HEADER NUCLEAR PROTEIN 16-JUN-10 2RR9 TITLE THE SOLUTION STRUCTURE OF THE K63-UB2:TUIMS COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN UIMC1; COMPND 7 CHAIN: C; COMPND 8 FRAGMENT: UNP RESIDUES 79-124; COMPND 9 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: UBC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET24A; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: UIMC1; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PET-ST2 KEYWDS LYS63-LINKED DIUBIQUITIN, UBIQUITIN-INTERACTING MOTIF, UBIQUITIN, KEYWDS 2 RAP80, DNA REPAIR, NUCLEAR PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.SEKIYAMA,J.JEE,S.ISOGAI,K.AKAGI,T.HUANG,M.ARIYOSHI,H.TOCHIO, AUTHOR 2 M.SHIRAKAWA REVDAT 1 06-JUL-11 2RR9 0 JRNL AUTH N.SEKIYAMA,J.JEE,S.ISOGAI,K.AKAGI,T.HUANG,M.ARIYOSHI, JRNL AUTH 2 H.TOCHIO,M.SHIRAKAWA JRNL TITL THE SOLUTION STRUCTURE OF THE K63-UB2:TUIMS COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RR9 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-10. REMARK 100 THE RCSB ID CODE IS RCSB150190. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.4 MM UBIQUITIN 1-1, 2.4 MM REMARK 210 UBIQUITIN 2-2, 2.4 MM [U-13C; U- REMARK 210 15N] TANDEM UIMS OF RAP80-3, 1 MM REMARK 210 DTT-4, 50 MM SODIUM PHOSPHATE-5, REMARK 210 90% H2O/10% D2O; 2 MM UBIQUITIN REMARK 210 1-6, 2 MM UBIQUITIN 2-7, 2 MM [U- REMARK 210 13C; U-15N; U-70% 2H] TANDEM UIMS REMARK 210 OF RAP80-8, 1 MM DTT-9, 50 MM REMARK 210 SODIUM PHOSPHATE-10, 90% H2O/10% REMARK 210 D2O; 2.9 MM [U-13C; U-15N] REMARK 210 UBIQUITIN 1-11, 2.9 MM UBIQUITIN REMARK 210 2-12, 2.9 MM TANDEM UIMS OF REMARK 210 RAP80-13, 1 MM DTT-14, 50 MM REMARK 210 SODIUM PHOSPHATE-15, 90% H2O/10% REMARK 210 D2O; 2.9 MM UBIQUITIN 1-16, 2.9 REMARK 210 MM [U-13C; U-15N] UBIQUITIN 2-17, REMARK 210 2.9 MM TANDEM UIMS OF RAP80-18, 1 REMARK 210 MM DTT-19, 50 MM SODIUM PHOSPHATE REMARK 210 -20, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D C(CO) REMARK 210 NH; 3D H(CCO)NH; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D 15N-EDITED/15N,13C-FILTERED REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CANDID REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 ARG C 111 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG C 111 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 ARG C 111 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG B 74 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES 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 ARG A 72 -101.51 -138.89 REMARK 500 1 ARG A 74 156.01 63.38 REMARK 500 1 ARG B 72 -139.95 58.28 REMARK 500 1 SER C 120 109.37 -160.84 REMARK 500 2 GLU A 64 19.40 59.48 REMARK 500 2 ARG A 74 -144.00 52.90 REMARK 500 3 GLU A 64 19.49 59.51 REMARK 500 3 ARG A 72 75.47 59.04 REMARK 500 4 GLU A 64 19.48 59.72 REMARK 500 4 ARG A 72 30.39 -148.86 REMARK 500 4 LEU A 73 -149.34 55.34 REMARK 500 5 GLU A 64 19.44 59.64 REMARK 500 6 LEU A 71 46.96 -144.90 REMARK 500 6 LEU A 73 -22.96 -162.15 REMARK 500 6 GLU B 64 18.86 59.01 REMARK 500 6 ARG B 74 -46.52 -154.22 REMARK 500 6 SER C 120 45.25 -144.32 REMARK 500 7 GLU A 64 19.89 59.48 REMARK 500 7 ARG A 72 15.78 -146.45 REMARK 500 7 GLU B 64 19.74 59.31 REMARK 500 7 ARG B 72 175.72 64.36 REMARK 500 7 SER C 120 80.31 -162.09 REMARK 500 8 ARG A 74 -83.52 -123.16 REMARK 500 9 ALA A 46 28.37 49.46 REMARK 500 9 LEU A 73 164.34 62.44 REMARK 500 9 LEU B 73 -179.58 56.87 REMARK 500 9 ARG B 74 -70.61 -139.31 REMARK 500 10 GLU A 64 19.73 59.61 REMARK 500 10 LEU A 73 46.02 -79.36 REMARK 500 10 GLU B 64 19.43 59.44 REMARK 500 10 LEU B 73 34.60 -146.52 REMARK 500 10 SER C 120 68.80 -159.40 REMARK 500 11 GLU A 64 19.58 59.61 REMARK 500 11 LEU A 73 -115.31 -99.85 REMARK 500 11 ARG A 74 -59.29 -146.93 REMARK 500 12 GLU A 64 19.28 59.36 REMARK 500 12 ARG A 72 -0.13 71.03 REMARK 500 12 ARG A 74 144.91 67.72 REMARK 500 12 ARG B 72 160.14 65.19 REMARK 500 12 LEU B 73 -51.90 -155.79 REMARK 500 12 ARG B 74 44.68 -87.22 REMARK 500 13 GLU A 64 19.63 59.55 REMARK 500 13 ARG A 72 -89.87 -138.66 REMARK 500 13 ARG A 74 164.44 64.81 REMARK 500 14 ALA A 46 29.19 49.16 REMARK 500 14 GLU A 64 19.57 59.63 REMARK 500 14 ARG A 72 -84.13 -151.33 REMARK 500 14 GLU B 64 19.27 59.31 REMARK 500 15 GLU A 64 19.76 59.60 REMARK 500 15 ARG A 72 -52.85 -170.43 REMARK 500 REMARK 500 THIS ENTRY HAS 70 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2RR9 A 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 2RR9 B 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 2RR9 C 79 124 UNP C9JR12 C9JR12_HUMAN 79 124 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 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 SEQRES 1 C 46 MET THR GLU GLU GLU GLN PHE ALA LEU ALA LEU LYS MET SEQRES 2 C 46 SER GLU GLN GLU ALA ARG GLU VAL ASN SER GLN GLU GLU SEQRES 3 C 46 GLU GLU GLU GLU LEU LEU ARG LYS ALA ILE ALA GLU SER SEQRES 4 C 46 LEU ASN SER CYS ARG PRO SER HELIX 1 1 THR A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 GLN A 41 5 5 HELIX 3 3 THR A 55 ASN A 60 5 6 HELIX 4 4 THR B 22 GLY B 35 1 14 HELIX 5 5 PRO B 37 GLN B 41 5 5 HELIX 6 6 GLU C 81 SER C 120 1 40 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 THR A 66 VAL A 70 1 O LEU A 69 N LYS A 6 SHEET 4 A 5 ARG A 42 PHE A 45 -1 N ARG A 42 O VAL A 70 SHEET 5 A 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 B 5 THR B 12 GLU B 16 0 SHEET 2 B 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 B 5 THR B 66 VAL B 70 1 O LEU B 69 N LYS B 6 SHEET 4 B 5 ARG B 42 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 B 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK C GLY A 76 NZ LYS B 63 1555 1555 1.34 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