PDB Short entry for 2KWV HEADER PROTEIN BINDING/SIGNALING PROTEIN 20-APR-10 2KWV TITLE SOLUTION STRUCTURE OF UBM1 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 487-532); 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-2; 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 5 14-JUN-23 2KWV 1 REMARK REVDAT 4 05-FEB-20 2KWV 1 REMARK SEQADV REVDAT 3 16-FEB-11 2KWV 1 JRNL REVDAT 2 19-JAN-11 2KWV 1 JRNL REVDAT 1 06-OCT-10 2KWV 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 2KWV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000101673. 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 UBM1, 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- REMARK 210 2 MM [U-95% 13C; U-99% 15N] DNA REMARK 210 POLYMERASE IOTA UBM1, 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- REMARK 210 8 MM DNA POLYMERASE IOTA UBM1, 1- REMARK 210 2 MM [U-99% 15N] UBIQUITIN, 25 REMARK 210 MM SODIUM PHOSPHATE, 25 MM REMARK 210 SODIUM CHLORIDE, 100 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM CHAPS, REMARK 210 0.15 MM PMSF, 0.2 % W/V SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O; 4-8 MM REMARK 210 DNA POLYMERASE IOTA UBM1, 1-2 MM REMARK 210 [U-95% 13C; U-99% 15N] UBIQUITIN, REMARK 210 25 MM SODIUM PHOSPHATE, 25 MM REMARK 210 SODIUM CHLORIDE, 100 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM CHAPS, REMARK 210 0.15 MM PMSF, 0.2 % W/V SODIUM REMARK 210 AZIDE, 95% H2O/5% D2O; 1.0 MM REMARK 210 DNA POLYMERASE IOTA UBM1, 4 MM REMARK 210 [U-95% 13C; U-99% 15N] UBIQUITIN, REMARK 210 25 MM SODIUM PHOSPHATE, 25 MM REMARK 210 SODIUM CHLORIDE, 100 MM REMARK 210 POTASSIUM CHLORIDE, 2 MM CHAPS, REMARK 210 0.15 MM PMSF, 0.2 % W/V SODIUM REMARK 210 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; REMARK 210 3D HCCH-COSY; 2D 1H-15N HSQC; 2D REMARK 210 1H-13C HSQC; 3D 1H-13C-FILTERED- REMARK 210 13C-EDITED NOESY; 3D 1H-13C- REMARK 210 AROMATIC 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, REMARK 210 UNIO'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 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 A 485 REMARK 465 SER A 486 REMARK 465 ASP A 487 REMARK 465 THR A 488 REMARK 465 SER A 489 REMARK 465 ASP A 490 REMARK 465 GLY A 527 REMARK 465 LYS A 528 REMARK 465 GLY A 529 REMARK 465 SER A 530 REMARK 465 LEU A 531 REMARK 465 SER A 532 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 492 -166.92 -77.57 REMARK 500 1 LEU A 493 28.40 -65.06 REMARK 500 1 ASN A 524 28.79 -148.29 REMARK 500 1 LEU A 525 6.88 50.92 REMARK 500 1 LEU B 8 1.66 -65.89 REMARK 500 1 PRO B 19 2.24 -58.45 REMARK 500 1 GLU B 34 -31.25 -138.94 REMARK 500 1 ALA B 46 13.77 49.53 REMARK 500 1 ARG B 54 -154.40 -112.47 REMARK 500 1 ASN B 60 18.91 48.54 REMARK 500 1 THR B 66 128.19 61.36 REMARK 500 1 ARG B 74 -32.05 62.28 REMARK 500 2 LEU A 493 32.47 -68.40 REMARK 500 2 LYS A 520 -179.96 -61.54 REMARK 500 2 ASN A 524 19.40 -152.37 REMARK 500 2 LEU A 525 -15.10 63.02 REMARK 500 2 PRO B 19 3.57 -55.46 REMARK 500 2 GLU B 34 -34.53 -137.68 REMARK 500 2 ALA B 46 13.64 49.69 REMARK 500 2 ARG B 54 -154.13 -115.26 REMARK 500 2 ASN B 60 25.68 46.75 REMARK 500 2 THR B 66 135.79 60.99 REMARK 500 2 ARG B 74 -28.07 59.94 REMARK 500 3 PRO A 492 -164.03 -74.54 REMARK 500 3 LEU A 493 32.95 -70.33 REMARK 500 3 GLU A 498 35.82 -77.55 REMARK 500 3 SER A 518 27.66 -142.16 REMARK 500 3 LYS A 520 9.26 -64.41 REMARK 500 3 ASN A 524 32.17 -150.25 REMARK 500 3 LEU A 525 5.20 50.95 REMARK 500 3 PRO B 19 5.42 -58.69 REMARK 500 3 GLU B 34 -32.10 -135.16 REMARK 500 3 ARG B 54 -150.20 -121.14 REMARK 500 3 ARG B 74 -27.85 61.90 REMARK 500 4 PRO A 492 -163.74 -76.18 REMARK 500 4 LEU A 493 31.62 -67.94 REMARK 500 4 ASN A 524 10.70 -149.05 REMARK 500 4 LEU B 8 7.12 -67.33 REMARK 500 4 PRO B 19 2.86 -57.85 REMARK 500 4 GLU B 34 -32.80 -138.00 REMARK 500 4 ALA B 46 12.29 49.96 REMARK 500 4 ARG B 54 -154.04 -110.56 REMARK 500 4 ASN B 60 20.06 48.33 REMARK 500 4 THR B 66 126.07 59.87 REMARK 500 4 ARG B 74 -27.67 61.19 REMARK 500 5 PRO A 492 -162.64 -61.20 REMARK 500 5 LEU A 493 31.65 -87.05 REMARK 500 5 SER A 518 15.80 -146.38 REMARK 500 5 ASN A 524 17.43 -144.27 REMARK 500 5 PRO B 19 1.57 -54.72 REMARK 500 REMARK 500 THIS ENTRY HAS 241 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: 2KWU RELATED DB: PDB REMARK 900 RELATED ID: 16885 RELATED DB: BMRB DBREF 2KWV A 487 532 UNP Q6R3M4 POLI_MOUSE 487 532 DBREF 2KWV B 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 2KWV GLY A 485 UNP Q6R3M4 EXPRESSION TAG SEQADV 2KWV SER A 486 UNP Q6R3M4 EXPRESSION TAG SEQADV 2KWV SER A 518 UNP Q6R3M4 TYR 518 VARIANT SEQRES 1 A 48 GLY SER ASP THR SER ASP LEU PRO LEU GLN ALA LEU PRO SEQRES 2 A 48 GLU GLY VAL ASP GLN GLU VAL PHE LYS GLN LEU PRO ALA SEQRES 3 A 48 ASP ILE GLN GLU GLU ILE LEU SER GLY LYS SER ARG GLU SEQRES 4 A 48 ASN LEU LYS GLY LYS GLY SER LEU SER 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 GLN A 502 GLN A 507 5 6 HELIX 2 2 ALA A 510 LEU A 517 1 8 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 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