PDB Short entry for 1YX4 HEADER HYDROLASE 19-FEB-05 1YX4 TITLE STRUCTURE OF S5A BOUND TO MONOUBIQUITIN PROVIDES A MODEL FOR TITLE 2 POLYUBIQUITIN RECOGNITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: (POLY)UBIQUITIN BINDING REGION; COMPND 5 SYNONYM: 26S PROTEASOME REGULATORY SUBUNIT S5A, RPN10, MULTIUBIQUITIN COMPND 6 CHAIN BINDING PROTEIN, ANTISECRETORY FACTOR-1, AF, ASF; COMPND 7 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: PET KEYWDS POLYUBIQUITIN, PROTEASOME, S5A, UIM, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Q.WANG,P.YOUNG,K.J.WALTERS REVDAT 3 02-MAR-22 1YX4 1 REMARK SEQADV REVDAT 2 24-FEB-09 1YX4 1 VERSN REVDAT 1 19-APR-05 1YX4 0 JRNL AUTH Q.WANG,P.YOUNG,K.J.WALTERS JRNL TITL STRUCTURE OF S5A BOUND TO MONOUBIQUITIN PROVIDES A MODEL FOR JRNL TITL 2 POLYUBIQUITIN RECOGNITION JRNL REF J.MOL.BIOL. V. 348 727 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15826667 JRNL DOI 10.1016/J.JMB.2005.03.007 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YX4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032022. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 283 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 100 MM NACL; 100 MM NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.35 MM S5A U-15N, 13C; 1 MM S5A REMARK 210 U-15N; 0.5 MM S5A UNLABELED; 0.5 REMARK 210 MM S5A U-N15 AND 50% DEUTERATED; REMARK 210 1 MM S5A U-C13 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 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 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 1-15 REMARK 465 RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 SER A -7 REMARK 465 SER A -6 REMARK 465 GLY A -5 REMARK 465 HIS A -4 REMARK 465 ILE A -3 REMARK 465 GLU A -2 REMARK 465 GLY A -1 REMARK 465 ARG A 0 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 5 33.27 -151.52 REMARK 500 1 GLU A 11 58.63 -92.72 REMARK 500 1 VAL A 14 -40.34 -139.67 REMARK 500 1 GLU A 51 79.07 52.39 REMARK 500 1 THR A 59 55.63 -90.36 REMARK 500 1 GLU A 60 57.33 -91.50 REMARK 500 1 SER A 62 72.38 -117.56 REMARK 500 1 LEU A 81 111.76 -175.53 REMARK 500 1 SER A 86 41.15 -96.18 REMARK 500 1 GLN A 102 71.17 -112.40 REMARK 500 1 ALA A 104 103.70 -166.98 REMARK 500 1 PHE A 106 -60.18 -144.92 REMARK 500 1 GLN A 108 58.40 -102.14 REMARK 500 2 GLU A 11 34.69 -159.43 REMARK 500 2 PHE A 12 -43.68 -161.74 REMARK 500 2 PRO A 16 78.35 -61.33 REMARK 500 2 SER A 17 47.30 70.28 REMARK 500 2 ALA A 18 27.27 44.64 REMARK 500 2 ASP A 19 119.06 -169.44 REMARK 500 2 THR A 56 44.58 -167.15 REMARK 500 2 ASP A 61 97.22 -56.45 REMARK 500 2 SER A 62 79.54 -50.74 REMARK 500 2 LEU A 81 112.33 -180.00 REMARK 500 2 ASP A 83 74.77 52.45 REMARK 500 2 SER A 86 43.94 -94.06 REMARK 500 2 THR A 88 -177.93 -60.45 REMARK 500 2 LEU A 101 33.00 -94.67 REMARK 500 2 GLN A 102 35.20 -167.13 REMARK 500 2 ALA A 104 111.21 -168.08 REMARK 500 2 PHE A 106 -71.43 -118.43 REMARK 500 2 GLN A 108 56.89 -104.47 REMARK 500 2 SER A 111 31.45 -147.49 REMARK 500 3 ALA A 7 114.37 -161.71 REMARK 500 3 ASP A 15 167.52 -47.69 REMARK 500 3 ASP A 19 119.83 -168.72 REMARK 500 3 THR A 59 73.17 -112.00 REMARK 500 3 GLU A 105 54.61 -151.73 REMARK 500 3 PHE A 106 -69.58 -96.80 REMARK 500 3 GLN A 108 60.43 -116.97 REMARK 500 3 ALA A 109 -51.33 -166.91 REMARK 500 4 MET A 2 -47.15 -157.36 REMARK 500 4 LEU A 3 33.23 79.39 REMARK 500 4 PHE A 10 44.78 -171.45 REMARK 500 4 PHE A 12 -61.52 -166.26 REMARK 500 4 GLU A 51 -67.94 -97.01 REMARK 500 4 GLU A 60 78.49 -159.66 REMARK 500 4 ASP A 83 90.22 53.31 REMARK 500 4 LEU A 101 46.21 -93.90 REMARK 500 4 GLN A 102 -70.53 -165.36 REMARK 500 4 GLU A 105 -136.04 -97.14 REMARK 500 REMARK 500 THIS ENTRY HAS 207 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 27 0.29 SIDE CHAIN REMARK 500 1 ARG A 34 0.24 SIDE CHAIN REMARK 500 1 ARG A 36 0.26 SIDE CHAIN REMARK 500 1 ARG A 42 0.32 SIDE CHAIN REMARK 500 1 ARG A 43 0.20 