HEADER LIGASE 30-OCT-24 9KBF TITLE CRYO-EM STRUCTURE OF THE SKP1-FBXO3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-PHASE KINASE-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: CYCLIN-A/CDK2-ASSOCIATED PROTEIN P19,P19A,ORGAN OF CORTI COMPND 5 PROTEIN 2,OCP-2,ORGAN OF CORTI PROTEIN II,OCP-II,RNA POLYMERASE II COMPND 6 ELONGATION FACTOR-LIKE PROTEIN,SIII,TRANSCRIPTION ELONGATION FACTOR B COMPND 7 POLYPEPTIDE 1-LIKE,P19SKP1; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: F-BOX ONLY PROTEIN 3; COMPND 11 CHAIN: C; COMPND 12 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: SKP1, EMC19, OCP2, SKP1A, TCEB1L; 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: FBXO3, FBX3; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CRYO-EM, PROTEIN BINDING, LIGASE EXPDTA ELECTRON MICROSCOPY AUTHOR J.WEI,C.XU REVDAT 2 26-FEB-25 9KBF 1 JRNL REVDAT 1 19-FEB-25 9KBF 0 JRNL AUTH J.WEI,C.XU JRNL TITL STRUCTURAL INSIGHT INTO THE SKP1-CUL1-FBXO3-RBX1 COMPLEX. JRNL REF PROTEINS 2025 JRNL REFN ESSN 1097-0134 JRNL PMID 39921442 JRNL DOI 10.1002/PROT.26809 REMARK 2 REMARK 2 RESOLUTION. 3.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL 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 : AB INITIO MODEL 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) : 3.740 REMARK 3 NUMBER OF PARTICLES : 185640 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 9KBF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 02-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053231. 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 : CRYO-EM OF THE CUL1-RBX1-SKP1 REMARK 245 -FBXO3 SCF UBIQUITION LIGASE REMARK 245 COMPLEX 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 : CRYO-EM OF THE CUL1-RBX1-SKP1 REMARK 245 -FBXO3 SCF UBIQUITION LIGASE COMPLEX 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 : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2900.00 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) : 5562.00 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: B, C 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 LYS B 163 REMARK 465 MET C 4 REMARK 465 GLU C 5 REMARK 465 THR C 6 REMARK 465 GLU C 7 REMARK 465 THR C 8 REMARK 465 ALA C 9 REMARK 465 PRO C 417 REMARK 465 ASP C 418 REMARK 465 GLU C 419 REMARK 465 TYR C 420 REMARK 465 GLU C 421 REMARK 465 GLU C 422 REMARK 465 MET C 423 REMARK 465 GLU C 424 REMARK 465 GLU C 425 REMARK 465 GLU C 426 REMARK 465 GLU C 427 REMARK 465 GLU C 428 REMARK 465 GLU C 429 REMARK 465 GLU C 430 REMARK 465 GLU C 431 REMARK 465 GLU C 432 REMARK 465 GLU C 433 REMARK 465 ASP C 434 REMARK 465 GLU C 435 REMARK 465 ASP C 436 REMARK 465 ASP C 437 REMARK 465 ASP C 438 REMARK 465 SER C 439 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 GLU B 76 -95.99 58.38 REMARK 500 TRP C 53 47.26 -91.09 REMARK 500 CYS C 111 108.67 -43.08 REMARK 500 LEU C 160 33.15 -97.27 REMARK 500 ILE C 200 -56.99 61.38 REMARK 500 ILE C 241 -60.15 -100.50 REMARK 500 ARG C 270 53.66 -92.07 REMARK 500 ARG C 332 77.70 -101.05 REMARK 500 VAL C 349 47.49 37.