HEADER LIGASE 29-FEB-24 8S7E TITLE CRYO-EM STRUCTURE OF SKP1-FBXO22 COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-PHASE KINASE-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: A; 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 OTHER_DETAILS: S-PHASE KINASE-ASSOCIATED PROTEIN 1 (SKP1); COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: F-BOX ONLY PROTEIN 22; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: F-BOX PROTEIN FBX22P44; COMPND 14 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: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: FBXO22, FBX22; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS SKP1-FBXO22 E3 LIGASE SCF F-BOX PROTEIN, LIGASE EXPDTA ELECTRON MICROSCOPY AUTHOR M.KHOSHOUEI REVDAT 1 11-DEC-24 8S7E 0 JRNL AUTH M.KHOSHOUEI JRNL TITL CRYO-EM STRUCTURE OF SKP1-FBXO22 AT 3.4A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.40 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 : 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 717992 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8S7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292136936. 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 : SKP1-FBXO22 COMPLEX REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 16.00 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 TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 800.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1600.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 PRO A 2 REMARK 465 SER A 3 REMARK 465 ILE A 4 REMARK 465 LYS A 5 REMARK 465 LEU A 6 REMARK 465 GLN A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 ASP A 10 REMARK 465 GLY A 11 REMARK 465 GLU A 12 REMARK 465 ILE A 13 REMARK 465 PHE A 14 REMARK 465 GLU A 15 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 MET A 36 REMARK 465 ASP A 37 REMARK 465 ASP A 38 REMARK 465 GLU A 39 REMARK 465 GLY A 40 REMARK 465 ASP A 41 REMARK 465 ASP A 42 REMARK 465 ASP A 43 REMARK 465 PRO A 44 REMARK 465 GLU A 73 REMARK 465 ASP A 74 REMARK 465 ASP A 75 REMARK 465 GLU A 76 REMARK 465 ASN A 77 REMARK 465 LYS A 78 REMARK 465 GLY B 9 REMARK 465 GLY B 10 REMARK 465 SER B 11 REMARK 465 GLY B 12 REMARK 465 SER B 13 REMARK 465 SER B 14 REMARK 465 VAL B 15 REMARK 465 ASP B 16 REMARK 465 PRO B 17 REMARK 465 ARG B 18 REMARK 465 THR B 110 REMARK 465 PHE B 111 REMARK 465 ILE B 112 REMARK 465 SER B 113 REMARK 465 LEU B 114 REMARK 465 GLU B 115 REMARK 465 GLU B 116 REMARK 465 CYS B 117 REMARK 465 ARG B 118 REMARK 465 GLY B 119 REMARK 465 HIS B 120 REMARK 465 LYS B 121 REMARK 465 ARG B 122 REMARK 465 ALA B 123 REMARK 465 ARG B 124 REMARK 465 LYS B 125 REMARK 465 LYS B 197 REMARK 465 ASN B 198 REMARK 465 LEU B 199 REMARK 465 THR B 200 REMARK 465 CYS B 227 REMARK 465 CYS B 228 REMARK 465 LYS B 229 REMARK 465 VAL B 230 REMARK 465 GLY B 231 REMARK 465 ALA B 232 REMARK 465 SER B 233 REMARK 465 ASN B 234 REMARK 465 SER B 263 REMARK 465 GLU B 264 REMARK 465 LYS B 265 REMARK 465 ASN B 266 REMARK 465 PRO B 267 REMARK 465 LEU B 268 REMARK 465 ASP B 269 REMARK 465 ILE B 270 REMARK 465 ASP B 271 REMARK 465 ALA B 272 REMARK 465 SER B 273 REMARK 