HEADER PROTEIN TURNOVER 10-APR-05 1ZC1 TITLE UFD1 EXHIBITS THE AAA-ATPASE FOLD WITH TWO DISTINCT UBIQUITIN TITLE 2 INTERACTION SITES COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN FUSION DEGRADATION PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N DOMAIN, RESIDUES 1-208; COMPND 5 SYNONYM: UB FUSION PROTEIN 1, POLYMERASE-INTERACTING PROTEIN 3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: UFD1, PIP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UFD1, DOUBLE-PSI-BETA-BARREL, PROTEIN TURNOVER EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.PARK,R.ISAACSON,H.T.KIM,P.A.SILVER,G.WAGNER REVDAT 4 22-MAY-24 1ZC1 1 REMARK REVDAT 3 02-MAR-22 1ZC1 1 REMARK REVDAT 2 24-FEB-09 1ZC1 1 VERSN REVDAT 1 26-JUL-05 1ZC1 0 JRNL AUTH S.PARK,R.ISAACSON,H.T.KIM,P.A.SILVER,G.WAGNER JRNL TITL UFD1 EXHIBITS THE AAA-ATPASE FOLD WITH TWO DISTINCT JRNL TITL 2 UBIQUITIN INTERACTION SITES JRNL REF STRUCTURE V. 13 995 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 16004872 JRNL DOI 10.1016/J.STR.2005.04.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0, CNS 1.0 REMARK 3 AUTHORS : BRUNGER, A. (CNS), BRUNGER, A. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ZC1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032550. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 307 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 20 MM PHOSPHATE 50MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2MM UFD1 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: 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 LEU A 85 -78.83 -92.03 REMARK 500 1 LEU A 121 108.32 64.57 REMARK 500 1 SER A 131 135.14 66.79 REMARK 500 1 GLU A 189 -79.94 -90.08 REMARK 500 1 THR A 190 41.41 -168.05 REMARK 500 2 LEU A 85 -79.88 -91.84 REMARK 500 2 SER A 131 137.21 67.87 REMARK 500 2 GLU A 189 -79.94 -90.02 REMARK 500 2 THR A 190 42.87 -161.18 REMARK 500 3 LEU A 85 -80.03 -93.38 REMARK 500 3 LEU A 121 100.77 70.11 REMARK 500 3 VAL A 132 27.21 36.84 REMARK 500 3 VAL A 187 67.83 -170.11 REMARK 500 3 PRO A 205 82.56 -61.86 REMARK 500 4 LEU A 85 -79.07 -90.14 REMARK 500 4 PRO A 108 0.09 -62.61 REMARK 500 4 LEU A 121 92.68 61.23 REMARK 500 4 SER A 131 160.61 56.77 REMARK 500 4 VAL A 187 64.91 -155.05 REMARK 500 5 LEU A 85 -78.16 -91.33 REMARK 500 5 SER A 131 130.68 69.55 REMARK 500 5 VAL A 187 -55.47 -178.16 REMARK 500 5 ILE A 188 -1.84 68.66 REMARK 500 6 PRO A 108 -3.41 -57.75 REMARK 500 6 SER A 131 166.97 71.05 REMARK 500 6 GLU A 189 -79.79 -89.97 REMARK 500 6 THR A 190 -158.70 -169.84 REMARK 500 6 PRO A 205 95.10 -56.70 REMARK 500 7 PRO A 18 160.79 -48.15 REMARK 500 7 LEU A 85 -77.39 -92.62 REMARK 500 7 ILE A 88 -5.73 -141.83 REMARK 500 7 LEU A 121 100.39 67.96 REMARK 500 7 SER A 131 133.28 70.17 REMARK 500 7 GLU A 189 -79.96 -91.03 REMARK 500 7 THR A 190 30.78 -168.97 REMARK 500 8 LEU A 85 -79.05 -92.22 REMARK 500 8 PRO A 108 -1.97 -59.93 REMARK 500 8 VAL A 132 24.36 41.95 REMARK 500 8 VAL A 187 121.36 77.06 REMARK 500 8 ASP A 191 94.57 70.47 REMARK 500 9 ASN A 74 139.59 62.27 REMARK 500 9 LEU A 85 -79.58 -92.75 REMARK 500 9 SER A 131 146.76 60.98 REMARK 500 9 LEU A 174 -70.46 -84.04 REMARK 500 9 ILE A 188 -67.81 -97.18 REMARK 500 9 PRO A 205 107.50 -57.90 REMARK 500 10 PRO A 18 167.45 -49.60 REMARK 500 10 ASN A 74 148.46 61.77 REMARK 500 10 LEU A 85 -79.21 -89.99 REMARK 500 10 SER A 131 131.05 75.90 REMARK 500 REMARK 500 THIS ENTRY HAS 74 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 THE AUTOMATICALLY GENERATED BETA SHEET NAMING IN THIS PDB REMARK 700 FILE IS SLIGHTLY DIFFERENT FROM THOSE IN THE CITATION DBREF 1ZC1 A 1 208 UNP P53044 UFD1_YEAST 1 208 SEQRES 1 A 208 MET PHE SER GLY PHE SER SER PHE GLY GLY GLY ASN GLY SEQRES 2 A 208 PHE VAL ASN MET PRO GLN THR PHE GLU GLU PHE PHE ARG SEQRES 3 A 208 CYS TYR PRO ILE ALA MET MET ASN ASP ARG ILE ARG LYS SEQRES 4 A 208 ASP ASP ALA ASN PHE GLY GLY LYS ILE PHE LEU PRO PRO SEQRES 5 A 208 SER ALA LEU SER LYS LEU SER MET LEU ASN ILE ARG TYR SEQRES 6 A 208 PRO MET LEU PHE LYS LEU THR ALA ASN GLU THR GLY ARG SEQRES 7 A 208 VAL THR HIS GLY GLY VAL LEU GLU PHE ILE ALA GLU GLU SEQRES 8 A 208 GLY ARG VAL TYR LEU PRO GLN TRP MET MET GLU THR LEU SEQRES 9 A 208 GLY ILE GLN PRO GLY SER LEU LEU GLN ILE SER SER THR SEQRES 10 A 208 ASP VAL PRO LEU GLY GLN PHE VAL LYS LEU GLU PRO GLN SEQRES 11 A 208 SER VAL ASP PHE LEU ASP ILE SER ASP PRO LYS ALA VAL SEQRES 12 A 208 LEU GLU ASN VAL LEU ARG ASN PHE SER THR LEU THR VAL SEQRES 13 A 208 ASP ASP VAL ILE GLU ILE SER TYR ASN GLY LYS THR PHE SEQRES 14 A 208 LYS ILE LYS ILE LEU GLU VAL LYS PRO GLU SER SER SER SEQRES 15 A 208 LYS SER ILE CYS VAL ILE GLU THR ASP LEU VAL THR ASP SEQRES 16 A 208 PHE ALA PRO PRO VAL GLY TYR VAL GLU PRO ASP TYR LYS HELIX 1 1 ASP A 40 PHE A 44 5 5 HELIX 2 2 PRO A 52 MET A 60 1 9 HELIX 3 3 GLN A 98 LEU A 104 1 7 HELIX 4 4 SER A 131 LEU A 135 1 5 HELIX 5 5 PRO A 140 ASN A 150 1 11 SHEET 1 A 7 GLN A 19 PRO A 29 0 SHEET 2 A 7 ARG A 93 LEU A 96 1 O VAL A 94 N TYR A 28 SHEET 3 A 7 LYS A 47 LEU A 50 -1 N PHE A 49 O TYR A 95 SHEET 4 A 7 VAL A 79 PHE A 87 1 O LEU A 85 N ILE A 48 SHEET 5 A 7 PHE A 69 THR A 72 -1 N LEU A 71 O THR A 80 SHEET 6 A 7 LEU A 111 ASP A 118 -1 O SER A 115 N LYS A 70 SHEET 7 A 7 GLN A 19 PRO A 29 -1 N PHE A 21 O SER A 116 SHEET 1 B 4 VAL A 159 TYR A 164 0 SHEET 2 B 4 LYS A 167 LYS A 177 -1 O PHE A 169 N ILE A 162 SHEET 3 B 4 PHE A 124 GLU A 128 -1 N PHE A 124 O LYS A 177 SHEET 4 B 4 VAL A 193 PHE A 196 1 O VAL A 193 N VAL A 125 SHEET 1 C 2 LEU A 154 THR A 155 0 SHEET 2 C 2 SER A 184 ILE A 185 -1 O ILE A 185 N LEU A 154 CISPEP 1 TYR A 65 PRO A 66 1 0.86 CISPEP 2 TYR A 65 PRO A 66 2 0.53 CISPEP 3 TYR A 65 PRO A 66 3 0.70 CISPEP 4 TYR A 65 PRO A 66 4 0.73 CISPEP 5 TYR A 65 PRO A 66 5 0.73 CISPEP 6 TYR A 65 PRO A 66 6 0.67 CISPEP 7 TYR A 65 PRO A 66 7 0.68 CISPEP 8 TYR A 65 PRO A 66 8 0.72 CISPEP 9 TYR A 65 PRO A 66 9 0.12 CISPEP 10 TYR A 65 PRO A 66 10 0.42 CISPEP 11 TYR A 65 PRO A 66 11 0.73 CISPEP 12 TYR A 65 PRO A 66 12 0.32 CISPEP 13 TYR A 65 PRO A 66 13 0.62 CISPEP 14 TYR A 65 PRO A 66 14 0.41 CISPEP 15 TYR A 65 PRO A 66 15 0.90 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