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62223 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF THE SKP1-FBXO3 COMPLEX DBREF 9KBF B 1 163 UNP P63208 SKP1_HUMAN 1 163 DBREF 9KBF C 4 439 UNP Q9UK99 FBX3_HUMAN 4 439 SEQRES 1 B 163 MET PRO SER ILE LYS LEU GLN SER SER ASP GLY GLU ILE SEQRES 2 B 163 PHE GLU VAL ASP VAL GLU ILE ALA LYS GLN SER VAL THR SEQRES 3 B 163 ILE LYS THR MET LEU GLU ASP LEU GLY MET ASP ASP GLU SEQRES 4 B 163 GLY ASP ASP ASP PRO VAL PRO LEU PRO ASN VAL ASN ALA SEQRES 5 B 163 ALA ILE LEU LYS LYS VAL ILE GLN TRP CYS THR HIS HIS SEQRES 6 B 163 LYS ASP ASP PRO PRO PRO PRO GLU ASP ASP GLU ASN LYS SEQRES 7 B 163 GLU LYS ARG THR ASP ASP ILE PRO VAL TRP ASP GLN GLU SEQRES 8 B 163 PHE LEU LYS VAL ASP GLN GLY THR LEU PHE GLU LEU ILE SEQRES 9 B 163 LEU ALA ALA ASN TYR LEU ASP ILE LYS GLY LEU LEU ASP SEQRES 10 B 163 VAL THR CYS LYS THR VAL ALA ASN MET ILE LYS GLY LYS SEQRES 11 B 163 THR PRO GLU GLU ILE ARG LYS THR PHE ASN ILE LYS ASN SEQRES 12 B 163 ASP PHE THR GLU GLU GLU GLU ALA GLN VAL ARG LYS GLU SEQRES 13 B 163 ASN GLN TRP CYS GLU GLU LYS SEQRES 1 C 436 MET GLU THR GLU THR ALA PRO LEU THR LEU GLU SER LEU SEQRES 2 C 436 PRO THR ASP PRO LEU LEU LEU ILE LEU SER PHE LEU ASP SEQRES 3 C 436 TYR ARG ASP LEU ILE ASN CYS CYS TYR VAL SER ARG ARG SEQRES 4 C 436 LEU SER GLN LEU SER SER HIS ASP PRO LEU TRP ARG ARG SEQRES 5 C 436 HIS CYS LYS LYS TYR TRP LEU ILE SER GLU GLU GLU LYS SEQRES 6 C 436 THR GLN LYS ASN GLN CYS TRP LYS SER LEU PHE ILE ASP SEQRES 7 C 436 THR TYR SER ASP VAL GLY ARG TYR ILE ASP HIS TYR ALA SEQRES 8 C 436 ALA ILE LYS LYS ALA TRP ASP ASP LEU LYS LYS TYR LEU SEQRES 9 C 436 GLU PRO ARG CYS PRO ARG MET VAL LEU SER LEU LYS GLU SEQRES 10 C 436 GLY ALA ARG GLU GLU ASP LEU ASP ALA VAL GLU ALA GLN SEQRES 11 C 436 ILE GLY CYS LYS LEU PRO ASP ASP TYR ARG CYS SER TYR SEQRES 12 C 436 ARG ILE HIS ASN GLY GLN LYS LEU VAL VAL PRO GLY LEU SEQRES 13 C 436 LEU GLY SER MET ALA LEU SER ASN HIS TYR ARG SER GLU SEQRES 14 C 436 ASP LEU LEU ASP VAL ASP THR ALA ALA GLY GLY PHE GLN SEQRES 15 C 436 GLN ARG GLN GLY LEU LYS TYR CYS LEU PRO LEU THR PHE SEQRES 16 C 436 CYS ILE HIS THR GLY LEU SER GLN TYR ILE ALA VAL GLU SEQRES 17 C 436 ALA ALA GLU GLY ARG ASN LYS ASN GLU VAL PHE TYR GLN SEQRES 18 C 436 CYS PRO ASP GLN MET ALA ARG ASN PRO ALA ALA ILE ASP SEQRES 19 C 436 MET PHE ILE ILE GLY ALA THR PHE THR ASP TRP PHE THR SEQRES 20 C 436 SER TYR VAL LYS ASN VAL VAL SER GLY GLY PHE PRO ILE SEQRES 21 C 436 ILE ARG ASP GLN ILE PHE ARG TYR VAL HIS ASP PRO GLU SEQRES 22 C 436 CYS VAL ALA THR THR GLY ASP ILE THR VAL SER VAL SER SEQRES 23 C 436 THR SER PHE LEU PRO GLU LEU SER SER VAL HIS PRO PRO SEQRES 24 C 436 HIS TYR PHE PHE THR TYR ARG ILE ARG ILE GLU MET SER SEQRES 25 C 436 LYS ASP ALA LEU PRO GLU LYS ALA CYS GLN LEU ASP SER SEQRES 26 C 436 ARG TYR TRP ARG ILE THR ASN ALA LYS GLY ASP VAL GLU SEQRES 27 C 436 GLU VAL GLN GLY PRO GLY VAL VAL GLY GLU PHE PRO ILE SEQRES 28 C 436 ILE SER