HEADER RNA 08-MAY-02 1LPW TITLE SOLUTION STRUCTURE OF THE YEAST SPLICEOSOMAL U2 SNRNA- TITLE 2 INTRON BRANCH SITE HELIX FEATURING A CONSERVED TITLE 3 PSEUDOURIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*UP*GP*(PSU)P*AP*GP*UP*A)-3'; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: U2 SNRNA; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-R(*UP*AP*CP*UP*AP*AP*CP*AP*CP*C)-3'; COMPND 7 CHAIN: B; COMPND 8 OTHER_DETAILS: PRE-MRNA CONSERVED INTRON BRANCH SITE COMPND 9 SEQUENCE SITE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 7 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 8 ORGANISM_TAXID: 4932 KEYWDS U2 SNRNA, BRANCH SITE, NMR, PSEUDOURIDINE EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR M.I.NEWBY,N.L.GREENBAUM REVDAT 2 24-FEB-09 1LPW 1 VERSN REVDAT 1 27-NOV-02 1LPW 0 JRNL AUTH M.I.NEWBY,N.L.GREENBAUM JRNL TITL SCULPTING OF THE SPLICEOSOMAL BRANCH SITE JRNL TITL 2 RECOGNITION MOTIF BY A CONSERVED PSEUDOURIDINE JRNL REF NAT.STRUCT.BIOL. V. 12 958 2002 JRNL REFN ISSN 1072-8368 JRNL PMID 12426583 JRNL DOI 10.1038/NSB873 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 191 DISTANCE RESTRAINTS REMARK 3 WERE USED, NOT INCLUDING THE 40 HYDROGEN BOND DISTANCES REMARK 3 IMPOSED. INCLUDING THE 133 DIHEDRAL RESTRAINTS APPLIED IN REMARK 3 STRUCTURE CALCULATIONS, 353 TOTAL RESTRAINTS WERE APPLIED. REMARK 4 REMARK 4 1LPW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAY-02. REMARK 100 THE RCSB ID CODE IS RCSB016167. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 293 REMARK 210 PH : 6.4; 6.4 REMARK 210 IONIC STRENGTH : 50MM SODIUM CHLORIDE; 50MM REMARK 210 SODIUM CHLORIDE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM U2 SNRNA-INTRON DUPLEX; REMARK 210 10MM SODIUM PHOSPHATE; 1MM U2 REMARK 210 SNRNA-INTRON DUPLEX; 10MM REMARK 210 SODIUM PHOSPHATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 720 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 5.3, SPARKY 3.69, VNMR REMARK 210 3.851 REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR REMARK 210 DYNAMICS FOLLOWED BY CONJUGATE REMARK 210 GRADIENT MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 800 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY STRUCTURES THAT REMARK 210 DID NOT VIOLATE DATA FROM REMARK 210 FLUORESCENCE EXPERIMENTS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. NOESY SPECTRA WERE COLLECTED AT MANY REMARK 210 DIFFERENT MIXING TIMES, SO THAT THE BUILDUP OF CERTAIN NOES REMARK 210 COULD BE OBSERVED TO RESOLVE SOME SPECTRAL OVERLAP. 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 A A 9 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 U B 1 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 C B 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 A B 8 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 U A 3 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 A A 9 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 U B 1 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 A B 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 A B 8 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 3 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 U B 1 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 3 A B 2 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 3 A B 6 C4' - C3' - C2' ANGL. DEV. = -6.4 DEGREES REMARK 500 3 A B 8 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 3 C B 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 U B 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 A B 2 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 4 A B 6 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 A B 8 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 5 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 G A 2 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 5 U B 1 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 5 A B 2 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 C B 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 A B 5 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 5 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 A B 8 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 6 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 6 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 6 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 U B 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 6 A B 2 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 6 A B 8 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 6 C B 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 G A 2 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 7 U B 1 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 7 A B 2 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 C B 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 7 A B 6 C4' - C3' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 7 A B 5 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 65 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LMV RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE UNMODIFIED U2 SNRNA-INTRON BRANCH REMARK 900 SITE HELIX REMARK 999 REMARK 999 SEQUENCE REMARK 999 POSITION 35 IN U2 SNRNA SEQUENCES FROM S. REMARK 999 CEREVISIAE IS A PSEUDOURIDINE. THIS CORRESPONDS REMARK 999 TO POSITION 5 ON STRAND A, WHICH IS A URIDINE IN REMARK 999 1LMV, AND A PSEUDOURIDINE IN 1LPW. DBREF 1LPW A 1 9 PDB 1LPW 1LPW 1 9 DBREF 1LPW B 1 10 PDB 1LPW 1LPW 1 10 SEQRES 1 A 9 G G U G PSU A G U A SEQRES 1 B 10 U A C U A A C A C C MODRES 1LPW PSU A 5 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET PSU A 5 30 HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE FORMUL 1 PSU C9 H13 N2 O9 P LINK O3' G A 4 P PSU A 5 1555 1555 1.60 LINK O3' PSU A 5 P A A 6 1555 1555 1.61 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 141 0 1 0 0 0 0 6 0 0 0 2 END