HEADER PROTEIN BINDING 13-MAY-25 9OMF TITLE CRYO-EM STRUCTURE OF NEDDYLATED PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5- TITLE 2 PCMTD1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE DOMAIN- COMPND 3 CONTAINING PROTEIN 1; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: CULLIN-5; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: CUL-5,VASOPRESSIN-ACTIVATED CALCIUM-MOBILIZING RECEPTOR 1, COMPND 11 VACM-1; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: RING-BOX PROTEIN 2; COMPND 15 CHAIN: C; COMPND 16 SYNONYM: RBX2,RING FINGER PROTEIN 7,SENSITIVE TO APOPTOSIS GENE COMPND 17 PROTEIN; COMPND 18 EC: 2.3.2.27,2.3.2.32; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: ELONGIN-B; COMPND 22 CHAIN: D; COMPND 23 SYNONYM: ELOB,ELONGIN 18 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION COMPND 24 FACTOR SIII SUBUNIT B,SIII P18,TRANSCRIPTION ELONGATION FACTOR B COMPND 25 POLYPEPTIDE 2; COMPND 26 ENGINEERED: YES; COMPND 27 MOL_ID: 5; COMPND 28 MOLECULE: ELONGIN-C; COMPND 29 CHAIN: E; COMPND 30 SYNONYM: ELOC,ELONGIN 15 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION COMPND 31 FACTOR SIII SUBUNIT C,SIII P15,TRANSCRIPTION ELONGATION FACTOR B COMPND 32 POLYPEPTIDE 1; COMPND 33 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: PCMTD1; 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: CUL5, VACM1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 17 ORGANISM_COMMON: MOUSE; SOURCE 18 ORGANISM_TAXID: 10090; SOURCE 19 GENE: RNF7, RBX2, SAG; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 MOL_ID: 4; SOURCE 23 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 24 ORGANISM_COMMON: HUMAN; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 GENE: ELOB, TCEB2; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 29 MOL_ID: 5; SOURCE 30 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 31 ORGANISM_COMMON: HUMAN; SOURCE 32 ORGANISM_TAXID: 9606; SOURCE 33 GENE: ELOC, TCEB1; SOURCE 34 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 35 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CUL5-RING UBIQUITIN LIGASE COMPLEX, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR E.Z.PANG,B.ZHAO,C.FLOWERS,E.OROUDJEVA,J.B.WINTERS,V.PANDEY, AUTHOR 2 M.R.SAWAYA,W.WOHLSCHLEGEL,J.A.LOO,J.A.RODRIGUEZ,S.G.CLARKE REVDAT 3 03-DEC-25 9OMF 1 JRNL REVDAT 2 18-JUN-25 9OMF 1 JRNL REVDAT 1 04-JUN-25 9OMF 0 JRNL AUTH E.Z.PANG,B.ZHAO,C.FLOWERS,E.OROUDJEVA,J.B.WINTER,V.PANDEY, JRNL AUTH 2 M.R.SAWAYA,J.WOHLSCHLEGEL,J.A.LOO,J.A.RODRIGUEZ,S.G.CLARKE JRNL TITL STRUCTURAL BASIS FOR L-ISOASPARTYL-CONTAINING PROTEIN JRNL TITL 2 RECOGNITION BY THE HUMAN PCMTD1 CULLIN-RING E3 UBIQUITIN JRNL TITL 3 LIGASE. JRNL REF J.BIOL.CHEM. V. 301 10735 2025 JRNL REFN ESSN 1083-351X JRNL PMID 40975169 JRNL DOI 10.1016/J.JBC.2025.110735 