HEADER PROTEIN BINDING 06-JAN-09 2KDE TITLE NMR STRUCTURE OF MAJOR S5A (196-306):K48 LINKED DIUBIQUITIN SPECIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 196-306, S5A FRAGMENT; COMPND 5 SYNONYM: 26S PROTEASOME REGULATORY SUBUNIT S5A, RPN10, MULTIUBIQUITIN COMPND 6 CHAIN-BINDING PROTEIN, ANTISECRETORY FACTOR 1, ASF, AF; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: UBIQUITIN; COMPND 10 CHAIN: B, C; COMPND 11 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: PSMD4, MCB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET26B; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 11 ORGANISM_COMMON: CLAWED FROG,COMMON PLATANNA,PLATANNA; SOURCE 12 ORGANISM_TAXID: 8355; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 EXPRESSION_SYSTEM_VECTOR: PET3A KEYWDS PROTEIN COMPLEX, UBIQUITIN INTERACTING MOTIFS, CYTOPLASM, NUCLEUS, KEYWDS 2 UBL CONJUGATION, ALTERNATIVE SPLICING, PHOSPHOPROTEIN, PROTEASOME, KEYWDS 3 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 7 AUTHOR N.ZHANG,Q.WANG,A.EHLINGER,L.RANDLES,J.W.LARY,Y.KANG,A.HARIRINIA, AUTHOR 2 J.L.COLE,D.FUSHMAN,K.J.WALTERS REVDAT 3 20-NOV-24 2KDE 1 REMARK REVDAT 2 16-MAR-22 2KDE 1 REMARK LINK REVDAT 1 01-SEP-09 2KDE 0 JRNL AUTH N.ZHANG,Q.WANG,A.EHLINGER,L.RANDLES,J.W.LARY,Y.KANG, JRNL AUTH 2 A.HARIRINIA,A.J.STORASKA,J.L.COLE,D.FUSHMAN,K.J.WALTERS JRNL TITL STRUCTURE OF THE S5A:K48-LINKED DIUBIQUITIN COMPLEX AND ITS JRNL TITL 2 INTERACTIONS WITH RPN13. JRNL REF MOL.CELL V. 35 280 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 19683493 JRNL DOI 10.1016/J.MOLCEL.2009.06.010 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XEASY, X-PLOR REMARK 3 AUTHORS : BARTELS ET AL. (XEASY), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100981. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 20 MM NAPO4; 100 MM NACL; 20 MM REMARK 210 NAPO4; 50 MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-100% 15N; U-50% 2H] REMARK 210 S5A (196-306)-1, 1.2 MM K48 REMARK 210 LINKED DIUBIQUITIN-2, 90% H2O/10% REMARK 210 D2O; 0.5 MM [U-100% 13C] S5A REMARK 210 (196-306)-3, 1.5 MM K48 LINKED REMARK 210 DIUBIQUITIN-4, 100% D2O; 0.5 MM REMARK 210 [U-100% 13C OF THE PROXIMAL UB; REMARK 210 NATURAL ABUNDANCE OF THE DISTAL REMARK 210 SUBUNIT] K48 LINKED DIUBIQUITIN- REMARK 210 5, 1.0 MM S5A (196-306)-6, 100% REMARK 210 D2O; 0.5 MM [U-100% 13C OF THE REMARK 210 DISTAL SUBUNIT; NATURAL REMARK 210 ABUNDANCE OF THE PROXIMAL UB] REMARK 210 K48 LINKED DIUBIQUITIN-7, 1.0 MM REMARK 210 S5A (196-306)-8, 100% D2O; 0.4 REMARK 210 MM [U-100% 13C] S5A (196-306)-9, REMARK 210 1.2 MM [U-100% 2H OF THE REMARK 210 PROXIMAL UB; NATURAL ABUNDANCE REMARK 210 OF THE DISTAL SUBUNIT] ] K48 REMARK 210 LINKED DIUBIQUITIN-10, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D 13C-FILTERED 1H-13C REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7 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: 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: 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 199 86.37 52.55 REMARK 500 1 ALA A 201 50.31 -91.88 REMARK 500 1 SER A 202 -44.43 -135.83 REMARK 500 1 PHE A 206 -44.31 -162.81 REMARK 500 1 VAL A 208 -40.64 -135.29 REMARK 500 1 ALA A 246 56.23 -145.37 REMARK 500 1 ASP A 255 51.20 -115.31 REMARK 500 1 THR A 273 34.64 -140.28 REMARK 500 1 LEU A 275 147.98 -171.10 REMARK 500 1 THR A 282 -158.78 -72.30 REMARK 500 1 ALA A 298 48.36 -95.20 REMARK 500 1 PHE A 300 -59.73 -120.88 REMARK 500 1 GLN A 302 49.62 -141.50 REMARK 500 1 THR B 7 -166.32 -110.42 REMARK 500 1 THR B 55 -169.52 -106.88 REMARK 500 1 GLN B 62 -167.23 -119.71 REMARK 500 1 ARG B 74 52.59 -97.23 REMARK 500 1 THR C 131 -169.71 -108.15 REMARK 500 1 GLN C 138 -165.79 -102.60 REMARK 500 2 ALA A 201 -57.05 -160.06 REMARK 500 2 PHE A 204 -61.45 -97.77 REMARK 500 2 GLU A 205 70.64 51.65 REMARK 500 2 VAL A 208 -69.07 -122.47 REMARK 500 2 ASP A 213 118.54 -171.39 REMARK 500 2 ILE A 248 -40.37 -131.62 REMARK 500 2 ALA A 249 -168.34 -123.88 REMARK 500 2 GLU A 254 44.46 -153.82 REMARK 500 2 THR A 273 35.29 -151.31 REMARK 500 2 LEU A 275 147.99 -171.45 REMARK 500 2 MET A 281 -164.37 -78.99 REMARK 500 2 THR A 282 -156.16 -147.01 REMARK 500 2 ALA A 298 51.45 -146.39 REMARK 500 2 PHE A 300 81.19 -166.62 REMARK 500 2 GLU A 304 102.20 -167.99 REMARK 500 2 VAL B 17 -163.51 -112.64 REMARK 500 2 THR C 83 -165.59 -122.06 REMARK 500 2 THR C 85 28.20 -140.49 REMARK 500 2 VAL C 93 -162.40 -111.85 REMARK 500 2 THR C 131 -168.01 -105.25 REMARK 500 2 GLN C 138 -168.74 -104.90 REMARK 500 3 GLU A 205 45.61 -150.16 REMARK 500 3 PHE A 206 -46.41 -161.97 REMARK 500 3 VAL A 208 -40.58 -134.84 REMARK 500 3 ASP A 213 118.09 -169.79 REMARK 500 3 ILE A 248 74.42 -115.21 REMARK 500 3 ASP A 255 27.89 -140.83 REMARK 500 3 PHE A 270 76.78 -116.07 REMARK 500 3 LEU A 275 148.03 -171.36 REMARK 500 3 THR A 282 -157.63 -71.48 REMARK 500 3 ALA A 298 48.06 -141.20 REMARK 500 REMARK 500 THIS ENTRY HAS 131 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 221 0.30 SIDE CHAIN REMARK 500 1 ARG A 228 0.32 SIDE CHAIN REMARK 500 1 ARG A 230 0.32 SIDE CHAIN REMARK 500 1 ARG A 236 0.27 SIDE CHAIN REMARK 500 1 ARG A 237 0.27 SIDE CHAIN REMARK 500 1 ARG A 272 0.23 SIDE CHAIN REMARK 500 1 ARG B 42 0.26 SIDE CHAIN REMARK 500 1 ARG B 54 0.27 SIDE CHAIN REMARK 500 1 ARG B 72 0.29 SIDE CHAIN REMARK 500 1 ARG B 74 0.32 SIDE CHAIN REMARK 500 1 ARG C 118 0.31 SIDE CHAIN REMARK 500 1 ARG C 130 0.27 SIDE CHAIN REMARK 500 1 ARG C 148 0.32 SIDE CHAIN REMARK 500 1 ARG C 150 0.31 SIDE CHAIN REMARK 500 2 ARG A 221 0.24 SIDE CHAIN REMARK 500 2 ARG A 228 0.31 SIDE CHAIN REMARK 500 2 ARG A 230 0.31 SIDE CHAIN REMARK 500 2 ARG A 236 0.29 SIDE CHAIN REMARK 500 2 ARG A 237 0.29 SIDE CHAIN REMARK 500 2 ARG A 272 0.30 SIDE CHAIN REMARK 500 2 ARG B 42 0.30 SIDE CHAIN REMARK 500 2 ARG B 54 0.30 SIDE CHAIN REMARK 500 2 ARG B 72 0.23 SIDE CHAIN REMARK 500 2 ARG B 74 0.26 SIDE CHAIN REMARK 500 2 ARG C 118 0.25 SIDE CHAIN REMARK 500 2 ARG C 130 0.30 SIDE CHAIN REMARK 500 2 ARG C 148 0.32 SIDE CHAIN REMARK 500 2 ARG C 150 0.32 SIDE CHAIN REMARK 500 3 ARG A 221 0.27 SIDE CHAIN REMARK 500 3 ARG A 228 0.28 