HEADER TRANSFERASE 14-OCT-23 8QU8 TITLE PROTAC-MEDIATED COMPLEX OF KRAS WITH VHL/ELONGIN-B/ELONGIN-C/CULLIN- TITLE 2 2/RBX1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ELONGIN-B; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: ELOB,ELONGIN 18 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION COMPND 9 FACTOR SIII SUBUNIT B,SIII P18,TRANSCRIPTION ELONGATION FACTOR B COMPND 10 POLYPEPTIDE 2; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: ELONGIN-C; COMPND 14 CHAIN: C; COMPND 15 SYNONYM: ELOC,ELONGIN 15 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION COMPND 16 FACTOR SIII SUBUNIT C,SIII P15,TRANSCRIPTION ELONGATION FACTOR B COMPND 17 POLYPEPTIDE 1; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: CULLIN-2; COMPND 21 CHAIN: D; COMPND 22 SYNONYM: CUL-2; COMPND 23 ENGINEERED: YES; COMPND 24 MOL_ID: 5; COMPND 25 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RBX1, N-TERMINALLY PROCESSED; COMPND 26 CHAIN: E; COMPND 27 SYNONYM: E3 UBIQUITIN-PROTEIN TRANSFERASE RBX1,N-TERMINALLY COMPND 28 PROCESSED; COMPND 29 ENGINEERED: YES; COMPND 30 MOL_ID: 6; COMPND 31 MOLECULE: GTPASE KRAS; COMPND 32 CHAIN: F; COMPND 33 SYNONYM: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS; COMPND 34 EC: 3.6.5.2; COMPND 35 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: VHL; 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: ELOB, TCEB2; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: ELOC, TCEB1; 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: CUL2; 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: RBX1, RNF75, ROC1; SOURCE 34 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 35 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 36 MOL_ID: 6; SOURCE 37 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 38 ORGANISM_COMMON: HUMAN; SOURCE 39 ORGANISM_TAXID: 9606; SOURCE 40 GENE: KRAS, KRAS2, RASK2; SOURCE 41 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 42 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TARGETED PROTEIN DEGRADATION, PROTAC, GTPASE, TRANSFERASE EXPDTA ELECTRON MICROSCOPY AUTHOR G.FISCHER,D.PETER,S.ARCE-SOLANO REVDAT 2 24-JAN-24 8QU8 1 REMARK REVDAT 1 06-DEC-23 8QU8 0 JRNL AUTH J.POPOW,W.FARNABY,A.GOLLNER,C.KOFINK,G.FISCHER,M.WURM, JRNL AUTH 2 D.ZOLLMAN,A.WIJAYA,N.MISCHERIKOW,C.HASENOEHRL,P.PROKOFEVA, JRNL AUTH 3 H.ARNHOF,S.ARCE-SOLANO,S.BELL,G.BOECK,E.DIERS,A.FROST, JRNL AUTH 4 J.GOODWIN-TINDALL,J.KAROLYI-OEZGUER,S.KHAN,T.KLAWATSCH, JRNL AUTH 5 M.KOEGL,R.KOUSEK,B.KRATOCHVIL,K.KROPATSCH,A.LAUBER, JRNL AUTH 6 R.MCLENNAN,S.OLT,D.PETER,O.PETERMANN,V.ROESSLER, JRNL AUTH 7 P.STOLT-BERGNER,P.STRACK,E.STRAUSS,N.TRAINOR,V.VETMA, JRNL AUTH 8 C.WHITWORTH,S.ZHONG,J.QUANT,H.WEINSTABL,B.KUSTER,P.ETTMAYER, JRNL