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.Z.PANG,B.ZHAO,C.FLOWERS,E.OROUDJEVA,J.B.WINTER,V.PANDEY, REMARK 1 AUTH 2 M.R.SAWAYA,J.WOHLSCHLEGEL,J.A.LOO,J.A.RODRIGUEZ,S.G.CLARKE REMARK 1 TITL STRUCTURAL BASIS FOR L-ISOASPARTYL-CONTAINING PROTEIN REMARK 1 TITL 2 RECOGNITION BY THE PCMTD1 CULLIN-RING E3 UBIQUITIN LIGASE. REMARK 1 REF BIORXIV 2025 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 40475564 REMARK 1 DOI 10.1101/2025.05.21.654933 REMARK 2 REMARK 2 RESOLUTION. 9.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, ROSETTA, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 9OMA REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : ENERGY MINIMIZED AGAINST 3D MAP OF N8-CRL5 REMARK 3 -PCMTD1 WITH MODEL OF CRL5-PCMTD1 (PDB: 9OMA) THEN REFINED IN REMARK 3 PHENIX 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) : 9.720 REMARK 3 NUMBER OF PARTICLES : 7521 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 9OMF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000295867. 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 : NEDDYLATED COMPLEX OF PCMTD1, REMARK 245 ELONGINS B AND C, CULLIN-5, AND REMARK 245 RING-BOX PROTEIN 2 (N8-CRL5- REMARK 245 PCMTD1) REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.30 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 : 15192 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : TFS FALCON 4I (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 SER A 0 REMARK 465 MET A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 VAL A 5 REMARK 465 SER A 6 REMARK 465 ALA A 7 REMARK 465 GLY A 8 REMARK 465 GLU A 9 REMARK 465 ALA A 265 REMARK 465 LYS A 266 REMARK 465 GLY A 267 REMARK 465 ILE A 268 REMARK 465 PRO A 269 REMARK 465 GLN A 270 REMARK 465 ARG A 271 REMARK 465 ALA A 272 REMARK 465 PRO A 273 REMARK 465 PRO A 274 REMARK 465 LYS A 275 REMARK 465 ARG A 276 REMARK 465 LYS A 277 REMARK 465 ARG A 278 REMARK 465 LYS A 279 REMARK 465 ARG A 280 REMARK 465 VAL A 281 REMARK 465 LYS A 282 REMARK 465 GLN A 283 REMARK 465 ARG A 284 REMARK 465 ILE A 285 REMARK 465 ASN A 286 REMARK 465 THR A 287 REMARK 465 TYR A 288 REMARK 465 VAL A 289 REMARK 465 PHE A 290 REMARK 465 VAL A 291 REMARK 465 GLY A 292 REMARK 465 ASN A 293 REMARK 465 GLN A 294 REMARK 465 LEU A 295 REMARK 465 ILE A 296 REMARK 465 PRO A 297 REMARK 465 GLN A 298 REMARK 465 PRO A 299 REMARK 465 LEU A 300 REMARK 465 ASP A 301 REMARK 465 SER A 302 REMARK 465 GLU A 303 REMARK 465 GLU A 304 REMARK 465 ASP A 305 REMARK 465 GLU A 306 REMARK 465 LYS A 307 REMARK 465 MET A 308 REMARK 465 GLU A 309 REMARK 465 GLU A 310 REMARK 465 ASP A 311 REMARK 465 ILE A 312 REMARK 465 LYS A 313 REMARK 465 GLU A 314 REMARK 465 GLU A 315 REMARK 465 GLU A 316 REMARK 465 GLU A 317 REMARK 465 LYS A 318 REMARK 465 ASP A 319 REMARK 465 HIS A 320 REMARK 465 ASN A 321 REMARK 465 GLU A 322 