HEADER PROTEIN BINDING/SIGNALING PROTEIN 19-APR-10 2KWU TITLE SOLUTION STRUCTURE OF UBM2 OF MURINE POLYMERASE IOTA IN COMPLEX WITH TITLE 2 UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE IOTA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL UBIQUITIN-BINDING MOTIF (UNP RESIDUES 673-717); COMPND 5 SYNONYM: RAD30 HOMOLOG B; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: UBIQUITIN; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: POLI, RAD30B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 STAR DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-4T-1; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21 STAR DE3; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PET-19B KEYWDS POLYMERASE IOTA, UBIQUITIN, UBIQUITIN-BINDING MOTIF, UBM, TLS, KEYWDS 2 PROTEIN BINDING-SIGNALING PROTEIN COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.BURSCHOWSKY,F.RUDOLF,G.RABUT,T.HERRMANN,M.PETER,G.WIDER REVDAT 3 16-FEB-11 2KWU 1 JRNL REVDAT 2 19-JAN-11 2KWU 1 JRNL REVDAT 1 06-OCT-10 2KWU 0 JRNL AUTH D.BURSCHOWSKY,F.RUDOLF,G.RABUT,T.HERRMANN,P.MATTHIAS,G.WIDER JRNL TITL STRUCTURAL ANALYSIS OF THE CONSERVED UBIQUITIN-BINDING JRNL TITL 2 MOTIFS (UBMS) OF THE TRANSLESION POLYMERASE IOTA IN COMPLEX JRNL TITL 3 WITH UBIQUITIN. JRNL REF J.BIOL.CHEM. V. 286 1364 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 20929865 JRNL DOI 10.1074/JBC.M110.135038 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KWU COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB101672. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.189 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MM [U-99% 15N] DNA REMARK 210 POLYMERASE IOTA UBM2, 4-8 MM REMARK 210 UBIQUITIN, 25 MM SODIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 100 MM POTASSIUM CHLORIDE, 2 MM REMARK 210 CHAPS, 0.15 MM PMSF, 0.2 % W/V REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O; 1-2 REMARK 210 MM [U-95% 13C; U-99% 15N] DNA REMARK 210 POLYMERASE IOTA UBM2, 4-8 MM REMARK 210 UBIQUITIN, 25 MM SODIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 100 MM POTASSIUM CHLORIDE, 2 MM REMARK 210 CHAPS, 0.15 MM PMSF, 0.2 % W/V REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O; 4-8 REMARK 210 MM DNA POLYMERASE IOTA UBM2, 1-2 REMARK 210 MM [U-99% 15N] UBIQUITIN, 25 MM REMARK 210 SODIUM PHOSPHATE, 25 MM SODIUM REMARK 210 CHLORIDE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 2 MM CHAPS, 0.15 MM REMARK 210 PMSF, 0.2 % W/V SODIUM AZIDE, 95% REMARK 210 H2O/5% D2O; 4-8 MM DNA POLYMERASE REMARK 210 IOTA UBM2, 1-2 MM [U-95% 13C; U- REMARK 210 99% 15N] UBIQUITIN, 25 MM SODIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 100 MM POTASSIUM CHLORIDE, 2 MM REMARK 210 CHAPS, 0.15 MM PMSF, 0.2 % W/V REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O; 1.7 REMARK 210 MM DNA POLYMERASE IOTA UBM2, 6.8 REMARK 210 MM [U-95% 13C; U-99% 15N] REMARK 210 UBIQUITIN, 25 MM SODIUM REMARK 210 PHOSPHATE, 25 MM SODIUM CHLORIDE, REMARK 210 100 MM POTASSIUM CHLORIDE, 2 MM REMARK 210 CHAPS, 0.15 MM PMSF, 0.2 % W/V REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D 1H-15N NOESY; 3D REMARK 210 1H-15N TOCSY; 3D 1H-13C NOESY; 3D REMARK 210 HCCH-COSY; 2D 1H-15N HSQC; 2D 1H- REMARK 210 13C HSQC; 3D 1H-13C-FILTERED-13C- REMARK 