AUTH 9 A.CIULLI JRNL TITL TARGETING CANCER WITH SMALL MOLECULE PAN-KRAS DEGRADERS JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2023.10.24.563163 REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, EPU, CRYOSPARC, COOT, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 5N4W 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 217000 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: CRYOSPARC 3DFLEX RECONSTRUCTION REMARK 4 REMARK 4 8QU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1292133993. 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 : REMARK 245 KRAS/ACBI3/VHL/ELOB/ELOC/CUL2/RBX1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.92 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 : PROTAC-MEDIATED COMPLEX OF KRAS REMARK 245 WITH VHL/ELONGIN-B/ELONGIN-C/CULLIN-2/RBX1 REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 7634 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) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 165000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 74930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 ARG A 3 REMARK 465 ARG A 4 REMARK 465 ALA A 5 REMARK 465 GLU A 6 REMARK 465 ASN A 7 REMARK 465 TRP A 8 REMARK 465 ASP A 9 REMARK 465 GLU A 10 REMARK 465 ALA A 11 REMARK 465 GLU A 12 REMARK 465 VAL A 13 REMARK 465 GLY A 14 REMARK 465 ALA A 15 REMARK 465 GLU A 16 REMARK 465 GLU A 17 REMARK 465 ALA A 18 REMARK 465 GLY A 19 REMARK 465 VAL A 20 REMARK 465 GLU A 21 REMARK 465 GLU A 22 REMARK 465 TYR A 23 REMARK 465 GLY A 24 REMARK 465 PRO A 25 REMARK 465 GLU A 26 REMARK 465 GLU A 27 REMARK 465 ASP A 28 REMARK 465 GLY A 29 REMARK 465 GLY A 30 REMARK 465 GLU A 31 REMARK 465 GLU A 32 REMARK 465 SER A 33 REMARK 465 GLY A 34 REMARK 465 ALA A 35 REMARK 465 GLU A 36 REMARK 465 GLU A 37 REMARK 465 SER A 38 REMARK 465 GLY A 39 REMARK 465 PRO A 40 REMARK 465 GLU A 41 REMARK 465 GLU A 42 REMARK 465 SER A 43 REMARK 465 GLY A 44 REMARK 465 PRO A 45 REMARK 465 GLU A 46 REMARK 465 GLU A 47 REMARK 465 LEU A 48 REMARK 465 GLY A 49 REMARK 465 ALA A 50 REMARK 465 GLU A 51 REMARK 465 GLU A 52 REMARK 465 GLU A 53 REMARK 465 MET A 54 REMARK 465 GLU A 55 REMARK 465 ALA A 56 REMARK 465 GLY A 57 REMARK 465 ARG A 58 REMARK 465 PRO A 59 REMARK 465 ARG A 60 REMARK 465 PRO A 61 REMARK 465 VAL A 62 REMARK 465 LEU A 63 REMARK 465 ARG A 64 REMARK 465 SER A 65 REMARK 465 ARG A 205 REMARK 465 ILE A 206 REMARK 465 ALA A 207 REMARK 465 HIS A 208 REMARK 465 GLN A 209 REMARK 465 ARG A 210 REMARK 465 MET A 211 REMARK 465 GLY A 212 REMARK 465 ASP A 213 REMARK 465 PRO B 105 REMARK 465 GLN B 106 REMARK 465 ASP B 107 REMARK 465 SER B 108 REMARK 465 GLY B 109 REMARK 465 SER B 110 REMARK 465 SER B 111 REMARK 465 ALA B 112 REMARK 465 