HEADER RIBOSOME/RNA 28-APR-99 1CK8 OBSLTE 25-JUL-06 1CK8 1T0K TITLE RPL30-MRNA COMPLEX FROM YEAST CAVEAT 1CK8 THERE ARE CHIRALITY ERRORS IN C-ALPHA CENTERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: L30 33 NUCLEOTIDE RNA YL32; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: YEAST L30 PRE-MRNA BINDING SITE; COMPND 5 SYNONYM: RPL32,YGL030W; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 60S RIBOSOMAL PROTEIN L30; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: RL30_YEAST, YL32,RP73; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 CELLULAR_LOCATION: NUCLEI; SOURCE 5 GENE: YSCRPL32; SOURCE 6 OTHER_DETAILS: SYNTHESIZED USING IN VITRO T7 POLYMERASE; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 9 ORGANISM_COMMON: YEAST; SOURCE 10 ORGANELLE: RIBOSOME,60S SUBUNIT; SOURCE 11 CELLULAR_LOCATION: CYTOPLASM; SOURCE 12 GENE: YSCRPL32; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 17 EXPRESSION_SYSTEM_PLASMID: PMALC-L30; SOURCE 18 EXPRESSION_SYSTEM_GENE: L30; SOURCE 19 OTHER_DETAILS: RECOMBINANT EXPRESSION AS A C-TERMINAL SOURCE 20 MALTOSE-BINDING PROTEIN FUSION IN ESCHERICHIA COLI STRAIN SOURCE 21 JM109 HOSTING PLASMID PMALC-30 KEYWDS RIBOSOMAL PROTEIN, PRE-MRNA, MRNA, AUTOREGULATION, PROTEIN- KEYWDS 2 RNA COMPLEX, NMR EXPDTA NMR, 21 STRUCTURES AUTHOR H.MAO,S.A.WHITE,J.R.WILLAMSON REVDAT 4 25-JUL-06 1CK8 1 OBSLTE REVDAT 3 01-APR-03 1CK8 1 JRNL REVDAT 2 27-MAR-00 1CK8 3 ATOM REVDAT 1 02-DEC-99 1CK8 0 JRNL AUTH H.MAO,S.A.WHITE,J.R.WILLIAMSON JRNL TITL A NOVEL LOOP-LOOP RECOGNITION MOTIF IN THE YEAST JRNL TITL 2 RIBOSOMAL PROTEIN L30 AUTOREGULATORY RNA COMPLEX. JRNL REF NAT.STRUCT.BIOL. V. 6 1139 1999 JRNL REFN ASTM NSBIEW US ISSN 1072-8368 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.LI,S.DALAL,J.KOHLER,J.VILARDELL,S.A.WHITE REMARK 1 TITL CHARACTERIZATION OF THE PRE-MRNA BINDING SITE FOR REMARK 1 TITL 2 YEAST RIBOSOMAL PROTEIN L32: THE IMPORTANCE OF A REMARK 1 TITL 3 PURINE-RICH LOOP REMARK 1 REF J.MOL.BIOL. V. 250 447 1995 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH F.J.ENG,J.R.WARNER REMARK 1 TITL STRUCTURAL BASIS FOR THE REGULATION OF SPLICING OF REMARK 1 TITL 2 A YEAST MESSENGER RNA REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 65 797 1991 REMARK 1 REFN ASTM CELLB5 US ISSN 0092-8674 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CONSTRAINTS: DISTANCE PROTEIN REMARK 3 INTRARESIDUE NOES: 898; INTERRESIDUE NOES: 1175; SEQUENTIAL (| REMARK 3 I-J|=1): 512; SHORT-RANGE (|I-J|<=4): 328; LONG-RANGE (|I-J|> REMARK 3 4): 335; HYDROGEN BONDS: 56; TOTAL: 2129. RNA INTRARESIDUE REMARK 3 NOES: 249; INTERRESIDUE NOES: 221 SEQUENTIAL (|I-J|=1): 159; REMARK 3 SHORT-RANGE (|I-J|<=4): 12; LONG-RANGE (| I-J|>1): 50; REMARK 3 HYDROGEN BONDS: 77; TOTAL 547. PROTEIN-RNA INTRARMOLECULE REMARK 3 NOES: 73; TORSION PROTEIN BACKBONE PHI: 76; SIDECHAIN KAI1: REMARK 3 59; TOTAL 135 RNA GLYCOSIDIC KAI, DELTA AND AMINO 107; TOTAL REMARK 3 107 REMARK 4 REMARK 4 1CK8 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-19) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-1999. REMARK 100 THE RCSB ID CODE IS RCSB000964. REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4' INSTEAD OF O1'. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 10% WATER/90% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, COSY, TOCSY, HNCA, REMARK 210 HNCO, HN(CO)CA, HNCACB, REMARK 210 HCCHTOCSY, NOESYHSQC, HNHA, REMARK 210 HMQC-J REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING MOLECULAR REMARK 210 DYNAMIC REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE REMARK 210 NMR SPECTROSCOPY ON 13C, 15N-LABELED L30 PROTEIN AND 13C, 15N- REMARK 210 LABELED RNA IN COMPLEXED WITH THEIR UNLABELED COUNTERPARTS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 12 GLU B 55 CB - CA - C ANGL. DEV. = 16.0 DEGREES REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 THR B 65 LYS B 66 1 -148.22 REMARK 500 ALA B 95 GLY B 96 1 -65.00 REMARK 500 ALA B 95 GLY B 96 2 -134.71 REMARK 500 ASP B 99 ILE B 100 2 -148.06 REMARK 500 LEU B 104 ALA B 105 2 143.41 REMARK 500 LYS B 5 SER B 6 3 -143.59 REMARK 500 ALA B 95 GLY B 96 3 -120.15 REMARK 500 ALA B 95 GLY B 96 4 -119.88 REMARK 500 LEU B 104 ALA B 105 4 148.84 REMARK 500 ALA B 95 GLY B 96 5 -111.47 REMARK 500 LYS B 40 LEU B 41 6 145.42 REMARK 500 ASN B 74 ASN B 75 6 149.35 REMARK 500 ALA B 95 GLY B 96 6 -136.51 REMARK 500 ASP B 99 ILE B 100 6 -149.69 REMARK 500 LEU B 104 ALA B 105 6 148.75 REMARK 500 LYS B 5 SER B 6 7 -144.21 REMARK 500 ALA B 95 GLY B 96 7 -138.59 REMARK 500 LEU B 104 ALA B 105 7 -141.55 REMARK 500 ALA B 95 GLY B 96 8 -62.35 REMARK 500 GLU B 8 SER B 9 9 147.55 REMARK 500 SER B 39 LYS B 40 9 145.83 REMARK 500 ALA B 95 GLY B 96 9 -137.32 REMARK 500 LEU B 104 ALA B 105 9 145.06 REMARK 500 SER B 39 LYS B 40 10 143.44 REMARK 500 ALA B 95 GLY B 96 10 -102.70 REMARK 500 SER B 39 LYS B 40 11 140.48 REMARK 500 ALA B 95 GLY B 96 11 -122.51 REMARK 500 GLU B 8 SER B 9 12 147.95 REMARK 500 SER B 39 LYS B 40 12 143.50 REMARK 500 ALA B 95 GLY B 96 12 -137.77 REMARK 500 ALA B 95 GLY B 96 13 -126.20 REMARK 500 LEU B 104 ALA B 105 13 145.69 REMARK 500 LYS B 5 SER B 6 14 -149.01 REMARK 500 ASN B 74 ASN B 75 14 144.31 REMARK 500 ALA B 95 GLY B 96 14 -136.49 REMARK 500 ALA B 95 GLY B 96 15 -142.68 REMARK 500 LEU B 104 ALA B 105 15 -146.49 REMARK 500 GLU B 8 SER B 9 16 149.59 REMARK 500 THR B 65 LYS B 66 16 -147.90 REMARK 500 ALA B 95 GLY B 96 16 -62.11 REMARK 500 LYS B 5 SER B 6 17 -147.80 REMARK 500 ASN B 74 ASN B 75 17 149.47 REMARK 500 ALA B 95 GLY B 96 17 -135.64 REMARK 500 ASP B 99 ILE B 100 17 -149.80 REMARK 500 SER B 39 LYS B 40 18 141.72 REMARK 500 ALA B 95 GLY B 96 19 -133.71 REMARK 500 ALA B 95 GLY B 96 20 -137.08 REMARK 500 ASP B 99 ILE B 100 20 -149.80 REMARK 500 GLU B 8 SER B 9 21 146.63 REMARK 500 ASN B 74 ASN B 75 21 149.93 REMARK 500 ALA B 95 GLY B 96 21 -115.14 REMARK 999 REMARK 999 SEQUENCE REFERENCES: REMARK 999 LI ET AL. (1995) J.MOL.BIOL. 250, P447. REMARK 999 DEBEVA ET AL. (1987) J.BIOL.CHEM. 262,P 16055. DBREF 1CK8 B 2 105 UNP P14120 RL30_YEAST 2 105 SEQRES 1 A 33 G G A C C G G A G U G U C SEQRES 2 A 33 G C A A G A C G C A G A G SEQRES 3 A 33 A U G G U C C SEQRES 1 B 104 ALA PRO VAL LYS SER GLN GLU SER ILE ASN GLN LYS LEU SEQRES 2 B 104 ALA LEU VAL ILE LYS SER GLY LYS TYR THR LEU GLY TYR SEQRES 3 B 104 LYS SER THR VAL LYS SER LEU ARG GLN GLY LYS SER LYS SEQRES 4 B 104 LEU ILE ILE ILE ALA ALA ASN THR PRO VAL LEU ARG LYS SEQRES 5 B 104 SER GLU LEU GLU TYR TYR ALA MET LEU SER LYS THR LYS SEQRES 6 B 104 VAL TYR TYR PHE GLN GLY GLY ASN ASN GLU LEU GLY THR SEQRES 7 B 104 ALA VAL GLY LYS LEU PHE ARG VAL GLY VAL VAL SER ILE SEQRES 8 B 104 LEU GLU ALA GLY ASP SER ASP ILE LEU THR THR LEU ALA HELIX 1 1 GLN B 7 ILE B 18 5 12 HELIX 2 2 LYS B 28 GLN B 36 1 9 HELIX 3 3 VAL B 17 SER B 63 1 47 HELIX 4 4 GLY B 73 ALA B 80 1 8 HELIX 5 5 ILE B 100 THR B 103 1 4 SHEET 1 A 4 TYR B 23 LEU B 25 0 SHEET 2 A 4 VAL B 89 ILE B 92 -1 N SER B 91 O THR B 24 SHEET 3 A 4 ILE B 42 ALA B 45 -1 N ILE B 10 O VAL B 90 SHEET 4 A 4 VAL B 67 PHE B 70 1 N TYR B 68 O ILE B 42 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