HEADER TRANSFERASE/PROTEIN BINDING 13-APR-09 2KHW TITLE SOLUTION STRUCTURE OF THE HUMAN POLYMERASE IOTA UBM2-UBIQUITIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN G-BINDING PROTEIN G, DNA POLYMERASE IOTA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 304-357, 676-715; COMPND 5 SYNONYM: IGG-BINDING PROTEIN G, RAD30 HOMOLOG B, ETA2; COMPND 6 EC: 2.7.7.7; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SP., HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 1320, 9606; SOURCE 4 GENE: SPG, POLI, RAD30B; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET30-GB1-FUSION; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS UBM, UBIQUITIN-BINDING DOMAIN, POLYMERASE IOTA, TRANSLESION KEYWDS 2 SYNTHESIS, TLS, CYTOPLASM, NUCLEUS, PROTEIN BINDING, TRANSCRIPTION KEYWDS 3 REGULATOR ACTIVITY, TRANSFERASE-PROTEIN BINDING COMPLEX EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR M.G.BOMAR,S.D'SOUZA,M.BIENKO,I.DIKIC,G.WALKER REVDAT 2 16-MAR-22 2KHW 1 REMARK SEQADV REVDAT 1 23-FEB-10 2KHW 0 JRNL AUTH M.G.BOMAR,S.D'SOUZA,M.BIENKO,I.DIKIC,G.WALKER,P.ZHOU JRNL TITL SOLUTION STRUCTURE OF THE HUMAN POLYMERASE IOTA JRNL TITL 2 UBM2-UBIQUITIN COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.19 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KHW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000101141. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298 REMARK 210 PH : 7; 7; 7; 7 REMARK 210 IONIC STRENGTH : 100; 100; 100; 100 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] ENTITY_1-1, 4 REMARK 210 MM ENTITY_2-2, 90% H2O/10% D2O; REMARK 210 3 MM [U-100% 15N] ENTITY_1-3, 3 REMARK 210 MM [U-100% 15N] ENTITY_2-4, 90% REMARK 210 H2O/10% D2O; 3 MM [U-100% 13C; U- REMARK 210 100% 15N] ENTITY_1-5, 3 MM [U- REMARK 210 100% 13C; U-100% 15N] ENTITY_2-6, REMARK 210 100% D2O; 1 MM [U-100% 13C; U- REMARK 210 100% 15N] ENTITY_1-7, 4 MM REMARK 210 ENTITY_2-8, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HN(COCA)CB; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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 1-25 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLN A 2 REMARK 465 TYR A 3 REMARK 465 LYS A 4 REMARK 465 LEU A 5 REMARK 465 ILE A 6 REMARK 465 LEU A 7 REMARK 465 ASN A 8 REMARK 465 GLY A 9 REMARK 465 LYS A 10 REMARK 465 THR A 11 REMARK 465 LEU A 12 REMARK 465 LYS A 13 REMARK 465 GLY A 14 REMARK 465 GLU A 15 REMARK 465 THR A 16 REMARK 465 THR A 17 REMARK 465 THR A 18 REMARK 465 GLU A 19 REMARK 465 ALA A 20 REMARK 465 VAL A 21 REMARK 465 ASP A 22 REMARK 465 ALA A 23 REMARK 465 ALA A 24 REMARK 465 THR A 25 REMARK 465 ALA A 26 REMARK 465 GLU A 27 REMARK 465 LYS A 28 REMARK 465 VAL A 29 REMARK 465 PHE A 30 REMARK 465 LYS A 31 REMARK 465 GLN A 32 REMARK 465 TYR A 33 REMARK 465 ALA A 34 REMARK 465 ASN A 35 REMARK 465 ASP A 36 REMARK 465 ASN A 37 REMARK 465 GLY A 38 REMARK 465 VAL A 39 REMARK 465 ASP A 40 REMARK 