REMARK 465 ALA A 323 REMARK 465 MET A 324 REMARK 465 LYS A 325 REMARK 465 PRO A 326 REMARK 465 GLU A 327 REMARK 465 GLU A 328 REMARK 465 PRO A 329 REMARK 465 PRO A 330 REMARK 465 ARG A 355 REMARK 465 ASP A 356 REMARK 465 LYS A 357 REMARK 465 GLY B -2 REMARK 465 GLU B -1 REMARK 465 PHE B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 THR B 3 REMARK 465 SER B 4 REMARK 465 ASN B 5 REMARK 465 LEU B 6 REMARK 465 LEU B 7 REMARK 465 LYS B 8 REMARK 465 ASN B 9 REMARK 465 LYS B 10 REMARK 465 GLY B 11 REMARK 465 SER B 12 REMARK 465 LEU B 13 REMARK 465 GLN B 14 REMARK 465 PHE B 15 REMARK 465 ILE B 116 REMARK 465 THR B 117 REMARK 465 LEU B 118 REMARK 465 MET B 119 REMARK 465 GLY B 120 REMARK 465 LYS B 121 REMARK 465 GLN B 122 REMARK 465 GLY B 123 REMARK 465 SER B 124 REMARK 465 ASN B 125 REMARK 465 LYS B 126 REMARK 465 LYS B 127 REMARK 465 SER B 128 REMARK 465 ASN B 129 REMARK 465 VAL B 130 REMARK 465 ALA B 380 REMARK 465 THR B 381 REMARK 465 ILE B 382 REMARK 465 PHE B 383 REMARK 465 LYS B 384 REMARK 465 LEU B 385 REMARK 465 GLU B 386 REMARK 465 LEU B 387 REMARK 465 PRO B 388 REMARK 465 LEU B 389 REMARK 465 LYS B 390 REMARK 465 GLN B 391 REMARK 465 LYS B 392 REMARK 465 GLY B 393 REMARK 465 VAL B 394 REMARK 465 GLY B 395 REMARK 465 LEU B 396 REMARK 465 LYS B 397 REMARK 465 THR B 398 REMARK 465 GLN B 399 REMARK 465 PRO B 400 REMARK 465 GLU B 401 REMARK 465 SER B 402 REMARK 465 ASN B 516 REMARK 465 ASN B 517 REMARK 465 LYS B 518 REMARK 465 LEU B 519 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 ASP C 3 REMARK 465 VAL C 4 REMARK 465 GLU C 5 REMARK 465 ASP C 6 REMARK 465 GLY C 7 REMARK 465 GLU C 8 REMARK 465 GLU C 9 REMARK 465 PRO C 10 REMARK 465 CYS C 11 REMARK 465 VAL C 12 REMARK 465 LEU C 13 REMARK 465 SER C 14 REMARK 465 SER C 15 REMARK 465 HIS C 16 REMARK 465 SER C 17 REMARK 465 GLY C 18 REMARK 465 SER C 19 REMARK 465 ALA C 20 REMARK 465 GLY C 21 REMARK 465 SER C 22 REMARK 465 LYS C 23 REMARK 465 SER C 24 REMARK 465 GLY C 25 REMARK 465 GLY C 26 REMARK 465 ASP C 27 REMARK 465 LYS C 28 REMARK 465 LYS C 69 REMARK 465 GLN C 70 REMARK 465 GLU C 71 REMARK 465 MET D 1 REMARK 465 ALA D 78 REMARK 465 PHE D 79 REMARK 465 ARG D 80 REMARK 465 ALA D 81 REMARK 465 ASP D 82 REMARK 465 ASP D 83 REMARK 465 THR D 84 REMARK 465 PHE D 85 REMARK 465 GLU D 86 REMARK 465 ASP D 107 REMARK 465 SER D 108 REMARK 465 GLY D 109 REMARK 465 SER D 110 REMARK 465 SER D 111 REMARK 465 ALA D 112 REMARK 465 ASN D 113 REMARK 465 GLU D 114 REMARK 465 GLN D 115 REMARK 465 ALA D 116 REMARK 465 VAL D 117 REMARK 465 GLN D 118 REMARK 465 GLY E 34 REMARK 465 GLN E 35 REMARK 465 PHE E 36 REMARK 465 ALA E 37 REMARK 465 GLU E 38 REMARK 465 ASN E 39 REMARK 465 GLU E 40 REMARK 465 THR E 41 REMARK 465 CYS E 96 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 ARG A 25 -49.52 68.37 REMARK 500 TYR A 46 -57.50 -128.90 REMARK 500 ASP A 48 -27.71 -140.79 REMARK 500 LEU A 54 -162.53 -163.07 REMARK 500 SER A 64 78.23 -151.10 REMARK 500 PRO A 66 -138.00 -68.05 REMARK 500 HIS A 158 -132.91 -118.65 REMARK 500 ILE A 338 76.07 -110.02 REMARK 500 TYR A 350 -38.84 -131.72 REMARK 500 ASP B 17 40.47 -179.11 REMARK 500 TRP B 19 58.68 -98.31 REMARK 500 ILE B 106 -55.16 -122.55 REMARK 500 PRO B 110 -170.52 -69.93 REMARK 500 PHE B 111 77.14 71.90 REMARK 500 ASP B 132 22.39 -144.71 REMARK 500 GLN B 196 -102.37 -139.45 REMARK 500 PHE B 202 -73.31 -150.18 REMARK 500 GLU B 203 -70.52 -38.05 REMARK 500 CYS B 255 -8.96 -169.56 REMARK 500 THR B 334 -71.12 60.00 REMARK 500 LYS B 418 77.71 -67.37 REMARK 500 ASN B 586 -155.21 -136.21 REMARK 500 ARG B 609 56.28 -153.17 REMARK 500 ALA B 639 53.83 -143.94 REMARK 500 LEU B 694 -153.34 -113.55 REMARK 500 MET B 745 -60.91 -136.22 REMARK 500 PHE B 746 92.78 -172.04 REMARK 500 CYS C 73 78.10 -67.84 REMARK 500 CYS C 102 -143.16 -126.39 REMARK 500 GLN C 109 -50.24 -127.21 REMARK 500 HIS D 10 -117.52 49.17 REMARK 500 THR D 16 -157.29 -130.37 REMARK 500 ASP D 48 -8.34 86.22 REMARK 500 ASP D 52 -144.18 53.30 REMARK 500 ALA D 67 54.17 -150.90 REMARK 500 VAL D 102 -62.91 65.97 REMARK 500 LEU E 30 -40.72 71.37 REMARK 500 PHE E 46 77.41 -119.20 REMARK 500 SER E 71 -83.67 -92.96 REMARK 500 LEU E 94 -38.75 -136.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B 252 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9OMA RELATED DB: PDB REMARK 900 9OMA CONTAINS THE SAME PROTEIN COMPLEX BUT WITHOUT NEDDYLATION REMARK 900 RELATED ID: EMD-70612 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF NEDDYLATED PCMTD1-ELOBC-CUL5-RBX2 (N8-CRL5- REMARK 900 PCMTD1) DBREF 9OMF A 1 357 UNP Q96MG8 PCMD1_HUMAN 1 357 DBREF 9OMF B 1 780 UNP Q93034 CUL5_HUMAN 1 780 DBREF 9OMF C 1 113 UNP Q9WTZ1 RBX2_MOUSE 1 113 DBREF 9OMF D 1 118 UNP Q15370 ELOB_HUMAN 1 118 DBREF 9OMF E 1 96 UNP Q15369 ELOC_HUMAN 17 112 SEQADV 9OMF SER A 0 UNP Q96MG8 EXPRESSION TAG SEQADV 9OMF ILE A 312 UNP Q96MG8 ASN 312 VARIANT SEQADV 9OMF GLY B -2 UNP Q93034 EXPRESSION TAG SEQADV 9OMF GLU B -1 UNP Q93034 EXPRESSION TAG SEQADV 9OMF PHE B 0 UNP Q93034 EXPRESSION TAG SEQADV 9OMF TYR B 567 UNP Q93034 SER 567 CONFLICT SEQADV 9OMF VAL B 619 UNP Q93034 LEU 619 CONFLICT SEQADV 9OMF LEU B 767 UNP Q93034 ARG 767 CONFLICT SEQRES 1 A 358 SER MET GLY GLY ALA VAL SER ALA GLY GLU ASP ASN ASP SEQRES 2 A 358 ASP LEU ILE ASP ASN LEU LYS GLU ALA GLN TYR ILE ARG SEQRES 3 A 358 THR GLU ARG VAL GLU GLN ALA PHE ARG ALA ILE ASP ARG SEQRES 4 A 358 GLY ASP TYR TYR LEU GLU GLY TYR ARG ASP ASN ALA TYR SEQRES 5 A 358 LYS ASP LEU ALA TRP LYS HIS GLY ASN ILE HIS LEU SER SEQRES 6 A 358 ALA PRO CYS ILE TYR SER GLU VAL MET GLU ALA LEU LYS SEQRES 7 A 358 LEU GLN PRO GLY LEU SER PHE LEU ASN LEU GLY SER GLY SEQRES 8 A 358 THR GLY TYR LEU