HEADER UBIQUITIN 22-DEC-04 2BGF TITLE NMR STRUCTURE OF LYS48-LINKED DI-UBIQUITIN USING CHEMICAL SHIFT TITLE 2 PERTURBATION DATA TOGETHER WITH RDCS AND 15N-RELAXATION DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DI-UBIQUITIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UBIQUITIN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ISOPEPTIDE BOND BETWEEN GLY76A AND LYS48B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEASOME, DEGRADATION, UBIQUITIN, POLYUBIQUITIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.D.J.VAN DIJK,D.FUSHMAN,A.M.J.J.BONVIN REVDAT 3 15-MAY-24 2BGF 1 REMARK REVDAT 2 24-FEB-09 2BGF 1 VERSN REVDAT 1 31-AUG-05 2BGF 0 JRNL AUTH A.D.J.VAN DIJK,D.FUSHMAN,A.M.J.J.BONVIN JRNL TITL VARIOUS STRATEGIES OF USING RESIDUAL DIPOLAR COUPLINGS IN JRNL TITL 2 NMR-DRIVEN PROTEIN DOCKING: APPLICATION TO LYS48-LINKED JRNL TITL 3 DI-UBIQUITIN AND VALIDATION AGAINST 15N-RELAXATION DATA JRNL REF PROTEINS: STRUCT., FUNCT., V. 60 367 2005 JRNL REF 2 BIOINF. JRNL REFN ISSN 0887-3585 JRNL PMID 15937902 JRNL DOI 10.1002/PROT.20476 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.VARADAN,O.WALKER,C.PICKART,D.FUSHMAN REMARK 1 TITL STRUCTURAL PROPERTIES OF POLYUBIQUITIN CHAINS IN SOLUTION REMARK 1 REF J.MOL.BIOL. V. 324 637 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12460567 REMARK 1 DOI 10.1016/S0022-2836(02)01198-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : DOMINGUEZ, BOELENS,BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IS DONE IN EXPLICIT SOLVENT. REMARK 3 REFINEMENT AND STRUCTURE CALCULATION DETAILS CAN BE FOUND IN REMARK 3 DOMINGUEZ ET AL, JACS 2003, 125, 173 REMARK 4 REMARK 4 2BGF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1290022088. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : OTHER REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK REMARK 210 METHOD USED : HADDOCK REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES OF REMARK 210 LOWEST ENERGY CLUSTER REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED WITH HADDOCK USING CHEMICAL REMARK 210 SHIFT PERTURBATION DATA AS AMBIGUOUS INTERACTION RESTRAINTS AND REMARK 210 RESIDUAL DIPOLAR COUPLINGS BOTH AS DIRECT RESTRAINTS (SANI) AND REMARK 210 INTERVECTOR PROJECTION ANGLE RESTRAINTS (VEAN). STRUCTURAL REMARK 210 CHARACTERISTICS OF ENSEMBLE OF 10 BEST: AVERAGE (STANDARD REMARK 210 DEVIATION) INTERMOLECULAR ENERGIES RAMACHANDRAN ANALYSIS: 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 400 REMARK 400 COMPOUND REMARK 400 FUNCTIONS INCLUDE ATP-DEPENDENT SELECTIVE DEGRADATION OF REMARK 400 CELLULAR PROTEINS, MAINTENANCE OF CHROMATIN STRUCTURE, REMARK 400 REGULATION OF GENE EXPRESSION, STRESS RESPONSE, AND REMARK 400 RIBOSOME BIOGENESIS 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 GLU A 16 79.95 -105.17 REMARK 500 1 LYS A 33 -83.42 -80.90 REMARK 500 1 ALA A 46 -2.29 65.45 REMARK 500 1 GLN A 62 -167.04 -119.23 REMARK 500 1 GLU A 64 12.26 59.83 REMARK 500 1 LYS B 11 140.38 -175.53 REMARK 500 1 LYS B 33 -76.46 -100.94 REMARK 500 2 LYS A 33 -80.51 -81.79 REMARK 500 2 ALA A 46 -9.34 69.20 REMARK 500 2 LYS B 33 -69.20 -108.80 REMARK 500 3 GLU A 16 77.00 -112.36 REMARK 500 3 LYS A 33 -83.72 -84.78 REMARK 500 3 LEU A 67 -164.70 -113.92 REMARK 500 3 LYS B 33 -76.21 -107.33 REMARK 500 4 GLU A 16 77.83 -105.40 REMARK 500 4 LYS A 33 -79.17 -80.93 REMARK 500 4 GLN A 62 -163.91 -123.43 REMARK 500 4 GLU A 64 14.44 56.51 REMARK 500 4 ALA B 46 17.30 57.58 REMARK 500 4 GLN B 62 -161.45 -110.16 REMARK 500 5 LYS A 33 -80.98 -84.09 REMARK 500 5 GLN A 62 -159.47 -127.23 REMARK 500 5 LYS B 33 -73.54 -111.25 REMARK 500 5 LEU B 73 -109.12 -80.53 REMARK 500 5 ARG B 74 -36.52 -170.11 REMARK 500 6 GLU A 16 78.62 -114.41 REMARK 500 6 LYS A 33 -83.37 -76.60 REMARK 500 6 GLN A 62 -165.24 -128.22 REMARK 500 6 ARG A 72 57.64 -90.39 REMARK 500 6 LYS B 33 -66.94 -108.94 REMARK 500 6 GLN B 62 -165.57 -103.43 REMARK 500 7 GLU A 16 76.47 -103.55 REMARK 500 7 LYS A 33 -84.80 -79.60 REMARK 500 7 GLU A 64 10.15 58.33 REMARK 500 7 ARG A 72 64.67 -112.26 REMARK 500 7 LYS B 33 -76.92 -108.60 REMARK 500 7 GLN B 62 -167.84 -105.01 REMARK 500 8 LYS A 33 -83.02 -81.68 REMARK 500 8 LYS B 33 -68.22 -108.96 REMARK 500 8 ASN B 60 32.62 71.71 REMARK 500 8 ARG B 74 62.25 -119.42 REMARK 500 9 LYS A 33 -77.61 -85.35 REMARK 500 9 GLN A 62 -159.10 -136.98 REMARK 500 9 LEU A 73 -164.66 -105.75 REMARK 500 9 GLN B 62 -164.76 -105.08 REMARK 500 10 LYS A 33 -78.54 -90.03 REMARK 500 10 ALA A 46 -43.67 72.81 REMARK 500 10 GLN A 62 -166.14 -118.18 REMARK 500 10 GLU A 64 13.04 58.95 REMARK 500 10 LEU A 73 -83.15 -82.14 REMARK 500 REMARK 500 THIS ENTRY HAS 54 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AAR RELATED DB: PDB REMARK 900 DI-UBIQUITIN REMARK 900 RELATED ID: 1E0Q RELATED DB: PDB REMARK 900 MUTANT PEPTIDE FROM THE FIRST N-TERMINAL 17 AMINO-ACID OF UBIQUITIN REMARK 900 RELATED ID: 1P3Q RELATED DB: PDB REMARK 900 MECHANISM OF UBIQUITIN RECOGNITION BY THE CUE DOMAIN OF VPS9 REMARK 900 RELATED ID: 1UZX RELATED DB: PDB REMARK 900 A COMPLEX OF THE VPS23 UEV WITH UBIQUITIN DBREF 2BGF A 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2BGF B 1 76 UNP P62988 UBIQ_HUMAN 1 76 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 HELIX 1 1 THR A 22 GLU A 34 1 13 HELIX 2 2 PRO A 37 ASP A 39 5 3 HELIX 3 3 LEU A 56 ASN A 60 5 5 HELIX 4 4 THR B 22 GLU B 34 1 13 HELIX 5 5 PRO B 37 ASP B 39 5 3 HELIX 6 6 LEU B 56 ASN B 60 5 5 SHEET 1 AA 5 LYS A 11 GLU A 16 0 SHEET 2 AA 5 GLN A 2 THR A 7 -1 O ILE A 3 N LEU A 15 SHEET 3 AA 5 THR A 66 LEU A 71 1 O LEU A 67 N LYS A 6 SHEET 4 AA 5 GLN A 41 PHE A 45 -1 O ARG A 42 N VAL A 70 SHEET 5 AA 5 LYS A 48 GLN A 49 -1 O LYS A 48 N PHE A 45 SHEET 1 BA 5 THR B 12 GLU B 16 0 SHEET 2 BA 5 GLN B 2 THR B 7 -1 O ILE B 3 N LEU B 15 SHEET 3 BA 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 BA 5 GLN B 41 PHE B 45 -1 O ARG B 42 N VAL B 70 SHEET 5 BA 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 MODEL 1