PDB Short entry for 2YUJ HEADER PROTEIN BINDING 06-APR-07 2YUJ TITLE SOLUTION STRUCTURE OF HUMAN UBIQUITIN FUSION DEGRADATION PROTEIN 1 TITLE 2 HOMOLOG UFD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN FUSION DEGRADATION 1-LIKE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UFD1; COMPND 5 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: AB1165_B04; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P061225-60; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS UBIQUITIN-DEPENDENT PROTEOLYTIC, DEGRADATION, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.SAITO,T.TOMIZAWA,T.KIGAWA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 29-JAN-20 2YUJ 1 AUTHOR REMARK SEQADV REVDAT 2 24-FEB-09 2YUJ 1 VERSN REVDAT 1 15-APR-08 2YUJ 0 JRNL AUTH K.SAITO,T.TOMIZAWA,T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF HUMAN UBIQUITIN FUSION DEGRADATION JRNL TITL 2 PROTEIN 1 HOMOLOG UFD1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YUJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027151. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM PROTEIN, 20MM D-TRIS-HCL, REMARK 210 100MM NACL, 1MM D-DTT, 0.02% REMARK 210 NAN3; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, NMRPIPE 2006, REMARK 210 NMRVIEW 5, CNS 1.1 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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 SER A 5 85.11 60.42 REMARK 500 1 ILE A 8 73.60 56.98 REMARK 500 1 PRO A 9 170.65 -52.86 REMARK 500 1 ARG A 10 32.43 -164.86 REMARK 500 1 PHE A 12 -47.94 -134.53 REMARK 500 1 GLN A 13 -177.65 -60.93 REMARK 500 1 ALA A 29 177.30 -59.05 REMARK 500 1 LYS A 69 31.27 -98.79 REMARK 500 1 SER A 71 25.92 -140.28 REMARK 500 1 PHE A 82 72.96 -103.51 REMARK 500 1 PRO A 92 -176.12 -52.37 REMARK 500 1 VAL A 154 86.35 -69.59 REMARK 500 1 TYR A 159 -50.03 -150.71 REMARK 500 1 ASN A 160 44.35 -96.78 REMARK 500 1 GLU A 181 87.63 61.37 REMARK 500 2 SER A 3 -46.37 -132.11 REMARK 500 2 ARG A 10 92.34 60.78 REMARK 500 2 PHE A 12 100.63 61.15 REMARK 500 2 GLN A 13 177.70 59.18 REMARK 500 2 ALA A 29 -59.79 -166.46 REMARK 500 2 ARG A 34 168.33 60.39 REMARK 500 2 LEU A 66 76.35 -69.99 REMARK 500 2 LYS A 69 33.94 -98.57 REMARK 500 2 VAL A 83 31.99 -157.39 REMARK 500 2 PRO A 92 -173.17 -53.41 REMARK 500 2 GLU A 103 84.03 -62.73 REMARK 500 2 TYR A 159 -40.42 -176.43 REMARK 500 2 ASN A 160 43.36 -105.28 REMARK 500 2 GLU A 181 88.18 60.29 REMARK 500 3 SER A 2 174.13 60.35 REMARK 500 3 VAL A 11 48.15 -143.57 REMARK 500 3 PHE A 12 82.49 61.24 REMARK 500 3 GLN A 13 -46.92 -138.76 REMARK 500 3 ASN A 14 99.61 60.50 REMARK 500 3 ALA A 29 -178.97 59.26 REMARK 500 3 LYS A 69 32.19 -98.52 REMARK 500 3 LEU A 80 -63.47 -122.09 REMARK 500 3 PHE A 82 79.97 -150.19 REMARK 500 3 VAL A 83 31.14 -148.71 REMARK 500 3 PRO A 92 178.74 -52.13 REMARK 500 3 TYR A 159 -46.99 -175.13 REMARK 500 3 ASN A 160 43.14 -100.82 REMARK 500 3 GLU A 181 66.10 60.75 REMARK 500 4 PRO A 9 -167.00 -72.23 REMARK 500 4 ARG A 10 173.20 64.48 REMARK 500 4 PHE A 16 98.40 -60.47 REMARK 500 4 LYS A 69 33.91 -98.50 REMARK 500 4 LEU A 80 -58.28 -151.56 REMARK 500 4 VAL A 83 32.07 -155.91 REMARK 500 4 PRO A 92 -174.38 -53.02 REMARK 500 REMARK 500 THIS ENTRY HAS 288 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO003008466.1 RELATED DB: TARGETDB DBREF 2YUJ A 8 190 UNP Q541A5 Q541A5_HUMAN 11 193 SEQADV 2YUJ GLY A 1 UNP Q541A5 EXPRESSION TAG SEQADV 2YUJ SER A 2 UNP Q541A5 EXPRESSION TAG SEQADV 2YUJ SER A 3 UNP Q541A5 EXPRESSION TAG SEQADV 2YUJ GLY