SIDE CHAIN REMARK 500 1 ARG A 78 0.29 SIDE CHAIN REMARK 500 2 ARG A 27 0.31 SIDE CHAIN REMARK 500 2 ARG A 34 0.24 SIDE CHAIN REMARK 500 2 ARG A 36 0.30 SIDE CHAIN REMARK 500 2 ARG A 42 0.29 SIDE CHAIN REMARK 500 2 ARG A 43 0.28 SIDE CHAIN REMARK 500 2 ARG A 78 0.22 SIDE CHAIN REMARK 500 3 ARG A 27 0.25 SIDE CHAIN REMARK 500 3 ARG A 34 0.21 SIDE CHAIN REMARK 500 3 ARG A 36 0.26 SIDE CHAIN REMARK 500 3 ARG A 42 0.21 SIDE CHAIN REMARK 500 3 ARG A 43 0.32 SIDE CHAIN REMARK 500 3 ARG A 78 0.21 SIDE CHAIN REMARK 500 4 ARG A 27 0.23 SIDE CHAIN REMARK 500 4 ARG A 34 0.26 SIDE CHAIN REMARK 500 4 ARG A 36 0.31 SIDE CHAIN REMARK 500 4 ARG A 42 0.23 SIDE CHAIN REMARK 500 4 ARG A 43 0.30 SIDE CHAIN REMARK 500 4 ARG A 78 0.23 SIDE CHAIN REMARK 500 5 ARG A 27 0.22 SIDE CHAIN REMARK 500 5 ARG A 34 0.23 SIDE CHAIN REMARK 500 5 ARG A 36 0.29 SIDE CHAIN REMARK 500 5 ARG A 42 0.25 SIDE CHAIN REMARK 500 5 ARG A 43 0.24 SIDE CHAIN REMARK 500 5 ARG A 78 0.30 SIDE CHAIN REMARK 500 6 ARG A 27 0.24 SIDE CHAIN REMARK 500 6 ARG A 34 0.28 SIDE CHAIN REMARK 500 6 ARG A 36 0.23 SIDE CHAIN REMARK 500 6 ARG A 42 0.26 SIDE CHAIN REMARK 500 6 ARG A 43 0.27 SIDE CHAIN REMARK 500 6 ARG A 78 0.21 SIDE CHAIN REMARK 500 7 ARG A 27 0.23 SIDE CHAIN REMARK 500 7 ARG A 34 0.28 SIDE CHAIN REMARK 500 7 ARG A 36 0.30 SIDE CHAIN REMARK 500 7 ARG A 42 0.21 SIDE CHAIN REMARK 500 7 ARG A 43 0.26 SIDE CHAIN REMARK 500 7 ARG A 78 0.32 SIDE CHAIN REMARK 500 8 ARG A 27 0.28 SIDE CHAIN REMARK 500 8 ARG A 34 0.29 SIDE CHAIN REMARK 500 8 ARG A 36 0.22 SIDE CHAIN REMARK 500 8 ARG A 42 0.28 SIDE CHAIN REMARK 500 8 ARG A 43 0.24 SIDE CHAIN REMARK 500 8 ARG A 78 0.23 SIDE CHAIN REMARK 500 9 ARG A 27 0.27 SIDE CHAIN REMARK 500 9 ARG A 34 0.22 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 90 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D3Z RELATED DB: PDB REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 1TBE RELATED DB: PDB REMARK 900 TETRA-UBIQUITIN DBREF 1YX4 A -2 112 UNP P55036 PSD4_HUMAN 192 306 SEQADV 1YX4 MET A -19 UNP P55036 CLONING ARTIFACT SEQADV 1YX4 GLY A -18 UNP P55036 CLONING ARTIFACT SEQADV 1YX4 HIS A -17 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -16 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -15 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -14 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -13 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -12 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -11 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -10 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -9 UNP P55036 EXPRESSION TAG SEQADV 1YX4 HIS A -8 UNP P55036 EXPRESSION TAG SEQADV 1YX4 SER A -7 UNP P55036 CLONING ARTIFACT SEQADV 1YX4 SER A -6 UNP P55036 CLONING ARTIFACT SEQADV 1YX4 GLY A -5 UNP P55036 CLONING ARTIFACT SEQADV 1YX4 HIS A -4 UNP P55036 CLONING ARTIFACT SEQADV 1YX4 ILE A -3 UNP P55036 CLONING ARTIFACT SEQADV 1YX4 ARG A 0 UNP P55036 GLY 194 CLONING ARTIFACT SEQADV 1YX4 HIS A 1 UNP P55036 ALA 195 CLONING ARTIFACT SEQRES 1 A 132 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 132 SER GLY HIS ILE GLU GLY ARG HIS MET LEU GLY LEU GLY SEQRES 3 A 132 ALA SER ASP PHE GLU PHE GLY VAL ASP PRO SER ALA ASP SEQRES 4 A 132 PRO GLU LEU ALA LEU ALA LEU ARG VAL SER MET GLU GLU SEQRES 5 A 132 GLN ARG GLN ARG GLN GLU GLU GLU ALA ARG ARG ALA ALA SEQRES 6 A 132 ALA ALA SER ALA ALA GLU ALA GLY ILE ALA THR THR GLY SEQRES 7 A 132 THR GLU ASP SER ASP ASP ALA LEU LEU LYS MET THR ILE SEQRES 8 A 132 SER GLN GLN GLU PHE GLY ARG THR GLY LEU PRO ASP LEU SEQRES 9 A 132 SER SER MET THR GLU GLU GLU GLN ILE ALA TYR ALA MET SEQRES 10 A 132 GLN MET SER LEU GLN GLY ALA GLU PHE GLY GLN ALA GLU SEQRES 11 A 132 SER ALA HELIX 1 1 PRO A 16 ALA A 18 5 3 HELIX 2 2 PRO A 20 GLU A 51 1 32 HELIX 3 3 ASP A 63 GLU A 75 1 13 HELIX 4 4 GLU A 89 SER A 100 1 12 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