HEADER UBIQUITIN-BINDING PROTEIN 02-AUG-16 5LN1 TITLE STRUCTURE OF UBIQUITYLATED-RPN10 FROM YEAST; COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN10; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-191; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: POLYUBIQUITIN-B; COMPND 8 CHAIN: U; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: RPN10, MCB1, SUN1, YHR200W; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: UBB; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, VWA, UBIQUITYLATION, PROTEASOME, UBIQUITIN-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KEREN-KAPLAN,I.ATTALI,O.LEVIN-KRAVETS,G.PRAG REVDAT 3 10-JAN-24 5LN1 1 REMARK REVDAT 2 08-MAY-19 5LN1 1 REMARK LINK REVDAT 1 19-OCT-16 5LN1 0 JRNL AUTH T.KEREN-KAPLAN,L.ZEEV PETERS,O.LEVIN-KRAVETS,I.ATTALI, JRNL AUTH 2 O.KLEIFELD,N.SHOHAT,S.ARTZI,O.ZUCKER,I.PILZER,N.REIS, JRNL AUTH 3 M.H.GLICKMAN,S.BEN-AROYA,G.PRAG JRNL TITL STRUCTURE OF UBIQUITYLATED-RPN10 PROVIDES INSIGHT INTO ITS JRNL TITL 2 AUTOREGULATION MECHANISM. JRNL REF NAT COMMUN V. 7 12960 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27698474 JRNL DOI 10.1038/NCOMMS12960 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.KEREN-KAPLAN,G.PRAG REMARK 1 TITL PURIFICATION AND CRYSTALLIZATION OF MONO-UBIQUITYLATED REMARK 1 TITL 2 UBIQUITIN RECEPTOR RPN10. REMARK 1 REF ACTA CRYSTALLOGR. SECT. F V. 68 1120 2012 REMARK 1 REF 2 STRUCT. BIOL. CRYST. COMMUN. REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 22949210 REMARK 1 DOI 10.1107/S1744309112034331 REMARK 2 REMARK 2 RESOLUTION. 3.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 5823 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.570 REMARK 3 FREE R VALUE TEST SET COUNT : 571 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 53.6486 - 3.2490 0.99 2803 140 0.1763 0.2099 REMARK 3 2 3.2490 - 3.1400 1.00 2754 126 0.2111 0.3164 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2098 REMARK 3 ANGLE : 1.409 2836 REMARK 3 CHIRALITY : 0.101 337 REMARK 3 PLANARITY : 0.006 371 REMARK 3 DIHEDRAL : 17.541 796 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5LN1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200000860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5824 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.140 REMARK 200 RESOLUTION RANGE LOW (A) : 61.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 9.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : 0.09800 REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.22500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2X5N, 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG 20000, 0.1M MES PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 292K, EVAPORATION, REMARK 280 RECRYSTALLIZATION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 53.64500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.64500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.85000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, U 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -52.87356 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 61.79770 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -3 REMARK 465 PRO A -2 REMARK 465 PRO A -1 REMARK 465 ARG A 0 REMARK 465 ASN A 150 REMARK 465 THR A 151 REMARK 465 GLU A 152 REMARK 465 GLY U -4 REMARK 465 ALA U -3 REMARK 465 MET U -2 REMARK 465 GLY U -1 REMARK 465 SER U 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 NZ LYS A 84 C GLY U 76 1.33 REMARK 500 O GLN A 149 N LEU A 153 2.06 REMARK 500 OE2 GLU A 4 NZ LYS A 40 2.18 REMARK 500 OD1 ASP A 11 OG SER A 13 2.19 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 ASN A 44 131.06 -175.83 REMARK 500 ALA A 57 3.82 156.78 REMARK 500 ASN A 58 104.93 158.09 REMARK 500 ASP A 78 -3.83 100.26 REMARK 500 ASN A 103 73.86 61.73 REMARK 500 ARG U 74 -80.63 -93.