465 PHE B 373 REMARK 465 ILE B 374 REMARK 465 LEU B 375 REMARK 465 ARG B 376 REMARK 465 LYS B 377 REMARK 465 CYS B 378 REMARK 465 ASN B 379 REMARK 465 GLU B 380 REMARK 465 VAL B 381 REMARK 465 LYS B 382 REMARK 465 ASP B 383 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 H LEU B 103 O LEU B 177 1.54 REMARK 500 H MET B 323 O PHE B 355 1.56 REMARK 500 O GLY B 224 H VAL B 255 1.57 REMARK 500 H VAL B 222 O ALA B 251 1.59 REMARK 500 H PHE B 322 O ALA B 395 1.59 REMARK 500 HE1 TRP B 68 O THR B 156 1.59 REMARK 500 O ARG B 32 OG1 THR B 35 1.90 REMARK 500 OE1 GLU B 316 OG SER B 351 1.99 REMARK 500 O LEU B 103 N LEU B 177 2.03 REMARK 500 OG1 THR A 131 OE1 GLU A 134 2.14 REMARK 500 O MET B 158 ND2 ASN B 163 2.17 REMARK 500 O CYS A 62 N LYS A 66 2.17 REMARK 500 O VAL A 153 ND2 ASN A 157 2.17 REMARK 500 OG1 THR B 150 O GLY B 152 2.17 REMARK 500 OH TYR B 334 OE2 GLU B 341 2.18 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 HIS B 63 34.91 -99.44 REMARK 500 ALA B 74 46.74 38.57 REMARK 500 SER B 160 141.68 -171.06 REMARK 500 LEU B 261 130.84 -170.35 REMARK 500 SER B 287 -179.44 -172.17 REMARK 500 ASN B 293 -168.64 -79.78 REMARK 500 LYS B 337 113.01 -160.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-19768 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SKP1-FBXO22 DBREF 8S7E A 2 163 UNP P63208 SKP1_HUMAN 2 163 DBREF 8S7E B 12 403 UNP Q8NEZ5 FBX22_HUMAN 12 403 SEQADV 8S7E GLY B 9 UNP Q8NEZ5 EXPRESSION TAG SEQADV 8S7E GLY B 10 UNP Q8NEZ5 EXPRESSION TAG SEQADV 8S7E SER B 11 UNP Q8NEZ5 EXPRESSION TAG SEQRES 1 A 162 PRO SER ILE LYS LEU GLN SER SER ASP GLY GLU ILE PHE SEQRES 2 A 162 GLU VAL ASP VAL GLU ILE ALA LYS GLN SER VAL THR ILE SEQRES 3 A 162 LYS THR MET LEU GLU ASP LEU GLY MET ASP ASP GLU GLY SEQRES 4 A 162 ASP ASP ASP PRO VAL PRO LEU PRO ASN VAL ASN ALA ALA SEQRES 5 A 162 ILE LEU LYS LYS VAL ILE GLN TRP CYS THR HIS HIS LYS SEQRES 6 A 162 ASP ASP PRO PRO PRO PRO GLU ASP ASP GLU ASN LYS GLU SEQRES 7 A 162 LYS ARG THR ASP ASP ILE PRO VAL TRP ASP GLN GLU PHE SEQRES 8 A 162 LEU LYS VAL ASP GLN GLY THR LEU PHE GLU LEU ILE LEU SEQRES 9 A 162 ALA ALA ASN TYR LEU ASP ILE LYS GLY LEU LEU ASP VAL SEQRES 10 A 162 THR CYS LYS THR VAL ALA ASN MET ILE LYS GLY LYS THR SEQRES 11 A 162 PRO GLU GLU ILE ARG LYS THR PHE ASN ILE LYS ASN ASP SEQRES 12 A 162 PHE THR GLU GLU GLU GLU ALA GLN VAL ARG LYS GLU ASN SEQRES 13 A 162 GLN TRP CYS GLU GLU LYS SEQRES 1 B 395 GLY GLY SER GLY SER SER VAL ASP PRO ARG SER THR PHE SEQRES 2 B 395 VAL LEU SER ASN LEU ALA GLU VAL VAL GLU ARG VAL LEU SEQRES 3 B 395 THR PHE LEU PRO ALA LYS ALA LEU LEU ARG VAL ALA CYS SEQRES 4 B 395 VAL CYS ARG LEU TRP ARG GLU CYS VAL ARG ARG VAL LEU SEQRES 5 B 395 ARG THR HIS ARG SER VAL THR TRP ILE SER ALA GLY LEU SEQRES 6 B 395 ALA GLU ALA GLY HIS LEU GLU GLY HIS CYS LEU VAL ARG SEQRES 7 B 395 VAL VAL ALA GLU GLU LEU GLU ASN VAL ARG ILE LEU PRO SEQRES 8 B 395 HIS THR VAL LEU TYR MET ALA ASP SER GLU THR PHE ILE SEQRES 9 B 395 SER LEU GLU GLU CYS ARG GLY HIS LYS ARG ALA ARG LYS SEQRES 10 B 395 ARG THR SER MET GLU THR ALA LEU ALA LEU GLU LYS LEU SEQRES 11 B 395 PHE PRO LYS GLN CYS GLN VAL LEU GLY ILE VAL THR PRO SEQRES 12 B 395 