ASN B 113 REMARK 465 GLU B 114 REMARK 465 GLN B 115 REMARK 465 ALA B 116 REMARK 465 VAL B 117 REMARK 465 GLN B 118 REMARK 465 ASP C 2 REMARK 465 GLY C 3 REMARK 465 GLU C 4 REMARK 465 GLU C 5 REMARK 465 LYS C 6 REMARK 465 THR C 7 REMARK 465 TYR C 8 REMARK 465 GLY C 9 REMARK 465 GLY C 10 REMARK 465 CYS C 11 REMARK 465 GLU C 12 REMARK 465 GLY C 13 REMARK 465 PRO C 14 REMARK 465 ASP C 15 REMARK 465 ALA C 16 REMARK 465 GLU D 563 REMARK 465 VAL D 564 REMARK 465 LYS D 565 REMARK 465 MET D 566 REMARK 465 ASN D 567 REMARK 465 TYR D 568 REMARK 465 LEU D 569 REMARK 465 GLY D 570 REMARK 465 LYS D 571 REMARK 465 PRO D 572 REMARK 465 TYR D 573 REMARK 465 VAL D 574 REMARK 465 ALA D 575 REMARK 465 MET D 576 REMARK 465 ALA D 745 REMARK 465 ALA E 2 REMARK 465 ALA E 3 REMARK 465 ALA E 4 REMARK 465 MET E 5 REMARK 465 ASP E 6 REMARK 465 VAL E 7 REMARK 465 ASP E 8 REMARK 465 THR E 9 REMARK 465 PRO E 10 REMARK 465 SER E 11 REMARK 465 GLY E 12 REMARK 465 THR E 13 REMARK 465 ASN E 14 REMARK 465 PHE E 103 REMARK 465 GLN E 104 REMARK 465 LYS E 105 REMARK 465 TYR E 106 REMARK 465 GLY E 107 REMARK 465 HIS E 108 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 90 CG OD1 ND2 REMARK 470 GLN E 57 CG CD OE1 NE2 REMARK 470 TRP E 101 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP E 101 CZ3 CH2 REMARK 470 VAL F 12 CG1 CG2 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 SG CYS E 53 NE2 HIS E 82 2.05 REMARK 500 OG1 THR A 124 OD1 ASP A 126 2.10 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 PRO A 71 49.00 -88.61 REMARK 500 ASP A 143 48.99 31.73 REMARK 500 HIS B 10 -97.47 52.91 REMARK 500 ASP B 47 -2.89 69.34 REMARK 500 ASP B 48 -37.55 -130.72 REMARK 500 PHE B 62 -94.84 59.40 REMARK 500 THR B 63 164.19 63.08 REMARK 500 ASP B 82 52.46 -92.08 REMARK 500 ASP B 83 7.26 55.68 REMARK 500 GLU B 91 74.11 53.09 REMARK 500 PRO B 100 -168.70 -71.92 REMARK 500 PRO C 49 -175.26 -69.12 REMARK 500 ALA C 53 -1.35 66.69 REMARK 500 THR C 57 21.71 47.86 REMARK 500 GLU C 59 62.22 37.61 REMARK 500 ASN C 85 40.15 37.03 REMARK 500 PHE D 10 -6.59 71.68 REMARK 500 MET D 26 17.51 52.24 REMARK 500 GLU D 81 -9.08 72.82 REMARK 500 TYR D 105 30.56 -94.60 REMARK 500 GLU D 134 123.53 -33.24 REMARK 500 PRO D 154 -1.78 -56.53 REMARK 500 ASP D 175 70.99 57.46 REMARK 500 ALA D 272 -3.71 69.69 REMARK 500 ARG D 379 -14.22 72.98 REMARK 500 VAL D 384 11.31 46.34 REMARK 500 CYS D 385 -5.44 66.75 REMARK 500 LYS D 386 -99.43 52.83 REMARK 500 THR D 526 -103.96 46.66 REMARK 500 VAL D 584 -69.37 62.85 REMARK 500 LEU D 585 -164.04 58.72 REMARK 500 VAL D 594 -126.67 35.20 REMARK 500 LYS D 597 51.58 -91.56 REMARK 500 ILE D 623 -63.12 -122.99 REMARK 500 GLU D 628 -139.41 60.22 REMARK 500 MET D 642 -95.25 59.82 REMARK 500 SER D 646 -119.23 