465 GLY A 41 REMARK 465 GLU A 42 REMARK 465 TRP A 43 REMARK 465 THR A 44 REMARK 465 TYR A 45 REMARK 465 ASP A 46 REMARK 465 ASP A 47 REMARK 465 ALA A 48 REMARK 465 THR A 49 REMARK 465 LYS A 50 REMARK 465 THR A 51 REMARK 465 PHE A 52 REMARK 465 THR A 53 REMARK 465 VAL A 54 REMARK 465 THR A 55 REMARK 465 GLU A 56 REMARK 465 GLY A 57 REMARK 465 SER A 58 REMARK 465 ASP A 59 REMARK 465 GLU A 60 REMARK 465 SER A 93 REMARK 465 ASP A 94 REMARK 465 PHE A 95 REMARK 465 HIS A 96 REMARK 465 ILE A 97 REMARK 465 GLY A 98 REMARK 465 HIS A 99 REMARK 465 LYS A 100 REMARK 465 LEU A 101 REMARK 465 GLU A 102 REMARK 465 HIS A 103 REMARK 465 HIS A 104 REMARK 465 HIS A 105 REMARK 465 HIS A 106 REMARK 465 HIS A 107 REMARK 465 HIS A 108 REMARK 465 GLY B 198 REMARK 465 SER B 199 REMARK 465 HIS B 200 REMARK 465 GLY B 275 REMARK 465 GLY B 276 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 PRO A 65 164.84 -49.10 REMARK 500 1 GLU B 264 9.90 56.40 REMARK 500 1 ARG B 272 -139.05 -91.06 REMARK 500 2 PRO A 65 164.30 -48.22 REMARK 500 2 GLU B 264 10.48 59.18 REMARK 500 2 ARG B 272 -140.00 -95.04 REMARK 500 2 LEU B 273 -52.03 -124.84 REMARK 500 3 PRO A 65 165.36 -47.89 REMARK 500 3 GLU B 264 14.26 57.99 REMARK 500 3 ARG B 272 -137.57 -95.25 REMARK 500 4 PRO A 65 164.75 -48.04 REMARK 500 4 GLU B 264 10.46 55.37 REMARK 500 4 ARG B 272 -138.62 -93.21 REMARK 500 5 PRO A 65 165.56 -47.66 REMARK 500 5 ASP B 252 3.20 -68.60 REMARK 500 5 GLU B 264 13.14 57.85 REMARK 500 5 ARG B 272 -137.15 -98.46 REMARK 500 6 PRO A 65 165.18 -48.19 REMARK 500 6 LYS B 263 160.42 -49.76 REMARK 500 6 GLU B 264 13.58 56.58 REMARK 500 6 ARG B 272 -137.12 -96.33 REMARK 500 7 PRO A 65 164.61 -48.72 REMARK 500 7 ASP B 252 3.83 -66.95 REMARK 500 7 GLU B 264 13.38 56.42 REMARK 500 7 ARG B 272 -137.80 -95.76 REMARK 500 8 PRO A 65 164.72 -48.47 REMARK 500 8 ASP B 252 3.91 -68.91 REMARK 500 8 LYS B 263 160.53 -49.93 REMARK 500 8 GLU B 264 11.68 58.08 REMARK 500 8 ARG B 272 -140.76 -92.13 REMARK 500 9 PRO A 65 164.34 -48.32 REMARK 500 9 ASP B 252 3.77 -69.18 REMARK 500 9 GLU B 264 11.28 57.31 REMARK 500 9 ARG B 272 -141.73 -92.38 REMARK 500 9 LEU B 273 -54.36 -124.62 REMARK 500 10 PRO A 65 165.25 -48.20 REMARK 500 10 GLU B 264 13.36 57.36 REMARK 500 10 ARG B 272 -136.16 -98.69 REMARK 500 11 PRO A 65 164.75 -47.64 REMARK 500 11 ARG B 272 -136.26 -96.94 REMARK 500 12 PRO A 65 164.81 -48.12 REMARK 500 12 ASP B 252 4.16 -69.58 REMARK 500 12 GLU B 264 12.67 56.04 REMARK 500 12 ARG B 272 -137.31 -96.46 REMARK 500 13 PRO A 65 164.84 -48.25 REMARK 500 13 GLU B 264 12.42 56.33 REMARK 500 13 ARG B 272 -136.31 -97.69 REMARK 500 14 PRO A 65 164.13 -48.09 REMARK 500 14 ASP B 252 3.45 -69.26 REMARK 500 14 GLU B 264 12.43 57.87 REMARK 500 REMARK 500 THIS ENTRY HAS 86 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KHU RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE UBIQUITIN-BINDING MOTIF OF HUMAN REMARK 900 POLYMERASE IOTA REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO THE AUTHORS THE N-TERMINAL PART IS A GB1 REMARK 999 TAG USED FOR ENHANCEMENT OF PROTEIN SOLUBILITY. THEY REMARK 999 CHOSE TO DEPOSIT ONLY THE C-TERMINAL PART OF THE SEQUENCE REMARK 999 CORRESPONDING TO DNA POLYMERASE IOTA. THESE 2 SEGMENTS REMARK 999 ARE LINKED BY THE RESIDUES GSDE DBREF 2KHW A 3 56 UNP P19909 SPG2_STRSG 304 357 DBREF 2KHW A 61 100 UNP Q9UNA4 POLI_HUMAN 676 715 DBREF 2KHW B 201 276 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 2KHW MET A 1 UNP P19909 EXPRESSION TAG SEQADV 2KHW GLN A 2 UNP P19909 EXPRESSION TAG SEQADV 2KHW GLY A 57 UNP Q9UNA4 SEE REMARK 999 SEQADV 2KHW SER A 58 UNP Q9UNA4 SEE REMARK 999 SEQADV 2KHW ASP A 59 UNP Q9UNA4 SEE REMARK 999 SEQADV 2KHW GLU A 60 UNP Q9UNA4 SEE REMARK 999 SEQADV 2KHW LEU A 101 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KHW GLU A 102 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KHW HIS A 103 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KHW HIS A 104 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KHW HIS A 105 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KHW HIS A 106 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KHW HIS A 107 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KHW HIS A 108 UNP Q9UNA4 EXPRESSION TAG SEQADV 2KHW GLY B 198 UNP P62988 EXPRESSION TAG SEQADV 2KHW SER B 199 UNP P62988 EXPRESSION TAG SEQADV 2KHW HIS B 200 UNP P62988 EXPRESSION TAG SEQRES 1 A 108 MET GLN TYR LYS LEU ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 A 108 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 A 108 GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL SEQRES 4 A 108 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 A 108 THR VAL THR GLU GLY SER ASP GLU LYS ILE THR PHE PRO SEQRES 6 A 108 SER ASP ILE ASP PRO GLN VAL PHE TYR GLU LEU PRO GLU SEQRES 7 A 108 ALA VAL GLN LYS GLU LEU LEU ALA GLU TRP LYS ARG THR SEQRES 8 A 108 GLY SER ASP PHE HIS ILE GLY HIS LYS LEU GLU HIS HIS SEQRES 9 A 108 HIS HIS HIS HIS SEQRES 1 B 79 GLY SER HIS MET GLN ILE PHE VAL LYS THR LEU THR GLY SEQRES 2 B 79 LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE SEQRES 3 B 79 GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE SEQRES 4 B 79 PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN SEQRES 5 B 79 LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN SEQRES 6 B 79 LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY SEQRES 7 B 79 GLY HELIX 1 1 ASP A 69 TYR A 74 1 6 HELIX 2 2 PRO A 77 GLY A 92 1 16 HELIX 3 3 THR B 222 GLY B 235 1 14 HELIX 4 4 THR B 255 ASN B 260 5 6 SHEET 1 A 5 THR B 212 GLU B 216 0 SHEET 2 A 5 GLN B 202 LYS B 206 -1 N VAL B 205 O ILE B 213 SHEET 3 A 5 SER B 265 LEU B 271 1 O SER B 265 N PHE B 204 SHEET 4 A 5 GLN B 241 PHE B 245 -1 N ARG B 242 O VAL B 270 SHEET 5 A 5 LYS B 248 GLN B 249 -1 O LYS B 248 N PHE B 245 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