HEADER RIBOSOMAL PROTEIN 04-JAN-19 6J3L TITLE SOLUTION STRUCTURE OF THE N-TERMINAL EXTENDED PROTUBERANT DOMAIN OF TITLE 2 EUKARYOTIC RIBOSOMAL STALK PROTEIN P0 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 60S ACIDIC RIBOSOMAL PROTEIN P0; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: GSHM IS THE CLONING ARTEFACT LEFT AFTER THROMBIN COMPND 6 DIGESTION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: SILK MOTH; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 GENE: P0; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3) PLYSS KEYWDS P0, RIBOSOMAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.H.A.CHOI,K.M.LEE,L.YANG,C.WING-HENG YU,D.K.BANFIELD,K.ITO, AUTHOR 2 T.UCHIUMI,K.B.WONG REVDAT 3 14-JUN-23 6J3L 1 REMARK REVDAT 2 25-SEP-19 6J3L 1 JRNL REVDAT 1 04-SEP-19 6J3L 0 JRNL AUTH K.A.CHOI,L.YANG,K.M.LEE,C.W.YU,D.K.BANFIELD,K.ITO,T.UCHIUMI, JRNL AUTH 2 K.B.WONG JRNL TITL STRUCTURAL AND MUTAGENESIS STUDIES EVINCE THE ROLE OF THE JRNL TITL 2 EXTENDED PROTUBERANT DOMAIN OF RIBOSOMAL PROTEIN UL10 IN JRNL TITL 3 PROTEIN TRANSLATION. JRNL REF BIOCHEMISTRY V. 58 3744 2019 JRNL REFN ISSN 0006-2960 JRNL PMID 31419120 JRNL DOI 10.1021/ACS.BIOCHEM.9B00528 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6J3L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1300010321. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] N REMARK 210 -TERMINAL EXTENDED PROTUBERANT REMARK 210 DOMAIN OF P0, 20 MM SODIUM REMARK 210 PHOSPHATE, 5 % V/V GLYCEROL, 150 REMARK 210 MM SODIUM CHLORIDE, 1 MM TCEP, REMARK 210 90% H2O/10% D2O; 1 MM [U-10% 13C] REMARK 210 N-TERMINAL EXTENDED PROTUBERANT REMARK 210 DOMAIN OF P0, 20 MM SODIUM REMARK 210 PHOSPHATE, 5 % V/V GLYCEROL, 150 REMARK 210 MM SODIUM CHLORIDE, 1 MM TCEP, REMARK 210 90% H2O/10% D2O; 1 MM UNLABEL N- REMARK 210 TERMINAL EXTENDED PROTUBERANT REMARK 210 DOMAIN OF P0, 20 MM SODIUM REMARK 210 PHOSPHATE, 5 % V/V GLYCEROL, 150 REMARK 210 MM SODIUM CHLORIDE, 1 MM TCEP, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 2D 1H-13C HSQC; 2D 1H REMARK 210 -15N HSQC; 2D 1H-1H NOESY; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; HSQC-NOESY-HSQC; 3D REMARK 210 HN(CO)CA; 3D HN(CA)CO; 3D 1H-15N REMARK 210 TOCSY; 3D (H)CC(CO)NH; 3D H(CC) REMARK 210 (CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.2, CNS 1.2, NMRVIEW J8, REMARK 210 TOPSPIN 3.2 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 900 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 101 REMARK 465 SER A 102 REMARK 465 HIS A 103 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 ASN A 105 -58.94 -138.95 REMARK 500 1 LYS A 106 54.79 -108.14 REMARK 500 1 PRO A 110 86.36 -63.79 REMARK 500 1 SER A 148 -83.33 -99.96 REMARK 500 1 LYS A 149 53.34 -113.36 REMARK 500 1 PRO A 163 101.87 -56.56 REMARK 500 1 PHE A 183 -79.21 -135.50 REMARK 500 2 ASN A 105 -38.18 -149.06 REMARK 500 2 PRO A 110 