60.08 REMARK 500 ARG D 648 -117.90 36.20 REMARK 500 LYS D 650 -8.71 73.36 REMARK 500 SER D 656 172.31 63.97 REMARK 500 LYS D 659 -6.68 71.56 REMARK 500 ASP D 660 -138.54 47.97 REMARK 500 THR D 661 74.52 51.59 REMARK 500 PRO D 662 -2.48 -58.51 REMARK 500 GLN D 701 -6.07 72.25 REMARK 500 ARG E 21 -131.23 62.54 REMARK 500 ASP E 36 -3.42 68.95 REMARK 500 ASN E 41 28.87 48.67 REMARK 500 CYS E 42 -137.70 58.19 REMARK 500 ARG E 46 48.79 38.66 REMARK 500 REMARK 500 THIS ENTRY HAS 53 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 42 SG REMARK 620 2 CYS E 45 SG 109.0 REMARK 620 3 HIS E 80 ND1 119.0 118.0 REMARK 620 4 CYS E 83 SG 111.5 112.4 84.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 53 SG REMARK 620 2 CYS E 56 SG 112.1 REMARK 620 3 CYS E 68 SG 112.9 113.0 REMARK 620 4 HIS E 82 NE2 55.3 152.7 94.2 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-18657 RELATED DB: EMDB REMARK 900 PROTAC-MEDIATED COMPLEX OF KRAS WITH VHL/ELONGIN-B/ELONGIN-C/CULLIN- REMARK 900 2/RBX1 DBREF 8QU8 A 2 213 UNP P40337 VHL_HUMAN 2 213 DBREF 8QU8 B 2 118 UNP Q15370 ELOB_HUMAN 2 118 DBREF 8QU8 C 2 112 UNP Q15369 ELOC_HUMAN 2 112 DBREF 8QU8 D 2 745 UNP Q13617 CUL2_HUMAN 2 745 DBREF 8QU8 E 2 108 UNP P62877 RBX1_HUMAN 2 108 DBREF 8QU8 F 1 164 UNP P01116 RASK_HUMAN 1 164 SEQADV 8QU8 GLY F 0 UNP P01116 EXPRESSION TAG SEQADV 8QU8 VAL F 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 8QU8 SER F 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQADV 8QU8 GLY F 151 UNP P01116 ARG 151 VARIANT SEQADV 8QU8 ASP F 153 UNP P01116 GLU 153 VARIANT SEQADV 8QU8 LYS F 165 UNP P01116 EXPRESSION TAG SEQADV 8QU8 HIS F 166 UNP P01116 EXPRESSION TAG SEQADV 8QU8 LYS F 167 UNP P01116 EXPRESSION TAG SEQADV 8QU8 GLU F 168 UNP P01116 EXPRESSION TAG SEQADV 8QU8 LYS F 169 UNP P01116 EXPRESSION TAG SEQRES 1 A 212 PRO ARG ARG ALA GLU ASN TRP ASP GLU ALA GLU VAL GLY SEQRES 2 A 212 ALA GLU GLU ALA GLY VAL GLU GLU TYR GLY PRO GLU GLU SEQRES 3 A 212 ASP GLY GLY GLU GLU SER GLY ALA GLU GLU SER GLY PRO SEQRES 4 A 212 GLU GLU SER GLY PRO GLU GLU LEU GLY ALA GLU GLU GLU SEQRES 5 A 212 MET GLU ALA GLY ARG PRO ARG PRO VAL LEU ARG SER VAL SEQRES 6 A 212 ASN SER ARG GLU PRO SER GLN VAL ILE PHE CYS ASN ARG SEQRES 7 A 212 SER PRO ARG VAL VAL LEU PRO VAL TRP LEU ASN PHE ASP SEQRES 8 A 212 GLY GLU PRO GLN PRO TYR PRO THR LEU PRO PRO GLY THR SEQRES 9 A 212 GLY ARG ARG ILE HIS SER TYR ARG GLY HIS LEU TRP LEU SEQRES 10 A 212 PHE ARG ASP ALA GLY THR HIS ASP GLY LEU LEU VAL ASN SEQRES 11 A 212 GLN THR GLU LEU PHE VAL PRO SER LEU ASN VAL ASP GLY SEQRES 12 A 212 GLN PRO ILE PHE ALA ASN ILE THR LEU PRO VAL TYR THR SEQRES 13 A 212 LEU LYS GLU ARG CYS LEU GLN VAL VAL ARG SER LEU VAL SEQRES 14 A 212 LYS PRO GLU ASN TYR ARG ARG LEU ASP ILE VAL