HEADER TRANSFERASE 06-APR-17 5VF0 TITLE SOLUTION NMR STRUCTURE OF HUMAN RAD18 (198-240) IN COMPLEX WITH TITLE 2 UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYUBIQUITIN-B; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RAD18; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: POSTREPLICATION REPAIR PROTEIN RAD18,HRAD18,RING FINGER COMPND 9 PROTEIN 73,RING-TYPE E3 UBIQUITIN TRANSFERASE RAD18; COMPND 10 EC: 2.3.2.27; COMPND 11 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: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: RAD18, RNF73; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PTEV KEYWDS UBIQUITIN LIGASE, UBIQUITIN, NUCLEOSOME, DNA DAMAGE RESPONSE, KEYWDS 2 TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Q.HU,M.V.BOTUYAN,G.MER REVDAT 5 14-JUN-23 5VF0 1 REMARK REVDAT 4 04-DEC-19 5VF0 1 REMARK REVDAT 3 20-SEP-17 5VF0 1 REMARK REVDAT 2 31-MAY-17 5VF0 1 JRNL REVDAT 1 17-MAY-17 5VF0 0 JRNL AUTH Q.HU,M.V.BOTUYAN,G.CUI,D.ZHAO,G.MER JRNL TITL MECHANISMS OF UBIQUITIN-NUCLEOSOME RECOGNITION AND JRNL TITL 2 REGULATION OF 53BP1 CHROMATIN RECRUITMENT BY RNF168/169 AND JRNL TITL 3 RAD18. JRNL REF MOL. CELL V. 66 473 2017 JRNL REFN ISSN 1097-4164 JRNL PMID 28506460 JRNL DOI 10.1016/J.MOLCEL.2017.04.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5VF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227316. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 50 MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-100% 13C; U-100% 15N] REMARK 210 RAD18, 3 MM UBIQUITIN, 25 MM MES- REMARK 210 BIS-TRIS, 50 MM KCL, 10 UM ZNCL2, REMARK 210 90% H2O/10% D2O; 3 MM RAD18, REMARK 210 0.6 MM [U-100% 13C; U-100% 15N] REMARK 210 UBIQUITIN, 25 MM MES-BIS-TRIS, REMARK 210 50 MM KCL, 10 UM ZNCL2, 90% H2O/ REMARK 210 10% D2O; 0.9 MM [U-15N] RAD18, REMARK 210 25 MM MES-BIS-TRIS, 50 MM KCL, REMARK 210 10 UM ZNCL2, 90% H2O/10% D2O; REMARK 210 0.9 MM [U-100% 13C; U-100% 15N] REMARK 210 RAD18, 25 MM MES-BIS-TRIS, 50 MM REMARK 210 KCL, 10 UM ZNCL2, 90% H2O/10% REMARK 210 D2O; 0.2 MM [U-100% 15N] RAD18, REMARK 210 1.0 MM UBIQUITIN, 25 MM MES-BIS- REMARK 210 TRIS, 50 MM KCL, 10 UM ZNCL2, 5 % REMARK 210 ALKYL-POLYETHYLENE GLYCOL REMARK 210 (C12E5)/N-HEXANOL MIXTURE, 90% REMARK 210 H2O/10% D2O; 1.0 MM RAD18, 0.2 REMARK 210 MM [U-100% 15N] UBIQUITIN, 25 MM REMARK 210 MES-BIS-TRIS, 50 MM KCL, 10 UM REMARK 210 ZNCL2, 5 % ALKYL-POLYETHYLENE REMARK 210 GLYCOL (C12E5)/N-HEXANOL MIXTURE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 15N/13C-FILTERED EDITED NOESY; REMARK 210 2D 1H-15N IPAP HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY B 195 REMARK 465 HIS B 196 REMARK 465 MET B 197 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 1 GLU A 64 83.65 55.19 REMARK 500 1 LEU A 73 -84.84 -47.03 REMARK 500 2 GLU A 64 84.98 54.42 REMARK 500 2 LYS B 230 38.38 -89.10 REMARK 500 2 SER B 232 34.84 73.05 REMARK 500 3 GLU A 64 99.00 54.28 REMARK 500 3 SER B 236 86.07 56.35 REMARK 500 4 ALA A 46 20.47 48.82 REMARK 500 4 GLU A 64 89.16 56.66 REMARK 500 5 GLU A 64 93.91 56.51 REMARK 500 5 SER B 232 91.71 -60.52 REMARK 500 6 GLU A 64 82.94 52.06 REMARK 500 7 GLU A 64 82.69 56.01 REMARK 500 7 GLU B 231 90.71 -69.94 REMARK 500 8 GLU A 64 89.50 51.78 REMARK 500 9 GLU A 64 83.80 56.66 REMARK 500 9 