GLY ILE VAL VAL THR PRO MET GLY SER GLY SER ASN ARG SEQRES 13 B 395 PRO GLN GLU ILE GLU ILE GLY GLU SER GLY PHE ALA LEU SEQRES 14 B 395 LEU PHE PRO GLN ILE GLU GLY ILE LYS ILE GLN PRO PHE SEQRES 15 B 395 HIS PHE ILE LYS ASP PRO LYS ASN LEU THR LEU GLU ARG SEQRES 16 B 395 HIS GLN LEU THR GLU VAL GLY LEU LEU ASP ASN PRO GLU SEQRES 17 B 395 LEU ARG VAL VAL LEU VAL PHE GLY TYR ASN CYS CYS LYS SEQRES 18 B 395 VAL GLY ALA SER ASN TYR LEU GLN GLN VAL VAL SER THR SEQRES 19 B 395 PHE SER ASP MET ASN ILE ILE LEU ALA GLY GLY GLN VAL SEQRES 20 B 395 ASP ASN LEU SER SER LEU THR SER GLU LYS ASN PRO LEU SEQRES 21 B 395 ASP ILE ASP ALA SER GLY VAL VAL GLY LEU SER PHE SER SEQRES 22 B 395 GLY HIS ARG ILE GLN SER ALA THR VAL LEU LEU ASN GLU SEQRES 23 B 395 ASP VAL SER ASP GLU LYS THR ALA GLU ALA ALA MET GLN SEQRES 24 B 395 ARG LEU LYS ALA ALA ASN ILE PRO GLU HIS ASN THR ILE SEQRES 25 B 395 GLY PHE MET PHE ALA CYS VAL GLY ARG GLY PHE GLN TYR SEQRES 26 B 395 TYR ARG ALA LYS GLY ASN VAL GLU ALA ASP ALA PHE ARG SEQRES 27 B 395 LYS PHE PHE PRO SER VAL PRO LEU PHE GLY PHE PHE GLY SEQRES 28 B 395 ASN GLY GLU ILE GLY CYS ASP ARG ILE VAL THR GLY ASN SEQRES 29 B 395 PHE ILE LEU ARG LYS CYS ASN GLU VAL LYS ASP ASP ASP SEQRES 30 B 395 LEU PHE HIS SER TYR THR THR ILE MET ALA LEU ILE HIS SEQRES 31 B 395 LEU GLY SER SER LYS HELIX 1 AA1 ASP A 17 SER A 24 1 8 HELIX 2 AA2 SER A 24 ASP A 33 1 10 HELIX 3 AA3 ASN A 51 LYS A 66 1 16 HELIX 4 AA4 PRO A 86 LYS A 94 1 9 HELIX 5 AA5 ASP A 96 ASP A 111 1 16 HELIX 6 AA6 ILE A 112 LYS A 128 1 17 HELIX 7 AA7 THR A 131 PHE A 139 1 9 HELIX 8 AA8 THR A 146 ASN A 157 1 12 HELIX 9 AA9 GLN A 158 GLU A 162 5 5 HELIX 10 AB1 LEU B 26 PHE B 36 1 11 HELIX 11 AB2 PRO B 38 CYS B 47 1 10 HELIX 12 AB3 CYS B 49 THR B 62 1 14 HELIX 13 AB4 HIS B 82 LEU B 92 1 11 HELIX 14 AB5 GLU B 130 PHE B 139 1 10 HELIX 15 AB6 GLU B 202 VAL B 209 1 8 HELIX 16 AB7 LEU B 236 ASP B 245 1 10 HELIX 17 AB8 ASP B 298 ALA B 312 1 15 HELIX 18 AB9 ASN B 339 PHE B 349 1 11 SHEET 1 AA1 3 GLN B 144 VAL B 145 0 SHEET 2 AA1 3 PRO B 99 ASP B 107 1 N VAL B 102 O GLN B 144 SHEET 3 AA1 3 ALA B 176 PRO B 180 -1 O LEU B 177 N LEU B 103 SHEET 1 AA2 4 GLN B 144 VAL B 145 0 SHEET 2 AA2 4 PRO B 99 ASP B 107 1 N VAL B 102 O GLN B 144 SHEET 3 AA2 4 ILE B 148 THR B 150 1 O ILE B 148 N TYR B 104 SHEET 4 AA2 4 ASN B 257 LEU B 258 -1 O ASN B 257 N VAL B 149 SHEET 1 AA3 7 GLN B 166 ILE B 168 0 SHEET 2 AA3 7 GLY B 152 VAL B 155 -1 N ILE B 153 O ILE B 168 SHEET 3 AA3 7 LEU B 354 GLY B 359 -1 O PHE B 358 N GLY B 152 SHEET 4 AA3 7 THR B 319 CYS B 326 1 N MET B 323 O PHE B 355 SHEET 5 AA3 7 THR B 392 HIS B 398 -1 O ILE B 397 N ILE B 320 SHEET 6 AA3 7 GLN B 286 LEU B 291 -1 N GLN B 286 O HIS B 398 SHEET 7 AA3 7 ILE B 368 THR B 370 -1 O VAL B 369 N SER B 287 SHEET 1 AA4 6 GLN B 188 PHE B 192 0 SHEET 2 AA4 6 VAL B 275 SER B 281 -1 O SER B 279 N GLN B 188 SHEET 3 AA4 6 LEU B 217 TYR B 225 -1 N ARG B 218 O PHE B 280 SHEET 4 AA4 6 ILE B 249 VAL B 255 1 O ALA B 251 N VAL B 222 SHEET 5 AA4 6 GLU B 362 ILE B 363 -1 O ILE B 363 N GLY B 252 SHEET 6 AA4 6 PHE B 387 HIS B 388 -1 O HIS B 388 N GLU B 362 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