210 EDITED NOESY; 3D 1H-13C-AROMATIC REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, MOLMOL 2K.2, UNIO' REMARK 210 08 1.0.4, DYANA, CARA 1.8.4 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 A 668 REMARK 465 SER A 669 REMARK 465 PRO A 670 REMARK 465 GLU A 671 REMARK 465 PHE A 672 REMARK 465 ASP A 673 REMARK 465 SER A 674 REMARK 465 ALA A 711 REMARK 465 ARG A 712 REMARK 465 PRO A 713 REMARK 465 SER A 714 REMARK 465 ALA A 715 REMARK 465 HIS A 716 REMARK 465 ARG A 717 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 O GLU A 695 H LYS A 699 1.69 REMARK 500 OD2 ASP B 39 HH12 ARG B 74 1.75 REMARK 500 O LEU A 693 HE21 GLN A 698 1.76 REMARK 500 O ASN B 60 HE21 GLN B 62 1.79 REMARK 500 HZ1 LYS B 27 OD1 ASP B 52 1.79 REMARK 500 O GLU B 16 HZ3 LYS B 29 1.81 REMARK 500 O PRO B 37 H GLN B 40 1.81 REMARK 500 HZ1 LYS B 11 OE2 GLU B 34 1.81 REMARK 500 OE2 GLU A 704 H LEU B 73 1.83 REMARK 500 H THR B 7 O LYS B 11 1.84 REMARK 500 O PRO A 683 H ILE A 685 1.85 REMARK 500 OE2 GLU A 704 HH21 ARG A 707 1.85 REMARK 500 O ASP A 686 H VAL A 689 1.85 REMARK 500 O ASP A 686 H GLN A 688 1.86 REMARK 500 OE1 GLU A 700 HH22 ARG B 42 1.86 REMARK 500 O LEU B 73 H GLY B 75 1.86 REMARK 500 O ILE B 30 H GLU B 34 1.88 REMARK 500 O PHE B 45 H LYS B 48 1.88 REMARK 500 HE21 GLN B 40 O ARG B 72 1.88 REMARK 500 H LYS B 6 O LEU B 67 1.89 REMARK 500 O GLN B 40 H ARG B 72 1.90 REMARK 500 O LYS B 27 HE22 GLN B 41 1.90 REMARK 500 OE1 GLU A 700 HH12 ARG B 42 1.92 REMARK 500 OD1 ASP B 21 HD21 ASN B 25 1.92 REMARK 500 O GLN A 698 H MET A 702 1.94 REMARK 500 O VAL B 5 H ILE B 13 1.95 REMARK 500 HE21 GLN B 2 OE2 GLU B 16 1.97 REMARK 500 O ASN B 25 H LYS B 29 1.98 REMARK 500 O LEU B 56 H ILE B 61 1.98 REMARK 500 O LEU A 679 H PHE A 681 1.99 REMARK 500 O THR B 22 H ASN B 25 2.00 REMARK 500 O LYS B 29 H LYS B 33 2.02 REMARK 500 O LYS B 27 H GLN B 31 2.03 REMARK 500 O ILE B 44 H HIS B 68 2.03 REMARK 500 O VAL B 26 H ILE B 30 2.03 REMARK 500 O GLU B 18 H ASP B 21 2.04 REMARK 500 C ASP A 686 H GLN A 688 2.04 REMARK 500 C GLY B 47 H GLN B 49 2.05 REMARK 500 O ALA A 675 H GLU A 677 2.05 REMARK 500 OE2 GLU A 704 H ARG B 74 2.07 REMARK 500 O TYR A 691 H LEU A 693 2.07 REMARK 500 O PHE B 4 H LEU B 67 2.07 REMARK 500 H ILE B 44 O HIS B 68 2.08 REMARK 500 O THR B 7 H GLY B 10 2.09 REMARK 500 O PRO A 694 H VAL A 697 2.10 REMARK 500 H VAL B 5 O ILE B 13 2.11 REMARK 500 H GLU B 18 OD2 ASP B 21 2.12 REMARK 500 O THR B 7 H THR B 9 2.13 REMARK 500 O LYS B 29 H ASP B 32 2.13 REMARK 500 O THR B 14 HE3 LYS B 33 2.14 REMARK 500 REMARK 500 THIS ENTRY HAS 1097 CLOSE CONTACTS 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 GLU A 676 33.53 -77.42 REMARK 500 1 LEU A 679 170.07 -58.47 REMARK 500 1 PRO A 680 10.60 -60.89 REMARK 500 1 ASP A 684 -25.00 60.54 REMARK 500 1 PRO A 687 32.97 -76.16 REMARK 500 1 GLU A 692 37.64 -80.17 REMARK 500 1 GLU A 696 -15.45 -46.91 REMARK 500 1 GLN B 2 116.53 -179.39 REMARK 500 1 LEU B 8 13.14 -64.00 REMARK 500 1 PRO B 19 6.12 -69.68 REMARK 500 1 ARG B 42 55.63 -144.13 REMARK 500 1 ALA B 46 18.59 54.33 REMARK 500 1 LYS B 48 21.64 -79.50 REMARK 500 1 GLN B 49 92.57 10.81 REMARK 500 1 GLU B 51 -148.10 -100.15 REMARK 500 1 ASP B 52 22.46 -149.24 REMARK 500 1 ARG B 54 -164.74 -117.32 REMARK 500 1 GLU