SER THR MET VAL GLY LEU ILE LEU GLY SEQRES 9 A 358 PRO PHE GLY ILE ASN HIS GLY ILE GLU LEU HIS SER ASP SEQRES 10 A 358 VAL VAL GLU TYR ALA LYS GLU LYS LEU GLU SER PHE ILE SEQRES 11 A 358 LYS ASN SER ASP SER PHE ASP LYS PHE GLU PHE CYS GLU SEQRES 12 A 358 PRO ALA PHE VAL VAL GLY ASN CYS LEU GLN ILE ALA SER SEQRES 13 A 358 ASP SER HIS GLN TYR ASP ARG ILE TYR CYS GLY ALA GLY SEQRES 14 A 358 VAL GLN LYS ASP HIS GLU ASN TYR MET LYS ILE LEU LEU SEQRES 15 A 358 LYS VAL GLY GLY ILE LEU VAL MET PRO ILE GLU ASP GLN SEQRES 16 A 358 LEU THR GLN ILE MET ARG THR GLY GLN ASN THR TRP GLU SEQRES 17 A 358 SER LYS ASN ILE LEU ALA VAL SER PHE ALA PRO LEU VAL SEQRES 18 A 358 GLN PRO SER LYS ASN ASP ASN GLY LYS PRO ASP SER VAL SEQRES 19 A 358 GLY LEU PRO PRO CYS ALA VAL ARG ASN LEU GLN ASP LEU SEQRES 20 A 358 ALA ARG ILE TYR ILE ARG ARG THR LEU ARG ASN PHE ILE SEQRES 21 A 358 ASN ASP GLU MET GLN ALA LYS GLY ILE PRO GLN ARG ALA SEQRES 22 A 358 PRO PRO LYS ARG LYS ARG LYS ARG VAL LYS GLN ARG ILE SEQRES 23 A 358 ASN THR TYR VAL PHE VAL GLY ASN GLN LEU ILE PRO GLN SEQRES 24 A 358 PRO LEU ASP SER GLU GLU ASP GLU LYS MET GLU GLU ASP SEQRES 25 A 358 ILE LYS GLU GLU GLU GLU LYS ASP HIS ASN GLU ALA MET SEQRES 26 A 358 LYS PRO GLU GLU PRO PRO GLN ASN LEU LEU ARG GLU LYS SEQRES 27 A 358 ILE MET LYS LEU PRO LEU PRO GLU SER LEU LYS ALA TYR SEQRES 28 A 358 LEU THR TYR PHE ARG ASP LYS SEQRES 1 B 783 GLY GLU PHE MET ALA THR SER ASN LEU LEU LYS ASN LYS SEQRES 2 B 783 GLY SER LEU GLN PHE GLU ASP LYS TRP ASP PHE MET ARG SEQRES 3 B 783 PRO ILE VAL LEU LYS LEU LEU ARG GLN GLU SER VAL THR SEQRES 4 B 783 LYS GLN GLN TRP PHE ASP LEU PHE SER ASP VAL HIS ALA SEQRES 5 B 783 VAL CYS LEU TRP ASP ASP LYS GLY PRO ALA LYS ILE HIS SEQRES 6 B 783 GLN ALA LEU LYS GLU ASP ILE LEU GLU PHE ILE LYS GLN SEQRES 7 B 783 ALA GLN ALA ARG VAL LEU SER HIS GLN ASP ASP THR ALA SEQRES 8 B 783 LEU LEU LYS ALA TYR ILE VAL GLU TRP ARG LYS PHE PHE SEQRES 9 B 783 THR GLN CYS ASP ILE LEU PRO LYS PRO PHE CYS GLN LEU SEQRES 10 B 783 GLU ILE THR LEU MET GLY LYS GLN GLY SER ASN LYS LYS SEQRES 11 B 783 SER ASN VAL GLU ASP SER ILE VAL ARG LYS LEU MET LEU SEQRES 12 B 783 ASP THR TRP ASN GLU SER ILE PHE SER ASN ILE LYS ASN SEQRES 13 B 783 ARG LEU GLN ASP SER ALA MET LYS LEU VAL HIS ALA GLU SEQRES 14 B 783 ARG LEU GLY GLU ALA PHE ASP SER GLN LEU VAL ILE GLY SEQRES 15 B 783 VAL ARG GLU SER TYR VAL ASN LEU CYS SER ASN PRO GLU SEQRES 16 B 783 ASP LYS LEU GLN ILE TYR ARG ASP ASN PHE GLU LYS ALA SEQRES 17 B 783 TYR LEU ASP SER THR GLU ARG PHE TYR ARG THR GLN ALA SEQRES 18 B 783 PRO SER TYR LEU GLN GLN ASN GLY VAL GLN ASN TYR MET SEQRES 19 B 783 LYS TYR ALA ASP ALA LYS LEU LYS GLU GLU GLU LYS ARG SEQRES 20 B 783 ALA LEU ARG TYR LEU GLU THR ARG ARG GLU CYS ASN SER SEQRES 21 B 783 VAL GLU ALA LEU MET GLU CYS CYS VAL ASN ALA LEU VAL SEQRES 22 B 783 THR SER