HEADER RNA 08-MAY-02 1LPW TITLE SOLUTION STRUCTURE OF THE YEAST SPLICEOSOMAL U2 SNRNA-INTRON BRANCH TITLE 2 SITE HELIX FEATURING A CONSERVED 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 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, PSEUDOURIDINE, RNA EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR M.I.NEWBY,N.L.GREENBAUM REVDAT 3 23-FEB-22 1LPW 1 REMARK LINK 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 RECOGNITION MOTIF JRNL TITL 2 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 5.3, X-PLOR 3.851 REMARK 3 AUTHORS : VARIAN, INC. (VNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 191 DISTANCE RESTRAINTS WERE REMARK 3 USED, NOT INCLUDING THE 40 HYDROGEN BOND DISTANCES IMPOSED. REMARK 3 INCLUDING THE 133 DIHEDRAL RESTRAINTS APPLIED IN STRUCTURE REMARK 3 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 DEPOSITION ID IS D_1000016167. 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; 10MM REMARK 210 SODIUM PHOSPHATE; 1MM U2 SNRNA- REMARK 210 INTRON DUPLEX; 10MM SODIUM REMARK 210 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 : SPARKY 3.69, VNMR 3.851 REMARK 210 METHOD USED : TORSION ANGLE MOLECULAR DYNAMICS REMARK 210 FOLLOWED BY CONJUGATE GRADIENT REMARK 210 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL 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. = 5.2 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 5 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 7 A B 6 C4' - C3' - C2' ANGL. DEV. = -6.1 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 SITE REMARK 900 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 MODEL 1