HEADER SIGNALING PROTEIN 25-APR-19 6OQ2 TITLE NMR STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UBIQUITIN; COMPND 8 CHAIN: D; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: UBIQUITIN; COMPND 13 CHAIN: E; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBB; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: UBB; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.J.BOUGHTON,D.FUSHMAN REVDAT 4 22-JAN-20 6OQ2 1 JRNL REVDAT 3 01-JAN-20 6OQ2 1 REMARK REVDAT 2 20-NOV-19 6OQ2 1 JRNL REVDAT 1 23-OCT-19 6OQ2 0 JRNL AUTH A.J.BOUGHTON,S.KRUEGER,D.FUSHMAN JRNL TITL BRANCHING VIA K11 AND K48 BESTOWS UBIQUITIN CHAINS WITH A JRNL TITL 2 UNIQUE INTERDOMAIN INTERFACE AND ENHANCED AFFINITY FOR JRNL TITL 3 PROTEASOMAL SUBUNIT RPN1. JRNL REF STRUCTURE V. 28 29 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 31677892 JRNL DOI 10.1016/J.STR.2019.10.008 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE INITIAL HADDOCK INPUT WAS THE REMARK 3 CRYSTAL STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN (PDB REMARK 3 ID 6OQ1). AMBIGUOUS DISTANCE RESTRAINTS WERE FROM CHEMICAL SHIFT REMARK 3 PERTURBATIONS AND DISTANCE RESTRAINTS WERE BASED ON PRES. REMARK 4 REMARK 4 6OQ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000241089. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 120 UM [U-15N-DISTAL11] BRANCHED REMARK 210 K11/K48-LINKED TRI-UBIQUITIN, 95% REMARK 210 H2O/5% D2O; 100 UM [U-15N- REMARK 210 DISTAL48] BRANCHED K11/K48- REMARK 210 LINKED TRI-UBIQUITIN, 95% H2O/5% REMARK 210 D2O; 60 UM [U-15N-DISTAL11] REMARK 210 BRANCHED K11/K48-LINKED TRI- REMARK 210 UBIQUITIN, 95% H2O/5% D2O; 110 REMARK 210 UM [U-15N-DISTAL48] BRANCHED K11/ REMARK 210 K48-LINKED TRI-UBIQUITIN, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, HADDOCK REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, E 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 ARG E 74 REMARK 465 GLY E 75 REMARK 465 GLY E 76 REMARK 465 ASP E 77 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 GLY B 76 HZ3 LYS E 11 1.50 REMARK 500 O GLY D 76 HZ3 LYS E 48 1.56 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 THR B 7 -102.50 -87.67 REMARK 500 1 LEU B 8 -47.29 -143.53 REMARK 500 1 GLN D 62 -166.89 -120.96 REMARK 500 2 GLN B 62 -159.87 -111.77 REMARK 500 2 ARG D 42 97.59 -166.12 REMARK 500 2 ALA D 46 -37.64 69.11 REMARK 500 2 GLN D 62 -166.28 -110.56 REMARK 500 2 THR E 7 -166.81 -122.41 REMARK 500 2 GLN E 62 -140.68 -107.83 REMARK 500 3 ALA B 46 -67.49 66.97 REMARK 500 3 GLN E 62 -164.87 -100.38 REMARK 500 4 ALA B 46 -67.53 68.85 REMARK 500 4 GLN B 62 -162.51 -113.71 REMARK 500 4 GLU D 34 -83.53 -98.86 REMARK 500 4 ASN D 60 60.80 64.33 REMARK 500 4 GLN D 62 -155.72 -119.20 REMARK 500 5 GLN B 62 -161.68 -116.34 REMARK 500 5 ALA D 46 -22.24 68.38 REMARK 500 5 GLN D 62 -166.13 -107.26 REMARK 500 6 ARG B 42 74.26 -119.04 REMARK 500 6 ALA B 46 -71.03 68.52 REMARK 500 6 GLN B 62 -162.92 -112.13 REMARK 500 6 LYS D 33 -71.57 -77.08 REMARK 500 6 GLN D 62 -151.23 -99.51 REMARK 500 6 ARG D 72 63.41 -110.25 REMARK 500 6 LEU D 73 -85.65 -118.01 REMARK 500 7 ALA D 46 -37.50 71.43 REMARK 500 7 GLN D 62 -158.49 -118.44 REMARK 500 7 ARG D 72 69.37 -101.54 REMARK 500 7 ARG D 74 -73.40 -70.08 REMARK 500 7 GLU E 34 -103.00 -97.25 REMARK 500 8 ALA B 46 -66.14 70.22 REMARK 500 8 GLN B 62 -164.84 -122.12 REMARK 500 8 GLN D 62 -123.20 -126.13 REMARK 500 8 GLU E 34 -65.40 -97.29 REMARK 500 9 THR B 9 -132.82 -100.48 REMARK 500 9 GLU B 34 -72.14 -91.60 REMARK 500 9 GLN B 62 -162.45 -125.31 REMARK 500 9 ARG B 72 -63.04 -104.49 REMARK 500 9 ARG B 74 -40.34 -131.58 REMARK 500 9 GLN D 62 -168.92 -103.40 REMARK 500 10 LYS B 33 -61.91 -92.69 REMARK 500 10 ALA B 46 -40.60 69.34 REMARK 500 10 GLN B 62 -168.60 -112.29 REMARK 500 10 LYS E 33 -78.50 -69.70 REMARK 500 10 GLN E 62 -169.22 -105.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30602 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN REMARK 900 RELATED ID: 6OQ1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BRANCHED K11/K48-LINKED TRI-UBIQUITIN DBREF 6OQ2 B 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 6OQ2 D 1 76 UNP P0CG47 UBB_HUMAN 1 76 DBREF 6OQ2 E 1 77 UNP P0CG47 UBB_HUMAN 1 77 SEQADV 6OQ2 ARG B 11 UNP P0CG47 LYS 11 ENGINEERED MUTATION SEQADV 6OQ2 ARG B 48 UNP P0CG47 LYS 48 ENGINEERED MUTATION SEQADV 6OQ2 ARG B 63 UNP P0CG47 LYS 63 ENGINEERED MUTATION SEQADV 6OQ2 ARG D 48 UNP P0CG47 LYS 48 ENGINEERED MUTATION SEQADV 6OQ2 ASP E 77 UNP P0CG47 MET 77 ENGINEERED MUTATION SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY ARG 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 ARG GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 76 GLN GLN ARG LEU ILE PHE ALA GLY ARG GLN LEU GLU ASP SEQRES 5 D 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 E 77 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 77 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 77 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 77 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 E 77 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 E 77 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY ASP HELIX 1 AA1 THR B 22 GLU B 34 1 13 HELIX 2 AA2 PRO B 37 ASP B 39 5 3 HELIX 3 AA3 THR D 22 GLU D 34 1 13 HELIX 4 AA4 LEU D 56 ASN D 60 5 5 HELIX 5 AA5 THR E 22 GLU E 34 1 13 HELIX 6 AA6 PRO E 37 ASP E 39 5 3 HELIX 7 AA7 THR E 55 ASN E 60 5 6 SHEET 1 AA1 5 THR B 12 GLU B 16 0 SHEET 2 AA1 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 AA1 5 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 AA1 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 AA1 5 ARG B 48 GLN B 49 -1 O ARG B 48 N PHE B 45 SHEET 1 AA2 5 THR D 12 GLU D 16 0 SHEET 2 AA2 5 GLN D 2 LYS D 6 -1 N VAL D 5 O ILE D 13 SHEET 3 AA2 5 THR D 66 LEU D 71 1 O LEU D 67 N PHE D 4 SHEET 4 AA2 5 GLN D 41 PHE D 45 -1 N ARG D 42 O VAL D 70 SHEET 5 AA2 5 ARG D 48 GLN D 49 -1 O ARG D 48 N PHE D 45 SHEET 1 AA3 5 THR E 12 GLU E 16 0 SHEET 2 AA3 5 GLN E 2 THR E 7 -1 N ILE E 3 O LEU E 15 SHEET 3 AA3 5 THR E 66 LEU E 71 1 O LEU E 67 N LYS E 6 SHEET 4 AA3 5 GLN E 41 PHE E 45 -1 N ILE E 44 O HIS E 68 SHEET 5 AA3 5 LYS E 48 GLN E 49 -1 O LYS E 48 N PHE E 45 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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