ARG SER SEQRES 15 A 212 LEU TYR GLU ASP LEU GLU ASP HIS PRO ASN VAL GLN LYS SEQRES 16 A 212 ASP LEU GLU ARG LEU THR GLN GLU ARG ILE ALA HIS GLN SEQRES 17 A 212 ARG MET GLY ASP SEQRES 1 B 117 ASP VAL PHE LEU MET ILE ARG ARG HIS LYS THR THR ILE SEQRES 2 B 117 PHE THR ASP ALA LYS GLU SER SER THR VAL PHE GLU LEU SEQRES 3 B 117 LYS ARG ILE VAL GLU GLY ILE LEU LYS ARG PRO PRO ASP SEQRES 4 B 117 GLU GLN ARG LEU TYR LYS ASP ASP GLN LEU LEU ASP ASP SEQRES 5 B 117 GLY LYS THR LEU GLY GLU CYS GLY PHE THR SER GLN THR SEQRES 6 B 117 ALA ARG PRO GLN ALA PRO ALA THR VAL GLY LEU ALA PHE SEQRES 7 B 117 ARG ALA ASP ASP THR PHE GLU ALA LEU CYS ILE GLU PRO SEQRES 8 B 117 PHE SER SER PRO PRO GLU LEU PRO ASP VAL MET LYS PRO SEQRES 9 B 117 GLN ASP SER GLY SER SER ALA ASN GLU GLN ALA VAL GLN SEQRES 1 C 111 ASP GLY GLU GLU LYS THR TYR GLY GLY CYS GLU GLY PRO SEQRES 2 C 111 ASP ALA MET TYR VAL LYS LEU ILE SER SER ASP GLY HIS SEQRES 3 C 111 GLU PHE ILE VAL LYS ARG GLU HIS ALA LEU THR SER GLY SEQRES 4 C 111 THR ILE LYS ALA MET LEU SER GLY PRO GLY GLN PHE ALA SEQRES 5 C 111 GLU ASN GLU THR ASN GLU VAL ASN PHE ARG GLU ILE PRO SEQRES 6 C 111 SER HIS VAL LEU SER LYS VAL CYS MET TYR PHE THR TYR SEQRES 7 C 111 LYS VAL ARG TYR THR ASN SER SER THR GLU ILE PRO GLU SEQRES 8 C 111 PHE PRO ILE ALA PRO GLU ILE ALA LEU GLU LEU LEU MET SEQRES 9 C 111 ALA ALA ASN PHE LEU ASP CYS SEQRES 1 D 744 SER LEU LYS PRO ARG VAL VAL ASP PHE ASP GLU THR TRP SEQRES 2 D 744 ASN LYS LEU LEU THR THR ILE LYS ALA VAL VAL MET LEU SEQRES 3 D 744 GLU TYR VAL GLU ARG ALA THR TRP ASN ASP ARG PHE SER SEQRES 4 D 744 ASP ILE TYR ALA LEU CYS VAL ALA TYR PRO GLU PRO LEU SEQRES 5 D 744 GLY GLU ARG LEU TYR THR GLU THR LYS ILE PHE LEU GLU SEQRES 6 D 744 ASN HIS VAL ARG HIS LEU HIS LYS ARG VAL LEU GLU SER SEQRES 7 D 744 GLU GLU GLN VAL LEU VAL MET TYR HIS ARG TYR TRP GLU SEQRES 8 D 744 GLU TYR SER LYS GLY ALA ASP TYR MET ASP CYS LEU TYR SEQRES 9 D 744 ARG TYR LEU ASN THR GLN PHE ILE LYS LYS ASN LYS LEU SEQRES 10 D 744 THR GLU ALA ASP LEU GLN TYR GLY TYR GLY GLY VAL ASP SEQRES 11 D 744 MET ASN GLU PRO LEU MET GLU ILE GLY GLU LEU ALA LEU SEQRES 12 D 744 ASP MET TRP ARG LYS LEU MET VAL GLU PRO LEU GLN ALA SEQRES 13 D 744 ILE LEU ILE ARG MET LEU LEU ARG GLU ILE LYS ASN ASP SEQRES 14 D 744 ARG GLY GLY GLU ASP PRO ASN GLN LYS VAL ILE HIS GLY SEQRES 15 D 744 VAL ILE ASN SER PHE VAL HIS VAL GLU GLN TYR LYS LYS SEQRES 16 D 744 LYS PHE PRO LEU LYS PHE TYR GLN GLU ILE PHE GLU SER SEQRES 17 D 744 PRO PHE LEU THR GLU THR GLY GLU TYR TYR LYS GLN GLU SEQRES 18 D 744 ALA SER ASN LEU LEU GLN GLU SER ASN CYS SER GLN TYR SEQRES 19 D 744 MET GLU LYS VAL LEU GLY ARG LEU LYS ASP GLU GLU ILE SEQRES 20 D 744 ARG CYS ARG LYS TYR LEU HIS PRO SER SER TYR THR LYS SEQRES 21 D 744 