH ONVANSERTIB DBREF 22RD A 13 345 UNP P53350 PLK1_HUMAN 13 345 SEQADV 22RD VAL A 210 UNP P53350 THR 210 ENGINEERED MUTATION SEQRES 1 A 333 ALA PRO ALA ASP PRO GLY LYS ALA GLY VAL PRO GLY VAL SEQRES 2 A 333 ALA ALA PRO GLY ALA PRO ALA ALA ALA PRO PRO ALA LYS SEQRES 3 A 333 GLU ILE PRO GLU VAL LEU VAL ASP PRO ARG SER ARG ARG SEQRES 4 A 333 ARG TYR VAL ARG GLY ARG PHE LEU GLY LYS GLY GLY PHE SEQRES 5 A 333 ALA LYS CYS PHE GLU ILE SER ASP ALA ASP THR LYS GLU SEQRES 6 A 333 VAL PHE ALA GLY LYS ILE VAL PRO LYS SER LEU LEU LEU SEQRES 7 A 333 LYS PRO HIS GLN ARG GLU LYS MET SER MET GLU ILE SER SEQRES 8 A 333 ILE HIS ARG SER LEU ALA HIS GLN HIS VAL VAL GLY PHE SEQRES 9 A 333 HIS GLY PHE PHE GLU ASP ASN ASP PHE VAL PHE VAL VAL SEQRES 10 A 333 LEU GLU LEU CYS ARG ARG ARG SER LEU LEU GLU LEU HIS SEQRES 11 A 333 LYS ARG ARG LYS ALA LEU THR GLU PRO GLU ALA ARG TYR SEQRES 12 A 333 TYR LEU ARG GLN ILE VAL LEU GLY CYS GLN TYR LEU HIS SEQRES 13 A 333 ARG ASN ARG VAL ILE HIS ARG ASP LEU LYS LEU GLY ASN SEQRES 14 A 333 LEU PHE LEU ASN GLU ASP LEU GLU VAL LYS ILE GLY ASP SEQRES 15 A 333 PHE GLY LEU ALA THR LYS VAL GLU TYR ASP GLY GLU ARG SEQRES 16 A 333 LYS LYS VAL LEU CYS GLY THR PRO ASN TYR ILE ALA PRO SEQRES 17 A 333 GLU VAL LEU SER LYS LYS GLY HIS SER PHE GLU VAL ASP SEQRES 18 A 333 VAL TRP SER ILE GLY CYS ILE MET TYR THR LEU LEU VAL SEQRES 19 A 333 GLY LYS PRO PRO PHE GLU THR SER CYS LEU LYS GLU THR SEQRES 20 A 333 TYR LEU ARG ILE LYS LYS ASN GLU TYR SER ILE PRO LYS SEQRES 21 A 333 HIS ILE ASN PRO VAL ALA ALA SER LEU ILE GLN LYS MET SEQRES 22 A 333 LEU GLN THR ASP PRO THR ALA ARG PRO THR ILE ASN GLU SEQRES 23 A 333 LEU LEU ASN ASP GLU PHE PHE THR SER GLY TYR ILE PRO SEQRES 24 A 333 ALA ARG LEU PRO ILE THR CYS LEU THR ILE PRO PRO ARG SEQRES 25 A 333 PHE SER ILE ALA PRO SER SER LEU ASP PRO SER ASN ARG SEQRES 26 A 333 LYS PRO LEU THR VAL LEU ASN LYS HET 937 A 401 38 HETNAM 937 1-(2-HYDROXYETHYL)-8-[[5-(4-METHYLPIPERAZIN-1-YL)-2- HETNAM 2 937 (TRIFLUOROMETHOXY)PHENYL]AMINO]-4,5-DIHYDROPYRIMIDO[5, HETNAM 3 937 4-G]INDAZOLE-3-CARBOXAMIDE FORMUL 2 937 C24 H27 F3 N8 O3 HELIX 1 AA1 SER A 87 LEU A 90 5 4 HELIX 2 AA2 LYS A 91 LEU A 108 1 18 HELIX 3 AA3 SER A 137 ARG A 145 1 9 HELIX 4 AA4 THR A 149 ASN A 170 1 22 HELIX 5 AA5 ASP A 194 ALA A 198 5 5 HELIX 6 AA6 ALA A 219 SER A 224 1 6 HELIX 7 AA7 PHE A 230 VAL A 246 1 17 HELIX 8 AA8 CYS A 255 ASN A 266 1 12 HELIX 9 AA9 ASN A 275 LEU A 286 1 12 HELIX 10 AB1 GLU A 298 ASP A 302 5 5 SHEET 1 AA1 3 VAL A 43 VAL A 45 0 SHEET 2 AA1 3 ARG A 52 VAL A 54 -1 O TYR A 53 N LEU A 44 SHEET 3 AA1 3 SER A 71 ASP A 72 -1 O SER A 71 N VAL A 54 SHEET 1 AA2 5 PHE A 58 GLY A 62 0 SHEET 2 AA2 5 ALA A 65 PHE A 68 -1 O CYS A 67 N GLY A 60 SHEET 3 AA2 5 ALA A 80 PRO A 85 -1 O ILE A 83 N LYS A 66 SHEET 4 AA2 5 PHE A 125 LEU A 130 -1 O VAL A 128 N LYS A 82 SHEET 5 AA2 5 PHE A 116 ASP A 122 -1 N GLY A 118 O VAL A 129 SHEET 1 AA3 2 VAL A 172 ILE A 173 0 SHEET 2 AA3 2 THR A 199 LYS A 200 -1 O THR A 199 N ILE A 173 SHEET 1 AA4 2 LEU A 182 LEU A 184 0 SHEET 2 AA4 2 VAL A 190 ILE A 192 -1 O LYS A 191 N PHE A 183 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 CONECT 2196 2197 2199 CONECT 2197 2196 2198 2209 CONECT 2198 2197 2201 CONECT 2199 2196 2200 CONECT 2200 2199 2201 2203 CONECT 2201 2198 2200 2205 CONECT 2202 2203 2204 CONECT 2203 2200 2202 CONECT 2204 2202 2205 2208 CONECT 2205 2201 2204 2206 CONECT 2206 2205 2207 2224 CONECT 2207 2206 2208 CONECT 2208 2204 2207 2210 CONECT 2209 2197 2212 CONECT 2210 2208 2211 2223 CONECT 2211 2210 CONECT 2212 2209 2213 2217 CONECT 2213 2212 2214 CONECT 2214 2213 2215 2227 CONECT 2215 2214 2216 CONECT 2216 2215 2217 CONECT 2217 2212 2216 2218 CONECT 2218 2217 2219 CONECT 2219 2218 2220 2221 2222 CONECT 2220 2219 CONECT 2221 2219 CONECT 2222 2219 CONECT 2223 2210 CONECT 2224 2206 2225 CONECT 2225 2224 2226 CONECT 2226 2225 CONECT 2227 2214 2228 2232 CONECT 2228 2227 2229 CONECT 2229 2228 2230 CONECT 2230 2229 2231 2233 CONECT 2231 2230 2232 CONECT 2232 2227 2231 CONECT 2233 2230 MASTER 196 0 1 10 12 0 0 6 2232 1 38 26 END