PHE LYS GLU THR ILE LEU ALA GLU CYS GLN GLY SEQRES 23 B 783 MET ILE LYS ARG ASN GLU THR GLU LYS LEU HIS LEU MET SEQRES 24 B 783 PHE SER LEU MET ASP LYS VAL PRO ASN GLY ILE GLU PRO SEQRES 25 B 783 MET LEU LYS ASP LEU GLU GLU HIS ILE ILE SER ALA GLY SEQRES 26 B 783 LEU ALA ASP MET VAL ALA ALA ALA GLU THR ILE THR THR SEQRES 27 B 783 ASP SER GLU LYS TYR VAL GLU GLN LEU LEU THR LEU PHE SEQRES 28 B 783 ASN ARG PHE SER LYS LEU VAL LYS GLU ALA PHE GLN ASP SEQRES 29 B 783 ASP PRO ARG PHE LEU THR ALA ARG ASP LYS ALA TYR LYS SEQRES 30 B 783 ALA VAL VAL ASN ASP ALA THR ILE PHE LYS LEU GLU LEU SEQRES 31 B 783 PRO LEU LYS GLN LYS GLY VAL GLY LEU LYS THR GLN PRO SEQRES 32 B 783 GLU SER LYS CYS PRO GLU LEU LEU ALA ASN TYR CYS ASP SEQRES 33 B 783 MET LEU LEU ARG LYS THR PRO LEU SER LYS LYS LEU THR SEQRES 34 B 783 SER GLU GLU ILE GLU ALA LYS LEU LYS GLU VAL LEU LEU SEQRES 35 B 783 VAL LEU LYS TYR VAL GLN ASN LYS ASP VAL PHE MET ARG SEQRES 36 B 783 TYR HIS LYS ALA HIS LEU THR ARG ARG LEU ILE LEU ASP SEQRES 37 B 783 ILE SER ALA ASP SER GLU ILE GLU GLU ASN MET VAL GLU SEQRES 38 B 783 TRP LEU ARG GLU VAL GLY MET PRO ALA ASP TYR VAL ASN SEQRES 39 B 783 LYS LEU ALA ARG MET PHE GLN ASP ILE LYS VAL SER GLU SEQRES 40 B 783 ASP LEU ASN GLN ALA PHE LYS GLU MET HIS LYS ASN ASN SEQRES 41 B 783 LYS LEU ALA LEU PRO ALA ASP SER VAL ASN ILE LYS ILE SEQRES 42 B 783 LEU ASN ALA GLY ALA TRP SER ARG SER SER GLU LYS VAL SEQRES 43 B 783 PHE VAL SER LEU PRO THR GLU LEU GLU ASP LEU ILE PRO SEQRES 44 B 783 GLU VAL GLU GLU PHE TYR LYS LYS ASN HIS TYR GLY ARG SEQRES 45 B 783 LYS LEU HIS TRP HIS HIS LEU MET SER ASN GLY ILE ILE SEQRES 46 B 783 THR PHE LYS ASN GLU VAL GLY GLN TYR ASP LEU GLU VAL SEQRES 47 B 783 THR THR PHE GLN LEU ALA VAL LEU PHE ALA TRP ASN GLN SEQRES 48 B 783 ARG PRO ARG GLU LYS ILE SER PHE GLU ASN VAL LYS LEU SEQRES 49 B 783 ALA THR GLU LEU PRO ASP ALA GLU LEU ARG ARG THR LEU SEQRES 50 B 783 TRP SER LEU VAL ALA PHE PRO LYS LEU LYS ARG GLN VAL SEQRES 51 B 783 LEU LEU TYR GLU PRO GLN VAL ASN SER PRO LYS ASP PHE SEQRES 52 B 783 THR GLU GLY THR LEU PHE SER VAL ASN GLN GLU PHE SER SEQRES 53 B 783 LEU ILE LYS ASN ALA LYS VAL GLN LYS ARG GLY LYS ILE SEQRES 54 B 783 ASN LEU ILE GLY ARG LEU GLN LEU THR THR GLU ARG MET SEQRES 55 B 783 ARG GLU GLU GLU ASN GLU GLY ILE VAL GLN LEU ARG ILE SEQRES 56 B 783 LEU ARG THR GLN GLU ALA ILE ILE GLN ILE MET LYS MET SEQRES 57 B 783 ARG LYS LYS ILE SER ASN ALA GLN LEU GLN THR GLU LEU SEQRES 58 B 783 VAL GLU ILE LEU LYS ASN MET PHE LEU PRO GLN LYS LYS SEQRES 59 B 783 MET ILE LYS GLU GLN ILE GLU TRP LEU ILE GLU HIS LYS SEQRES 60 B 783 TYR ILE LEU ARG ASP GLU SER ASP ILE ASN THR PHE ILE SEQRES 61 B 783 TYR MET ALA SEQRES 1 C 113 MET ALA ASP VAL GLU ASP GLY GLU GLU PRO CYS VAL LEU SEQRES 2 C 113 SER SER HIS SER GLY SER ALA GLY SER LYS SER GLY GLY SEQRES 3 C 113 ASP LYS