VAL ILE HIS GLU CYS GLN GLN ARG MET VAL ALA ASP HIS SEQRES 22 D 744 LEU GLN PHE LEU HIS ALA GLU CYS HIS ASN ILE ILE ARG SEQRES 23 D 744 GLN GLU LYS LYS ASN ASP MET ALA ASN MET TYR VAL LEU SEQRES 24 D 744 LEU ARG ALA VAL SER THR GLY LEU PRO HIS MET ILE GLN SEQRES 25 D 744 GLU LEU GLN ASN HIS ILE HIS ASP GLU GLY LEU ARG ALA SEQRES 26 D 744 THR SER ASN LEU THR GLN GLU ASN MET PRO THR LEU PHE SEQRES 27 D 744 VAL GLU SER VAL LEU GLU VAL HIS GLY LYS PHE VAL GLN SEQRES 28 D 744 LEU ILE ASN THR VAL LEU ASN GLY ASP GLN HIS PHE MET SEQRES 29 D 744 SER ALA LEU ASP LYS ALA LEU THR SER VAL VAL ASN TYR SEQRES 30 D 744 ARG GLU PRO LYS SER VAL CYS LYS ALA PRO GLU LEU LEU SEQRES 31 D 744 ALA LYS TYR CYS ASP ASN LEU LEU LYS LYS SER ALA LYS SEQRES 32 D 744 GLY MET THR GLU ASN GLU VAL GLU ASP ARG LEU THR SER SEQRES 33 D 744 PHE ILE THR VAL PHE LYS TYR ILE ASP ASP LYS ASP VAL SEQRES 34 D 744 PHE GLN LYS PHE TYR ALA ARG MET LEU ALA LYS ARG LEU SEQRES 35 D 744 ILE HIS GLY LEU SER MET SER MET ASP SER GLU GLU ALA SEQRES 36 D 744 MET ILE ASN LYS LEU LYS GLN ALA CYS GLY TYR GLU PHE SEQRES 37 D 744 THR SER LYS LEU HIS ARG MET TYR THR ASP MET SER VAL SEQRES 38 D 744 SER ALA ASP LEU ASN ASN LYS PHE ASN ASN PHE ILE LYS SEQRES 39 D 744 ASN GLN ASP THR VAL ILE ASP LEU GLY ILE SER PHE GLN SEQRES 40 D 744 ILE TYR VAL LEU GLN ALA GLY ALA TRP PRO LEU THR GLN SEQRES 41 D 744 ALA PRO SER SER THR PHE ALA ILE PRO GLN GLU LEU GLU SEQRES 42 D 744 LYS SER VAL GLN MET PHE GLU LEU PHE TYR SER GLN HIS SEQRES 43 D 744 PHE SER GLY ARG LYS LEU THR TRP LEU HIS TYR LEU CYS SEQRES 44 D 744 THR GLY GLU VAL LYS MET ASN TYR LEU GLY LYS PRO TYR SEQRES 45 D 744 VAL ALA MET VAL THR THR TYR GLN MET ALA VAL LEU LEU SEQRES 46 D 744 ALA PHE ASN ASN SER GLU THR VAL SER TYR LYS GLU LEU SEQRES 47 D 744 GLN ASP SER THR GLN MET ASN GLU LYS GLU LEU THR LYS SEQRES 48 D 744 THR ILE LYS SER LEU LEU ASP VAL LYS MET ILE ASN HIS SEQRES 49 D 744 ASP SER GLU LYS GLU ASP ILE ASP ALA GLU SER SER PHE SEQRES 50 D 744 SER LEU ASN MET ASN PHE SER SER LYS ARG THR LYS PHE SEQRES 51 D 744 LYS ILE THR THR SER MET GLN LYS ASP THR PRO GLN GLU SEQRES 52 D 744 MET GLU GLN THR ARG SER ALA VAL ASP GLU ASP ARG LYS SEQRES 53 D 744 MET TYR LEU GLN ALA ALA ILE VAL ARG ILE MET LYS ALA SEQRES 54 D 744 ARG LYS VAL LEU ARG HIS ASN ALA LEU ILE GLN GLU VAL SEQRES 55 D 744 ILE SER GLN SER ARG ALA ARG PHE ASN PRO SER ILE SER SEQRES 56 D 744 MET ILE LYS LYS CYS ILE GLU VAL LEU ILE ASP LYS GLN SEQRES 57 D 744 TYR ILE GLU ARG SER GLN ALA SER ALA ASP GLU TYR SER SEQRES 58 D 744 TYR VAL ALA SEQRES 1 E 107 ALA ALA ALA MET ASP VAL ASP THR PRO SER GLY THR ASN SEQRES 2 E 107 SER GLY ALA GLY LYS LYS ARG PHE GLU VAL LYS LYS TRP SEQRES 3 E 107 ASN ALA VAL ALA LEU TRP ALA TRP ASP ILE VAL VAL