84.18 -63.29 REMARK 500 2 PRO A 132 6.58 -69.38 REMARK 500 2 PRO A 163 108.89 -44.85 REMARK 500 2 PHE A 183 -70.32 -120.23 REMARK 500 3 ASN A 105 -72.89 -160.56 REMARK 500 3 VAL A 107 70.95 -104.15 REMARK 500 3 GLN A 108 95.18 -162.39 REMARK 500 3 PRO A 110 74.68 -64.50 REMARK 500 3 HIS A 126 -56.69 -151.79 REMARK 500 3 LYS A 149 -67.77 -170.64 REMARK 500 3 PRO A 163 101.48 -44.00 REMARK 500 3 PHE A 183 -76.36 -113.85 REMARK 500 4 VAL A 107 -73.20 -72.48 REMARK 500 4 PRO A 110 78.69 -66.06 REMARK 500 4 LYS A 149 60.05 -156.18 REMARK 500 4 PRO A 163 100.82 -54.02 REMARK 500 4 PHE A 183 -73.85 -109.16 REMARK 500 5 ASN A 105 -56.49 -145.32 REMARK 500 5 GLN A 108 92.67 67.19 REMARK 500 5 LYS A 149 -70.88 -168.27 REMARK 500 5 PRO A 163 105.86 -54.64 REMARK 500 5 SER A 181 71.87 60.76 REMARK 500 5 PHE A 183 -61.37 -125.62 REMARK 500 6 PRO A 110 96.26 -58.40 REMARK 500 6 LYS A 149 81.76 -158.51 REMARK 500 6 PRO A 163 103.81 -51.32 REMARK 500 6 ALA A 169 -70.33 -70.11 REMARK 500 6 PHE A 183 -125.15 -120.90 REMARK 500 6 SER A 184 -73.39 -108.12 REMARK 500 7 ASN A 105 -60.60 -163.33 REMARK 500 7 LYS A 106 -72.25 -111.29 REMARK 500 7 VAL A 107 46.32 -160.87 REMARK 500 7 PRO A 110 93.84 -68.43 REMARK 500 7 LYS A 149 -58.73 -163.30 REMARK 500 7 PRO A 163 96.01 -55.86 REMARK 500 7 PHE A 183 -89.39 -130.30 REMARK 500 8 LYS A 106 76.52 55.03 REMARK 500 8 PRO A 110 106.51 -55.65 REMARK 500 8 HIS A 126 -50.53 -158.78 REMARK 500 8 ASN A 127 150.19 173.57 REMARK 500 8 SER A 148 -72.34 -74.86 REMARK 500 8 PRO A 163 106.15 -44.87 REMARK 500 REMARK 500 THIS ENTRY HAS 63 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36233 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE N-TERMINAL EXTENDED PROTUBERANT DOMAIN OF REMARK 900 EUKARYOTIC RIBOSOMAL STALK PROTEIN P0 DBREF 6J3L A 105 186 UNP Q70YZ3 Q70YZ3_BOMMO 105 186 SEQADV 6J3L GLY A 101 UNP Q70YZ3 CLONING ARTIFACT SEQADV 6J3L SER A 102 UNP Q70YZ3 CLONING ARTIFACT SEQADV 6J3L HIS A 103 UNP Q70YZ3 CLONING ARTIFACT SEQADV 6J3L MET A 104 UNP Q70YZ3 CLONING ARTIFACT SEQRES 1 A 86 GLY SER HIS MET ASN LYS VAL GLN ALA PRO ALA ARG PRO SEQRES 2 A 86 GLY ALA ILE ALA PRO LEU SER VAL VAL ILE PRO ALA HIS SEQRES 3 A 86 ASN THR GLY LEU GLY PRO GLU LYS THR SER PHE PHE GLN SEQRES 4 A 86 ALA LEU SER ILE PRO THR LYS ILE SER LYS GLY THR ILE SEQRES 5 A 86 GLU ILE ILE ASN ASP VAL HIS ILE LEU LYS PRO GLY ASP SEQRES 6 A 86 LYS VAL GLY ALA SER GLU ALA THR LEU LEU ASN MET LEU SEQRES 7 A 86 ASN ILE SER PRO PHE SER TYR GLY HELIX 1 AA1 LYS A 134 LEU A 141 1 8 HELIX 2 AA2 GLY A 168 LEU A 178 1 11 SHEET 1 AA1 2 GLY A 114 ALA A 117 0 SHEET 2 AA1 2 GLY A 164 VAL A 167 -1 O ASP A 165 N ALA A 117 SHEET 1 AA2 2 THR A 145 ILE A 147 0 SHEET 2 AA2 2 ILE A 152 ILE A 154 -1 O GLU A 153 N LYS A 146 SHEET 1 AA3 2 VAL A 121 ILE A 123 0 SHEET 2 AA3 2 VAL A 158 LEU A 161 -1 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