B 64 25.86 -141.05 REMARK 500 1 THR B 66 141.21 62.17 REMARK 500 1 ARG B 74 -65.85 64.28 REMARK 500 2 GLU A 677 17.03 -66.19 REMARK 500 2 PRO A 680 12.56 -65.35 REMARK 500 2 ASP A 684 -21.50 60.80 REMARK 500 2 GLU A 692 41.62 -72.40 REMARK 500 2 GLN B 2 -173.07 -170.04 REMARK 500 2 ASP B 21 -143.04 -70.48 REMARK 500 2 ALA B 46 26.23 179.43 REMARK 500 2 LYS B 48 94.98 -63.94 REMARK 500 2 LEU B 50 152.98 -49.85 REMARK 500 2 ARG B 54 -167.68 -120.81 REMARK 500 2 ILE B 61 122.74 -38.13 REMARK 500 2 GLU B 64 24.33 -148.92 REMARK 500 2 THR B 66 140.82 64.56 REMARK 500 2 VAL B 70 83.04 -66.87 REMARK 500 2 LEU B 73 -63.99 47.90 REMARK 500 2 ARG B 74 -57.92 60.80 REMARK 500 3 GLU A 676 42.65 -76.92 REMARK 500 3 PRO A 680 15.00 -63.25 REMARK 500 3 ASP A 684 -18.47 59.63 REMARK 500 3 GLU A 692 24.24 -72.74 REMARK 500 3 GLU A 695 -55.38 -16.96 REMARK 500 3 GLU A 696 -17.91 -48.21 REMARK 500 3 LEU B 8 17.48 -67.40 REMARK 500 3 ALA B 46 25.41 -178.47 REMARK 500 3 LYS B 48 76.12 -69.68 REMARK 500 3 ARG B 54 -169.06 -119.08 REMARK 500 3 LYS B 63 -90.28 -63.59 REMARK 500 3 GLU B 64 21.98 -67.37 REMARK 500 3 THR B 66 146.58 64.15 REMARK 500 3 VAL B 70 73.74 -152.24 REMARK 500 REMARK 500 THIS ENTRY HAS 331 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX: REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KHW RELATED DB: PDB REMARK 900 RELATED ID: 2KHU RELATED DB: PDB DBREF 2KWU A 673 717 UNP Q6R3M4 POLI_MOUSE 673 717 DBREF 2KWU B 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 2KWU GLY A 668 UNP Q6R3M4 EXPRESSION TAG SEQADV 2KWU SER A 669 UNP Q6R3M4 EXPRESSION TAG SEQADV 2KWU PRO A 670 UNP Q6R3M4 EXPRESSION TAG SEQADV 2KWU GLU A 671 UNP Q6R3M4 EXPRESSION TAG SEQADV 2KWU PHE A 672 UNP Q6R3M4 EXPRESSION TAG SEQRES 1 A 50 GLY SER PRO GLU PHE ASP SER ALA GLU GLU LYS LEU PRO SEQRES 2 A 50 PHE PRO PRO ASP ILE ASP PRO GLN VAL PHE TYR GLU LEU SEQRES 3 A 50 PRO GLU GLU VAL GLN LYS GLU LEU MET ALA GLU TRP GLU SEQRES 4 A 50 ARG ALA GLY ALA ALA ARG PRO SER ALA HIS ARG SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 1 PRO A 687 GLU A 692 1 6 HELIX 2 2 GLU A 695 ARG A 707 1 13 HELIX 3 4 PRO B 37 ASP B 39 5 3 HELIX 4 5 LEU B 56 ASN B 60 5 5 SHEET 1 A 5 THR B 12 GLU B 16 0 SHEET 2 A 5 GLN B 2 LYS B 6 -1 O ILE B 3 N LEU B 15 SHEET 3 A 5 THR B 66 LEU B 71 1 N LEU B 67 O PHE B 4 SHEET 4 A 5 GLN B 41 PHE B 45 -1 O ARG B 42 N VAL B 70 SHEET 5 A 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 CISPEP 1 PHE A 681 PRO A 682 1 -7.08 CISPEP 2 PHE A 681 PRO A 682 2 -7.48 CISPEP 3 PHE A 681 PRO A 682 3 -8.56 CISPEP 4 PHE A 681 PRO A 682 4 -8.39 CISPEP 5 PHE A 681 PRO A 682 5 -7.25 CISPEP 6 PHE A 681 PRO A 682 6 -6.41 CISPEP 7 PHE A 681 PRO A 682 7 -7.60 CISPEP 8 PHE A 681 PRO A 682 8 -6.41 CISPEP 9 PHE A 681 PRO A 682 9 -8.37 CISPEP 10 PHE A 681 PRO A 682 10 -8.08 CISPEP 11 PHE A 681 PRO A 682 11 -6.64 CISPEP 12 PHE A 681 PRO A 682 12 -10.46 CISPEP 13 PHE A 681 PRO A 682 13 -7.50 CISPEP 14 PHE A 681 PRO A 682 14 -7.27 CISPEP 15 PHE A 681 PRO A 682 15 -7.46 CISPEP 16 PHE A 681 PRO A 682 16 -6.65 CISPEP 17 PHE A 681 PRO A 682 17 -6.80 CISPEP 18 PHE A 681 PRO A 682 18 -8.02 CISPEP 19 PHE A 681 PRO A 682 19 -7.46 CISPEP 20 PHE A 681 PRO A 682 20 -5.81 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