ASP SEQRES 4 E 107 ASN CYS ALA ILE CYS ARG ASN HIS ILE MET ASP LEU CYS SEQRES 5 E 107 ILE GLU CYS GLN ALA ASN GLN ALA SER ALA THR SER GLU SEQRES 6 E 107 GLU CYS THR VAL ALA TRP GLY VAL CYS ASN HIS ALA PHE SEQRES 7 E 107 HIS PHE HIS CYS ILE SER ARG TRP LEU LYS THR ARG GLN SEQRES 8 E 107 VAL CYS PRO LEU ASP ASN ARG GLU TRP GLU PHE GLN LYS SEQRES 9 E 107 TYR GLY HIS SEQRES 1 F 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA VAL SEQRES 2 F 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 F 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 F 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 F 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 F 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 F 170 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 F 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 F 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 F 170 LYS SER ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 F 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 F 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 F 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 F 170 LYS HET ZN E 201 1 HET ZN E 202 1 HET GDP F 201 28 HET WYL F 202 72 HETNAM ZN ZINC ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM WYL (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-AZANYL-3- HETNAM 2 WYL CYANO-4-METHYL-6,7-DIHYDRO-5H-1-BENZOTHIOPHEN-4-YL]-1, HETNAM 3 WYL 2,4-OXADIAZOL-3-YL]PYRIMIDIN-2-YL]-3-METHYL-1,4- HETNAM 4 WYL DIAZEPAN-1-YL]BUTOXY]-1,2,3-TRIAZOL-1-YL]-3-METHYL- HETNAM 5 WYL BUTANOYL]-N-[(1R)-1-[4-(4-METHYL-1,3-THIAZOL-5-YL) HETNAM 6 WYL PHENYL]-2-OXIDANYL-ETHYL]-4-OXIDANYL-PYRROLIDINE-2- HETNAM 7 WYL CARBOXAMIDE FORMUL 7 ZN 2(ZN 2+) FORMUL 9 GDP C10 H15 N5 O11 P2 FORMUL 10 WYL C50 H62 N14 O6 S2 HELIX 1 AA1 THR A 157 VAL A 170 1 14 HELIX 2 AA2 SER A 183 ASP A 190 1 8 HELIX 3 AA3 ASN A 193 ARG A 200 1 8 HELIX 4 AA4 THR B 23 LYS B 36 1 14 HELIX 5 AA5 PHE B 62 ALA B 67 1 6 HELIX 6 AA6 PRO B 100 LYS B 104 5 5 HELIX 7 AA7 ARG C 33 LEU C 37 1 5 HELIX 8 AA8 SER C 39 SER C 47 1 9 HELIX 9 AA9 PRO C 66 THR C 84 1 19 HELIX 10 AB1 ALA C 96 GLU C 98 5 3 HELIX 11 AB2 ILE C 99 ASP C 111 1 13 HELIX 12 AB3 GLU D 12 VAL D 25 1 14 HELIX 13 AB4 MET D 26 GLU D 28 5 3 HELIX 14 AB5 GLU D 31 VAL D 47 1 17 HELIX 15 AB6 LEU D 53 SER D 79 1 27 HELIX 16 AB7 GLN D 82 TYR D 105 1 24 HELIX 17 AB8 TYR D 105 ALA D 121 1 17 HELIX 18 AB9 TYR D 127 GLU D 134 1 8 HELIX 19 AC1 GLU D 138 GLU D 153 1 16 HELIX 20 AC2 PRO D 154 LYS D 168 1 15 HELIX 21 AC3 ASN D 169 GLY D 172 5 4 HELIX 22 AC4 ASN D 177 VAL D 191 1 15 HELIX 23 AC5 LEU D 200 PHE D 207 1 8 HELIX 24 AC6 PHE D 207 GLN D 228 1 22 HELIX 25 AC7 ASN D 231 LEU D 254 1 24 HELIX 26 AC8 HIS D 255 SER D 257 5 3 