MET PHE SER LEU LYS LYS TRP ASN ALA VAL ALA SEQRES 4 C 113 MET TRP SER TRP ASP VAL GLU CYS ASP THR CYS ALA ILE SEQRES 5 C 113 CYS ARG VAL GLN VAL MET ASP ALA CYS LEU ARG CYS GLN SEQRES 6 C 113 ALA GLU ASN LYS GLN GLU ASP CYS VAL VAL VAL TRP GLY SEQRES 7 C 113 GLU CYS ASN HIS SER PHE HIS ASN CYS CYS MET SER LEU SEQRES 8 C 113 TRP VAL LYS GLN ASN ASN ARG CYS PRO LEU CYS GLN GLN SEQRES 9 C 113 ASP TRP VAL VAL GLN ARG ILE GLY LYS SEQRES 1 D 118 MET ASP VAL PHE LEU MET ILE ARG ARG HIS LYS THR THR SEQRES 2 D 118 ILE PHE THR ASP ALA LYS GLU SER SER THR VAL PHE GLU SEQRES 3 D 118 LEU LYS ARG ILE VAL GLU GLY ILE LEU LYS ARG PRO PRO SEQRES 4 D 118 ASP GLU GLN ARG LEU TYR LYS ASP ASP GLN LEU LEU ASP SEQRES 5 D 118 ASP GLY LYS THR LEU GLY GLU CYS GLY PHE THR SER GLN SEQRES 6 D 118 THR ALA ARG PRO GLN ALA PRO ALA THR VAL GLY LEU ALA SEQRES 7 D 118 PHE ARG ALA ASP ASP THR PHE GLU ALA LEU CYS ILE GLU SEQRES 8 D 118 PRO PHE SER SER PRO PRO GLU LEU PRO ASP VAL MET LYS SEQRES 9 D 118 PRO GLN ASP SER GLY SER SER ALA ASN GLU GLN ALA VAL SEQRES 10 D 118 GLN SEQRES 1 E 96 MET TYR VAL LYS LEU ILE SER SER ASP GLY HIS GLU PHE SEQRES 2 E 96 ILE VAL LYS ARG GLU HIS ALA LEU THR SER GLY THR ILE SEQRES 3 E 96 LYS ALA MET LEU SER GLY PRO GLY GLN PHE ALA GLU ASN SEQRES 4 E 96 GLU THR ASN GLU VAL ASN PHE ARG GLU ILE PRO SER HIS SEQRES 5 E 96 VAL LEU SER LYS VAL CYS MET TYR PHE THR TYR LYS VAL SEQRES 6 E 96 ARG TYR THR ASN SER SER THR GLU ILE PRO GLU PHE PRO SEQRES 7 E 96 ILE ALA PRO GLU ILE ALA LEU GLU LEU LEU MET ALA ALA SEQRES 8 E 96 ASN PHE LEU ASP CYS HELIX 1 AA1 ASN A 11 ALA A 21 1 11 HELIX 2 AA2 GLU A 27 ILE A 36 1 10 HELIX 3 AA3 ASP A 48 LYS A 52 5 5 HELIX 4 AA4 PRO A 66 LEU A 76 1 11 HELIX 5 AA5 GLY A 92 LEU A 102 1 11 HELIX 6 AA6 HIS A 114 SER A 132 1 19 HELIX 7 AA7 SER A 134 PHE A 138 5 5 HELIX 8 AA8 GLN A 170 HIS A 173 5 4 HELIX 9 AA9 GLU A 174 ILE A 179 1 6 HELIX 10 AB1 ASN A 242 MET A 263 1 22 HELIX 11 AB2 ASN A 332 GLU A 336 1 5 HELIX 12 AB3 PRO A 342 TYR A 350 1 9 HELIX 13 AB4 MET B 22 ARG B 31 1 10 HELIX 14 AB5 THR B 36 TRP B 53 1 18 HELIX 15 AB6 LYS B 56 SER B 82 1 27 HELIX 16 AB7 ASP B 85 CYS B 104 1 20 HELIX 17 AB8 SER B 133 ILE B 147 1 15 HELIX 18 AB9 ILE B 147 ARG B 167 1 21 HELIX 19 AC1 SER B 174 LEU B 187 1 14 HELIX 20 AC2 GLN B 196 PHE B 202 1 7 HELIX 21 AC3 PHE B 202 ALA B 218 1 17 HELIX 22 AC4 ALA B 218 GLN B 223 1 6 HELIX 23 AC5 GLY B 226 LEU B 249 1 24 HELIX 24 AC6 ASN B 256 VAL B 270 1 15 HELIX 25 AC7 VAL B 270 ARG B 287 1 18 HELIX 26 AC8 LYS B 292 ASP B 301 1 10 HELIX 27 AC9 VAL B 303 THR B 334 1 32 HELIX 28 AD1 ASP B 336 PHE B 359 1 24 HELIX 29 AD2 ASP B 362 LYS B 374 1 13 HELIX 30 AD3 GLU B 406 ARG B 417 1 12 HELIX 31 AD4 THR B 419 LEU B 425 1 7 HELIX 32 AD5 THR B 426 LYS B 442 1 17 HELIX 33 AD6 LYS B 447 LEU B 464 1 18 HELIX 34 AD7 ASP B 469 GLY B 484 1 16 HELIX 