ARG B 234 83.44 -65.64 REMARK 500 10 ALA A 46 19.74 49.92 REMARK 500 10 GLU A 64 90.32 53.66 REMARK 500 10 SER B 232 176.10 70.09 REMARK 500 10 LEU B 233 158.29 -44.65 REMARK 500 10 SER B 235 37.23 -151.18 REMARK 500 11 ALA A 46 25.72 44.23 REMARK 500 11 GLU A 64 92.86 55.96 REMARK 500 12 GLU A 64 79.46 54.38 REMARK 500 12 ARG A 74 155.72 58.27 REMARK 500 12 GLU B 231 -75.22 63.53 REMARK 500 12 ARG B 234 -81.15 4.04 REMARK 500 13 ALA A 46 22.16 48.58 REMARK 500 13 GLU A 64 75.32 58.54 REMARK 500 13 GLU B 231 82.50 39.92 REMARK 500 14 GLU A 64 90.56 54.25 REMARK 500 14 GLU B 231 163.23 -49.71 REMARK 500 14 SER B 232 -165.99 55.98 REMARK 500 14 LEU B 233 -36.55 -135.15 REMARK 500 15 ALA A 46 17.14 56.11 REMARK 500 15 GLU A 64 87.64 52.80 REMARK 500 15 LYS B 230 -73.72 -63.50 REMARK 500 15 GLU B 231 85.54 40.55 REMARK 500 16 GLU A 64 91.69 56.52 REMARK 500 16 SER B 236 111.53 -169.91 REMARK 500 17 ALA A 46 18.30 53.94 REMARK 500 17 GLU A 64 81.88 55.44 REMARK 500 17 SER B 232 88.72 54.42 REMARK 500 17 SER B 235 -41.48 -146.98 REMARK 500 18 GLU A 64 87.27 55.45 REMARK 500 18 LEU B 233 97.94 55.14 REMARK 500 19 ALA A 46 31.47 70.73 REMARK 500 20 GLU A 64 75.87 55.50 REMARK 500 20 SER B 232 -34.84 -168.54 REMARK 500 REMARK 500 THIS ENTRY HAS 52 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 B 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 204 SG REMARK 620 2 CYS B 207 SG 107.8 REMARK 620 3 HIS B 219 NE2 107.3 109.6 REMARK 620 4 CYS B 223 SG 112.6 109.8 109.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30276 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF HUMAN RAD18 (198-240) IN COMPLEX WITH REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 5VEY RELATED DB: PDB DBREF 5VF0 A 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 5VF0 B 198 240 UNP Q9NS91 RAD18_HUMAN 198 240 SEQADV 5VF0 GLY B 195 UNP Q9NS91 EXPRESSION TAG SEQADV 5VF0 HIS B 196 UNP Q9NS91 EXPRESSION TAG SEQADV 5VF0 MET B 197 UNP Q9NS91 EXPRESSION TAG SEQRES 1 A 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 A 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 A 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 A 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 B 46 GLY HIS MET GLN VAL THR LYS VAL ASP CYS PRO VAL CYS SEQRES 2 B 46 GLY VAL ASN ILE PRO GLU SER HIS ILE ASN LYS HIS LEU SEQRES 3 B 46 ASP SER CYS LEU SER ARG GLU GLU LYS LYS GLU SER LEU SEQRES 4 B 46 ARG SER SER VAL HIS LYS ARG HET ZN B 300 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 AA1 THR A 22 GLY A 35 1 14 HELIX 2 AA2 LEU A 56 ASN A 60 5 5 HELIX 3 AA3 HIS B 215 GLU B 231 1 17 SHEET 1 AA1 5 THR A 12 GLU A 16 0 SHEET 2 AA1 5 GLN A 2 THR A 7 -1 N ILE A 3 O LEU A 15 SHEET 3 AA1 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 4 AA1 5 GLN A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 AA1 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 AA2 2 LYS B 201 VAL B 202 0 SHEET 2 AA2 2 ILE B 211 PRO B 212 -1 O ILE B 211 N VAL B 202 LINK SG CYS B 204 ZN ZN B 300 1555 1555 2.30 LINK SG CYS B 207 ZN ZN B 300 1555 1555 2.30 LINK NE2 HIS B 219 ZN ZN B 300 1555 1555 1.98 LINK SG CYS B 223 ZN ZN B 300 1555 1555 2.33 SITE 1 AC1 4 CYS B 204 CYS B 207 HIS B 219 CYS B 223 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1