PRO GLY ARG VAL TYR GLU TYR THR SER CYS THR SEQRES 29 C 436 THR PHE SER THR THR SER GLY TYR MET GLU GLY TYR TYR SEQRES 30 C 436 THR PHE HIS PHE LEU TYR PHE LYS ASP LYS ILE PHE ASN SEQRES 31 C 436 VAL ALA ILE PRO ARG PHE HIS MET ALA CYS PRO THR PHE SEQRES 32 C 436 ARG VAL SER ILE ALA ARG LEU GLU MET GLY PRO ASP GLU SEQRES 33 C 436 TYR GLU GLU MET GLU GLU GLU GLU GLU GLU GLU GLU GLU SEQRES 34 C 436 GLU ASP GLU ASP ASP ASP SER HELIX 1 AA1 VAL B 18 LYS B 22 1 5 HELIX 2 AA2 SER B 24 LEU B 34 1 11 HELIX 3 AA3 LEU B 34 GLU B 39 1 6 HELIX 4 AA4 ASN B 51 HIS B 65 1 15 HELIX 5 AA5 ASP B 75 GLU B 79 5 5 HELIX 6 AA6 PRO B 86 LEU B 93 1 8 HELIX 7 AA7 ASP B 96 ASP B 111 1 16 HELIX 8 AA8 ILE B 112 MET B 126 1 15 HELIX 9 AA9 THR B 131 PHE B 139 1 9 HELIX 10 AB1 THR B 146 GLN B 158 1 13 HELIX 11 AB2 PRO C 17 PHE C 27 1 11 HELIX 12 AB3 ASP C 29 TYR C 38 1 10 HELIX 13 AB4 SER C 40 SER C 48 1 9 HELIX 14 AB5 PRO C 51 HIS C 56 1 6 HELIX 15 AB6 SER C 64 ASN C 72 1 9 HELIX 16 AB7 CYS C 74 GLY C 87 1 14 HELIX 17 AB8 TYR C 89 LEU C 107 1 19 HELIX 18 AB9 CYS C 111 LEU C 118 1 8 HELIX 19 AC1 ARG C 123 GLY C 135 1 13 HELIX 20 AC2 PRO C 139 HIS C 149 1 11 HELIX 21 AC3 ASP C 176 GLY C 183 1 8 HELIX 22 AC4 THR C 244 SER C 258 1 15 HELIX 23 AC5 GLY C 347 GLU C 351 5 5 HELIX 24 AC6 SER C 409 MET C 415 1 7 SHEET 1 AA1 3 ILE B 13 ASP B 17 0 SHEET 2 AA1 3 SER B 3 GLN B 7 -1 N LEU B 6 O PHE B 14 SHEET 3 AA1 3 VAL B 45 PRO B 46 1 O VAL B 45 N LYS B 5 SHEET 1 AA2 2 SER C 162 ALA C 164 0 SHEET 2 AA2 2 TYR C 169 SER C 171 -1 O ARG C 170 N MET C 163 SHEET 1 AA3 2 ASP C 173 LEU C 174 0 SHEET 2 AA3 2 THR C 197 PHE C 198 -1 O PHE C 198 N ASP C 173 SHEET 1 AA4 4 GLN C 185 GLN C 186 0 SHEET 2 AA4 4 LYS C 191 PRO C 195 -1 O CYS C 193 N GLN C 185 SHEET 3 AA4 4 TYR C 207 ALA C 209 -1 O ILE C 208 N LEU C 194 SHEET 4 AA4 4 VAL C 221 PHE C 222 -1 O PHE C 222 N TYR C 207 SHEET 1 AA5 3 GLN C 224 PRO C 226 0 SHEET 2 AA5 3 ILE C 236 PHE C 239 -1 O ASP C 237 N CYS C 225 SHEET 3 AA5 3 PHE C 406 ARG C 407 -1 O ARG C 407 N MET C 238 SHEET 1 AA6 2 ILE C 263 ILE C 264 0 SHEET 2 AA6 2 GLN C 267 ILE C 268 -1 O GLN C 267 N ILE C 264 SHEET 1 AA7 3 ILE C 284 THR C 285 0 SHEET 2 AA7 3 PHE C 306 MET C 314 -1 O GLU C 313 N THR C 285 SHEET 3 AA7 3 VAL C 288 PHE C 292 -1 N SER C 291 O THR C 307 SHEET 1 AA8 3 ILE C 284 THR C 285 0 SHEET 2 AA8 3 PHE C 306 MET C 314 -1 O GLU C 313 N THR C 285 SHEET 3 AA8 3 VAL C 360 THR C 367 -1 O TYR C 361 N ILE C 312 SHEET 1 AA9 4 ILE C 354 ILE C 355 0 SHEET 2 AA9 4 CYS C 324 GLN C 325 -1 N CYS C 324 O ILE C 355 SHEET 3 AA9 4 PHE C 382 PHE C 384 -1 O HIS C 383 N GLN C 325 SHEET 4 AA9 4 ILE C 391 PHE C 392 -1 O PHE C 392 N PHE C 382 SHEET 1 AB1 4 VAL C 340 VAL C 343 0 SHEET 2 AB1 4 TYR C 330 THR C 334 -1 N ILE C 333 O GLU C 341 SHEET 3 AB1 4 GLY C 378 TYR C 379 -1 O TYR C 379 N TYR C 330 SHEET 4 AB1 4 ALA C 395 ILE C 396 -1 O ILE C 396 N GLY C 378 CISPEP 1 VAL C 156 PRO C 157 0 3.19 CISPEP 2 HIS C 300 PRO C 301 0 -0.72 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