35 AD8 PRO B 486 ASN B 491 1 6 HELIX 36 AD9 ASN B 491 GLU B 512 1 22 HELIX 37 AE1 PRO B 522 ASP B 524 5 3 HELIX 38 AE2 GLY B 534 TRP B 536 5 3 HELIX 39 AE3 PRO B 548 ASP B 553 1 6 HELIX 40 AE4 LEU B 554 HIS B 566 1 13 HELIX 41 AE5 THR B 597 GLN B 608 1 12 HELIX 42 AE6 PHE B 616 GLU B 624 1 9 HELIX 43 AE7 PRO B 626 ALA B 639 1 14 HELIX 44 AE8 SER B 656 PHE B 660 5 5 HELIX 45 AE9 ILE B 689 LEU B 694 5 6 HELIX 46 AF1 GLU B 697 ARG B 726 1 30 HELIX 47 AF2 ASN B 731 LEU B 742 1 12 HELIX 48 AF3 LYS B 743 MET B 745 5 3 HELIX 49 AF4 GLN B 749 HIS B 763 1 15 HELIX 50 AF5 CYS C 61 GLN C 65 5 5 HELIX 51 AF6 CYS C 88 VAL C 93 1 6 HELIX 52 AF7 THR D 23 LYS D 36 1 14 HELIX 53 AF8 THR D 63 ALA D 67 5 5 HELIX 54 AF9 ARG E 17 LEU E 21 1 5 HELIX 55 AG1 SER E 23 MET E 29 1 7 HELIX 56 AG2 PRO E 50 TYR E 67 1 18 HELIX 57 AG3 ILE E 83 ASN E 92 1 10 SHEET 1 AA1 7 ALA A 144 VAL A 147 0 SHEET 2 AA1 7 ILE A 107 GLU A 112 1 N GLY A 110 O ALA A 144 SHEET 3 AA1 7 SER A 83 LEU A 87 1 N PHE A 84 O ILE A 107 SHEET 4 AA1 7 TYR A 160 CYS A 165 1 O TYR A 164 N LEU A 85 SHEET 5 AA1 7 LEU A 181 ILE A 191 1 O ILE A 186 N ILE A 163 SHEET 6 AA1 7 GLN A 194 ARG A 200 -1 O ILE A 198 N LEU A 187 SHEET 7 AA1 7 TRP A 206 ALA A 213 -1 O LYS A 209 N GLN A 197 SHEET 1 AA2 3 VAL B 526 ASN B 532 0 SHEET 2 AA2 3 LYS C 34 SER C 42 1 O ALA C 39 N LYS B 529 SHEET 3 AA2 3 LYS B 570 TRP B 573 -1 N HIS B 572 O MET C 40 SHEET 1 AA3 5 VAL B 526 ASN B 532 0 SHEET 2 AA3 5 LYS C 34 SER C 42 1 O ALA C 39 N LYS B 529 SHEET 3 AA3 5 ASN B 579 LYS B 585 -1 N ASN B 579 O ASN C 36 SHEET 4 AA3 5 GLN B 590 THR B 596 -1 O TYR B 591 N PHE B 584 SHEET 5 AA3 5 LYS B 685 ASN B 687 1 O ILE B 686 N GLU B 594 SHEET 1 AA4 3 ILE B 614 SER B 615 0 SHEET 2 AA4 3 LEU B 665 VAL B 668 -1 O PHE B 666 N ILE B 614 SHEET 3 AA4 3 LEU B 648 TYR B 650 -1 N LEU B 649 O SER B 667 SHEET 1 AA5 2 ILE B 675 LYS B 676 0 SHEET 2 AA5 2 LYS B 679 VAL B 680 -1 O LYS B 679 N LYS B 676 SHEET 1 AA6 3 LYS B 728 SER B 730 0 SHEET 2 AA6 3 ASP B 772 ILE B 777 -1 O PHE B 776 N ILE B 729 SHEET 3 AA6 3 LEU B 767 ASP B 769 -1 N LEU B 767 O ILE B 777 SHEET 1 AA7 2 VAL C 75 VAL C 76 0 SHEET 2 AA7 2 PHE C 84 HIS C 85 -1 O PHE C 84 N VAL C 76 SHEET 1 AA8 6 ALA D 73 VAL D 75 0 SHEET 2 AA8 6 VAL D 3 ARG D 9 1 N MET D 6 O ALA D 73 SHEET 3 AA8 6 THR D 12 ALA D 18 -1 O ILE D 14 N ILE D 7 SHEET 4 AA8 6 GLU E 12 LYS E 16 1 O ILE E 14 N THR D 13 SHEET 5 AA8 6 TYR E 2 ILE E 6 -1 N VAL E 3 O VAL E 15 SHEET 6 AA8 6 GLU E 43 ASN E 45 1 O VAL E 44 N LYS E 4 SSBOND 1 CYS C 50 CYS C 53 1555 1555 2.05 SSBOND 2 CYS C 61 CYS C 73 1555 1555 2.04 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 2233 PHE A 354 TER 8193 ALA B 780 TER 8857 LYS C 113 TER 9613 GLN D 106 TER 10305 ASP E 95 CONECT 8376 8395 CONECT 8395 8376 CONECT 8456 8526 CONECT 8526 8456 MASTER 398 0 0 57 31 0 0 610300 5 4 116 END