SIDE CHAIN REMARK 500 3 ARG A 230 0.31 SIDE CHAIN REMARK 500 3 ARG A 236 0.32 SIDE CHAIN REMARK 500 3 ARG A 237 0.32 SIDE CHAIN REMARK 500 3 ARG A 272 0.32 SIDE CHAIN REMARK 500 3 ARG B 42 0.28 SIDE CHAIN REMARK 500 3 ARG B 54 0.32 SIDE CHAIN REMARK 500 3 ARG B 72 0.30 SIDE CHAIN REMARK 500 3 ARG B 74 0.31 SIDE CHAIN REMARK 500 3 ARG C 118 0.28 SIDE CHAIN REMARK 500 3 ARG C 130 0.23 SIDE CHAIN REMARK 500 3 ARG C 148 0.32 SIDE CHAIN REMARK 500 3 ARG C 150 0.28 SIDE CHAIN REMARK 500 4 ARG A 221 0.27 SIDE CHAIN REMARK 500 4 ARG A 228 0.23 SIDE CHAIN REMARK 500 4 ARG A 230 0.29 SIDE CHAIN REMARK 500 4 ARG A 236 0.28 SIDE CHAIN REMARK 500 4 ARG A 237 0.29 SIDE CHAIN REMARK 500 4 ARG A 272 0.32 SIDE CHAIN REMARK 500 4 ARG B 42 0.28 SIDE CHAIN REMARK 500 4 ARG B 54 0.26 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 98 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YX4 RELATED DB: PDB REMARK 900 STRUCTURE OF S5A BOUND TO MONOUBIQUITIN PROVIDES A MODEL FOR REMARK 900 POLYUBIQUITIN RECOGNITION REMARK 900 RELATED ID: 1YX5 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF S5A UIM-1/UBIQUITIN COMPLEX REMARK 900 RELATED ID: 1YX6 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF S5A UIM-2/UBIQUITIN COMPLEX REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 UBIQUITIN NMR STRUCTURE REMARK 900 RELATED ID: 2KDF RELATED DB: PDB DBREF 2KDE B 1 76 UNP P62972 UBIQ_XENLA 1 76 DBREF 2KDE C 77 152 UNP P62972 UBIQ_XENLA 1 76 DBREF 2KDE A 196 306 UNP P55036 PSMD4_HUMAN 196 306 SEQRES 1 A 111 MET LEU GLY LEU GLY ALA SER ASP PHE GLU PHE GLY VAL SEQRES 2 A 111 ASP PRO SER ALA ASP PRO GLU LEU ALA LEU ALA LEU ARG SEQRES 3 A 111 VAL SER MET GLU GLU GLN ARG GLN ARG GLN GLU GLU GLU SEQRES 4 A 111 ALA ARG ARG ALA ALA ALA ALA SER ALA ALA GLU ALA GLY SEQRES 5 A 111 ILE ALA THR THR GLY THR GLU ASP SER ASP ASP ALA LEU SEQRES 6 A 111 LEU LYS MET THR ILE SER GLN GLN GLU PHE GLY ARG THR SEQRES 7 A 111 GLY LEU PRO ASP LEU SER SER MET THR GLU GLU GLU GLN SEQRES 8 A 111 ILE ALA TYR ALA MET GLN MET SER LEU GLN GLY ALA GLU SEQRES 9 A 111 PHE GLY GLN ALA GLU SER ALA 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 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 1 ASP A 209 ALA A 212 5 4 HELIX 2 2 ASP A 213 GLY A 247 1 35 HELIX 3 3 SER A 256 PHE A 270 1 15 HELIX 4 4 THR A 282 GLY A 297 1 16 HELIX 5 5 THR B 22 GLU B 34 1 13 HELIX 6 6 LEU B 56 ASN B 60 5 5 HELIX 7 7 THR C 98 GLU C 110 1 13 HELIX 8 8 PRO C 113 GLN C 117 5 5 HELIX 9 9 LEU C 132 ASN C 136 5 5 SHEET 1 A 4 THR B 12 GLU B 16 0 SHEET 2 A 4 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 A 4 THR B 66 LEU B 71 1 O LEU B 69 N LYS B 6 SHEET 4 A 4 GLN B 41 ILE B 44 -1 N ILE B 44 O HIS B 68 SHEET 1 B 5 THR C 88 GLU C 92 0 SHEET 2 B 5 GLN C 78 LYS C 82 -1 N ILE C 79 O LEU C 91 SHEET 3 B 5 THR C 142 VAL C 146 1 O LEU C 143 N PHE C 80 SHEET 4 B 5 ARG C 118 PHE C 121 -1 N ARG C 118 O VAL C 146 SHEET 5 B 5 LYS C 124 GLN C 125 -1 O LYS C 124 N PHE C 121 LINK C GLY B 76 NZ LYS C 124 1555 1555 1.31 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