HELIX 27 AC9 SER D 258 VAL D 271 1 14 HELIX 28 AD1 HIS D 274 GLU D 281 1 8 HELIX 29 AD2 GLU D 281 GLN D 288 1 8 HELIX 30 AD3 LYS D 290 VAL D 304 1 15 HELIX 31 AD4 GLY D 307 ASN D 329 1 23 HELIX 32 AD5 PRO D 336 VAL D 357 1 22 HELIX 33 AD6 ASP D 361 ASN D 377 1 17 HELIX 34 AD7 LYS D 386 ASP D 396 1 11 HELIX 35 AD8 ASN D 397 LEU D 399 5 3 HELIX 36 AD9 GLU D 410 LYS D 423 1 14 HELIX 37 AE1 ASP D 427 GLY D 446 1 20 HELIX 38 AE2 GLU D 454 CYS D 465 1 12 HELIX 39 AE3 CYS D 465 LYS D 495 1 31 HELIX 40 AE4 PRO D 530 SER D 549 1 20 HELIX 41 AE5 LEU D 610 SER D 616 1 7 HELIX 42 AE6 GLN D 663 GLN D 681 1 19 HELIX 43 AE7 ALA D 682 ARG D 691 1 10 HELIX 44 AE8 ARG D 695 ILE D 700 1 6 HELIX 45 AE9 GLN D 701 ARG D 708 1 8 HELIX 46 AF1 SER D 714 ASP D 727 1 14 HELIX 47 AF2 VAL E 38 CYS E 42 5 5 HELIX 48 AF3 ILE E 54 ALA E 58 5 5 HELIX 49 AF4 ILE E 84 ARG E 91 1 8 HELIX 50 AF5 GLY F 15 ASN F 26 1 12 HELIX 51 AF6 SER F 65 THR F 74 1 10 HELIX 52 AF7 ASN F 86 ASP F 92 1 7 HELIX 53 AF8 ASP F 92 ASP F 105 1 14 HELIX 54 AF9 ASP F 126 GLY F 138 1 13 HELIX 55 AG1 GLY F 151 LYS F 169 1 19 SHEET 1 AA1 4 GLY A 106 HIS A 110 0 SHEET 2 AA1 4 GLN A 73 ASN A 78 -1 N VAL A 74 O ILE A 109 SHEET 3 AA1 4 ILE A 147 THR A 152 1 O ILE A 151 N CYS A 77 SHEET 4 AA1 4 LEU A 129 VAL A 130 -1 N LEU A 129 O THR A 152 SHEET 1 AA2 2 VAL A 84 TRP A 88 0 SHEET 2 AA2 2 TRP A 117 ASP A 121 -1 O LEU A 118 N VAL A 87 SHEET 1 AA3 7 ARG B 43 TYR B 45 0 SHEET 2 AA3 7 ALA B 73 ALA B 78 -1 O ALA B 78 N ARG B 43 SHEET 3 AA3 7 VAL B 3 ARG B 9 1 N MET B 6 O VAL B 75 SHEET 4 AA3 7 THR B 12 ALA B 18 -1 O ALA B 18 N VAL B 3 SHEET 5 AA3 7 GLU C 28 LYS C 32 1 O GLU C 28 N THR B 13 SHEET 6 AA3 7 TYR C 18 ILE C 22 -1 N LEU C 21 O PHE C 29 SHEET 7 AA3 7 VAL C 60 ASN C 61 1 O VAL C 60 N LYS C 20 SHEET 1 AA4 3 PHE D 507 VAL D 511 0 SHEET 2 AA4 3 TRP E 27 LEU E 32 1 O ALA E 29 N TYR D 510 SHEET 3 AA4 3 THR D 554 TRP D 555 -1 N THR D 554 O LEU E 32 SHEET 1 AA5 2 ALA E 71 TRP E 72 0 SHEET 2 AA5 2 ALA E 78 PHE E 79 -1 O PHE E 79 N ALA E 71 SHEET 1 AA6 6 ASP F 38 ILE F 46 0 SHEET 2 AA6 6 GLU F 49 ASP F 57 -1 O ILE F 55 N TYR F 40 SHEET 3 AA6 6 GLU F 3 GLY F 10 1 N TYR F 4 O ASP F 54 SHEET 4 AA6 6 GLY F 77 ALA F 83 1 O LEU F 79 N VAL F 7 SHEET 5 AA6 6 MET F 111 ASN F 116 1 O ASN F 116 N PHE F 82 SHEET 6 AA6 6 PHE F 141 GLU F 143 1 O ILE F 142 N GLY F 115 LINK SG CYS E 42 ZN ZN E 201 1555 1555 2.32 LINK SG CYS E 45 ZN ZN E 201 1555 1555 2.32 LINK SG CYS E 53 ZN ZN E 202 1555 1555 2.32 LINK SG CYS E 56 ZN ZN E 202 1555 1555 2.32 LINK SG CYS E 68 ZN ZN E 202 1555 1555 2.32 LINK ND1 HIS E 80 ZN ZN E 201 1555 1555 2.11 LINK NE2 HIS E 82 ZN ZN E 202 1555 1555 2.08 LINK SG CYS E 83 ZN ZN E 201 1555 1555 2.32 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