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LN1 A 1 191 UNP P38886 RPN10_YEAST 1 191 DBREF 5LN1 U 1 76 UNP P0CG47 UBB_HUMAN 77 152 SEQADV 5LN1 GLY A -3 UNP P38886 EXPRESSION TAG SEQADV 5LN1 PRO A -2 UNP P38886 EXPRESSION TAG SEQADV 5LN1 PRO A -1 UNP P38886 EXPRESSION TAG SEQADV 5LN1 ARG A 0 UNP P38886 EXPRESSION TAG SEQADV 5LN1 GLY U -4 UNP P0CG47 EXPRESSION TAG SEQADV 5LN1 ALA U -3 UNP P0CG47 EXPRESSION TAG SEQADV 5LN1 MET U -2 UNP P0CG47 EXPRESSION TAG SEQADV 5LN1 GLY U -1 UNP P0CG47 EXPRESSION TAG SEQADV 5LN1 SER U 0 UNP P0CG47 EXPRESSION TAG SEQRES 1 A 195 GLY PRO PRO ARG MET VAL LEU GLU ALA THR VAL LEU VAL SEQRES 2 A 195 ILE ASP ASN SER GLU TYR SER ARG ASN GLY ASP PHE PRO SEQRES 3 A 195 ARG THR ARG PHE GLU ALA GLN ILE ASP SER VAL GLU PHE SEQRES 4 A 195 ILE PHE GLN ALA LYS ARG ASN SER ASN PRO GLU ASN THR SEQRES 5 A 195 VAL GLY LEU ILE SER GLY ALA GLY ALA ASN PRO ARG VAL SEQRES 6 A 195 LEU SER THR PHE THR ALA GLU PHE GLY LYS ILE LEU ALA SEQRES 7 A 195 GLY LEU HIS ASP THR GLN ILE GLU GLY LYS LEU HIS MET SEQRES 8 A 195 ALA THR ALA LEU GLN ILE ALA GLN LEU THR LEU LYS HIS SEQRES 9 A 195 ARG GLN ASN LYS VAL GLN HIS GLN ARG ILE VAL ALA PHE SEQRES 10 A 195 VAL CYS SER PRO ILE SER ASP SER ARG ASP GLU LEU ILE SEQRES 11 A 195 ARG LEU ALA LYS THR LEU LYS LYS ASN ASN VAL ALA VAL SEQRES 12 A 195 ASP ILE ILE ASN PHE GLY GLU ILE GLU GLN ASN THR GLU SEQRES 13 A 195 LEU LEU ASP GLU PHE ILE ALA ALA VAL ASN ASN PRO GLN SEQRES 14 A 195 GLU GLU THR SER HIS LEU LEU THR VAL THR PRO GLY PRO SEQRES 15 A 195 ARG LEU LEU TYR GLU ASN ILE ALA SER SER PRO ILE ILE SEQRES 1 U 81 GLY ALA MET GLY SER MET GLN ILE PHE VAL LYS THR LEU SEQRES 2 U 81 THR GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP SEQRES 3 U 81 THR ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU SEQRES 4 U 81 GLY ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 U 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 U 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 U 81 ARG GLY GLY HELIX 1 AA1 SER A 13 ARG A 17 5 5 HELIX 2 AA2 THR A 24 ASN A 44 1 21 HELIX 3 AA3 GLU A 68 HIS A 77 1 10 HELIX 4 AA4 HIS A 86 HIS A 100 1 15 HELIX 5 AA5 SER A 121 ASN A 135 1 15 HELIX 6 AA6 GLN A 149 GLN A 149 1 1 HELIX 7 AA7 LEU A 154 ASN A 162 1 9 HELIX 8 AA8 LEU A 180 SER A 188 1 9 HELIX 9 AA9 THR U 22 GLY U 35 1 14 HELIX 10 AB1 PRO U 37 ASP U 39 5 3 SHEET 1 AA1 6 ARG A 60 THR A 66 0 SHEET 2 AA1 6 THR A 48 SER A 53 -1 N VAL A 49 O THR A 66 SHEET 3 AA1 6 GLU A 4 ILE A 10 1 N LEU A 8 O GLY A 50 SHEET 4 AA1 6 HIS A 107 VAL A 114 1 O VAL A 111 N VAL A 7 SHEET 5 AA1 6 VAL A 137 ASN A 143 1 O ILE A 142 N ALA A 112 SHEET 6 AA1 6 LEU A 171 THR A 173 1 O LEU A 172 N ASN A 143 SHEET 1 AA2 5 THR U 12 GLU U 16 0 SHEET 2 AA2 5 GLN U 2 THR U 7 -1 N VAL U 5 O ILE U 13 SHEET 3 AA2 5 THR U 66 LEU U 71 1 O LEU U 67 N PHE U 4 SHEET 4 AA2 5 GLN U 41 PHE U 45 -1 N ILE U 44 O HIS U 68 SHEET 5 AA2 5 LYS U 48 GLN U 49 -1 O LYS U 48 N PHE U 45 CISPEP 1 PRO A 22 ARG A 23 0 -2.63 CRYST1 107.290 49.700 81.330 90.00 130.55 90.00 C 1 2 1 4 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 0.009321 0.000000 0.007975 0.00000 SCALE2 0.000000 0.020121 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016182 0.00000