A 4 UNP Q541A5 EXPRESSION TAG SEQADV 2YUJ SER A 5 UNP Q541A5 EXPRESSION TAG SEQADV 2YUJ SER A 6 UNP Q541A5 EXPRESSION TAG SEQADV 2YUJ GLY A 7 UNP Q541A5 EXPRESSION TAG SEQRES 1 A 190 GLY SER SER GLY SER SER GLY ILE PRO ARG VAL PHE GLN SEQRES 2 A 190 ASN ARG PHE SER THR GLN TYR ARG CYS PHE SER VAL SER SEQRES 3 A 190 MET LEU ALA GLY PRO ASN ASP ARG SER ASP VAL GLU LYS SEQRES 4 A 190 GLY GLY LYS ILE ILE MET PRO PRO SER ALA LEU ASP GLN SEQRES 5 A 190 LEU SER ARG LEU ASN ILE THR TYR PRO MET LEU PHE LYS SEQRES 6 A 190 LEU THR ASN LYS ASN SER ASP ARG MET THR HIS CYS GLY SEQRES 7 A 190 VAL LEU GLU PHE VAL ALA ASP GLU GLY ILE CYS TYR LEU SEQRES 8 A 190 PRO HIS TRP MET MET GLN ASN LEU LEU LEU GLU GLU GLY SEQRES 9 A 190 GLY LEU VAL GLN VAL GLU SER VAL ASN LEU GLN VAL ALA SEQRES 10 A 190 THR TYR SER LYS PHE GLN PRO GLN SER PRO ASP PHE LEU SEQRES 11 A 190 ASP ILE THR ASN PRO LYS ALA VAL LEU GLU ASN ALA LEU SEQRES 12 A 190 ARG ASN PHE ALA CYS LEU THR THR GLY ASP VAL ILE ALA SEQRES 13 A 190 ILE ASN TYR ASN GLU LYS ILE TYR GLU LEU ARG VAL MET SEQRES 14 A 190 GLU THR LYS PRO ASP LYS ALA VAL SER ILE ILE GLU CYS SEQRES 15 A 190 ASP MET ASN VAL ASP PHE ASP ALA HELIX 1 1 PRO A 46 LEU A 56 1 11 HELIX 2 2 HIS A 93 LEU A 100 1 8 HELIX 3 3 SER A 126 ILE A 132 1 7 HELIX 4 4 ASN A 134 ARG A 144 1 11 SHEET 1 A 7 SER A 17 PHE A 23 0 SHEET 2 A 7 CYS A 89 TYR A 90 1 O CYS A 89 N PHE A 23 SHEET 3 A 7 LYS A 42 ILE A 44 -1 N ILE A 44 O TYR A 90 SHEET 4 A 7 ARG A 73 GLU A 81 1 O LEU A 80 N ILE A 43 SHEET 5 A 7 LEU A 63 ASN A 68 -1 N PHE A 64 O CYS A 77 SHEET 6 A 7 GLY A 105 VAL A 112 -1 O GLN A 108 N THR A 67 SHEET 7 A 7 SER A 17 PHE A 23 -1 N CYS A 22 O GLY A 105 SHEET 1 B 4 VAL A 154 ASN A 158 0 SHEET 2 B 4 ILE A 163 THR A 171 -1 O TYR A 164 N ILE A 157 SHEET 3 B 4 TYR A 119 PRO A 124 -1 N LYS A 121 O GLU A 170 SHEET 4 B 4 ASN A 185 PHE A 188 1 O ASN A 185 N SER A 120 SHEET 1 C 2 CYS A 148 LEU A 149 0 SHEET 2 C 2 VAL A 177 SER A 178 -1 O VAL A 177 N LEU A 149 CISPEP 1 TYR A 60 PRO A 61 1 -0.15 CISPEP 2 LYS A 172 PRO A 173 1 0.09 CISPEP 3 TYR A 60 PRO A 61 2 0.03 CISPEP 4 LYS A 172 PRO A 173 2 -0.07 CISPEP 5 TYR A 60 PRO A 61 3 -0.02 CISPEP 6 LYS A 172 PRO A 173 3 0.11 CISPEP 7 TYR A 60 PRO A 61 4 -0.07 CISPEP 8 LYS A 172 PRO A 173 4 -0.01 CISPEP 9 TYR A 60 PRO A 61 5 0.11 CISPEP 10 LYS A 172 PRO A 173 5 0.10 CISPEP 11 TYR A 60 PRO A 61 6 0.09 CISPEP 12 LYS A 172 PRO A 173 6 0.01 CISPEP 13 TYR A 60 PRO A 61 7 -0.14 CISPEP 14 LYS A 172 PRO A 173 7 0.03 CISPEP 15 TYR A 60 PRO A 61 8 -0.04 CISPEP 16 LYS A 172 PRO A 173 8 0.13 CISPEP 17 TYR A 60 PRO A 61 9 0.02 CISPEP 18 LYS A 172 PRO A 173 9 0.00 CISPEP 19 TYR A 60 PRO A 61 10 0.01 CISPEP 20 LYS A 172 PRO A 173 10 -0.04 CISPEP 21 TYR A 60 PRO A 61 11 -0.02 CISPEP 22 LYS A 172 PRO A 173 11 0.04 CISPEP 23 TYR A 60 PRO A 61 12 0.05 CISPEP 24 LYS A 172 PRO A 173 12 0.06 CISPEP 25 TYR A 60 PRO A 61 13 -0.05 CISPEP 26 LYS A 172 PRO A 173 13 -0.08 CISPEP 27 TYR A 60 PRO A 61 14 0.09 CISPEP 28 LYS A 172 PRO A 173 14 0.06 CISPEP 29 TYR A 60 PRO A 61 15 0.02 CISPEP 30 LYS A 172 PRO A 173 15 0.00 CISPEP 31 TYR A 60 PRO A 61 16 0.05 CISPEP 32 LYS A 172 PRO A 173 16 -0.04 CISPEP 33 TYR A 60 PRO A 61 17 -0.13 CISPEP 34 LYS A 172 PRO A 173 17 0.02 CISPEP 35 TYR A 60 PRO A 61 18 0.06 CISPEP 36 LYS A 172 PRO A 173 18 -0.02 CISPEP 37 TYR A 60 PRO A 61 19 0.10 CISPEP 38 LYS A 172 PRO A 173 19 0.08 CISPEP 39 TYR A 60 PRO A 61 20 0.12 CISPEP 40 LYS A 172 PRO A 173 20 -0.10 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