HEADER RNA 06-JUL-04 1TXS TITLE STEM-LOOP D OF THE CLOVERLEAF DOMAIN OF ENTEROVIRAL 5'UTR RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENTEROVIRAL 5'-UTR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 4 RNA POLYMERASE KEYWDS TETRALOOP UACG, CLOSING WOBBLE UG PAIR, PYRIMIDINE-PYRIMIDINE KEYWDS 2 MISMATCHES, TWO-NUCLEOTIDE BULGE, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Z.DU,J.YU,N.B.ULYANOV,R.ANDINO,T.L.JAMES REVDAT 3 02-MAR-22 1TXS 1 REMARK REVDAT 2 24-FEB-09 1TXS 1 VERSN REVDAT 1 05-OCT-04 1TXS 0 JRNL AUTH Z.DU,J.YU,N.B.ULYANOV,R.ANDINO,T.L.JAMES JRNL TITL SOLUTION STRUCTURE OF A CONSENSUS STEM-LOOP D RNA DOMAIN JRNL TITL 2 THAT PLAYS IMPORTANT ROLES IN REGULATING TRANSLATION AND JRNL TITL 3 REPLICATION IN ENTEROVIRUSES AND RHINOVIRUSES JRNL REF BIOCHEMISTRY V. 43 11959 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15379536 JRNL DOI 10.1021/BI048973P REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, DYANA 1.5, XPLOR NIH REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT (DYANA), BRUNGER (XPLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TXS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023012. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298; 303 REMARK 210 PH : 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 25 MM SODIUM CHLORIDE, 25 MM REMARK 210 SODIUM PHOSPHATE; 25 MM SODIUM REMARK 210 CHLORIDE, 25 MM SODIUM PHOSPHATE; REMARK 210 25 MM SODIUM CHLORIDE, 25 MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MM UNLABELED RNA, 25 MM REMARK 210 SODIUM CHLORIDE, 25 MM SODIUM REMARK 210 PHOSPHATE; 1-2 MM UNLABELED RNA, REMARK 210 25 MM SODIUM CHLORIDE, 25 MM REMARK 210 SODIUM PHOSPHATE; 1-2 MM 13C&15N- REMARK 210 LABELED RNA, 25 MM SODIUM REMARK 210 CHLORIDE, 25 MM SODIUM PHOSPHATE; REMARK 210 1-2 MM 13C&15N-LABELED RNA, 25 REMARK 210 MM SODIUM CHLORIDE, 25 MM SODIUM REMARK 210 PHOSPHATE; 1-2 MM 13C&15N- REMARK 210 LABELED RNA, 25 MM SODIUM REMARK 210 CHLORIDE, 25 MM SODIUM PHOSPHATE, REMARK 210 2.5% (WEIGHT/VOLUME) OF C12E6/N- REMARK 210 HEXANOL MIXTURE (MOLAR RATIO REMARK 210 0.64) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D TOCSY; REMARK 210 3D_13C-SEPARATED_NOESY; 2D H(N) REMARK 210 CO; 2D HNN-COSY; 2D CT REMARK 210 NONDECOUPLED 13C-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, SPARKY 3.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING 541 NOE RESTRAINTS REMARK 210 AND 136 RDC RESTRAINTS. 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 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 C A 21 C4' C A 21 C3' 0.069 REMARK 500 2 C A 21 C4' C A 21 C3' 0.073 REMARK 500 3 C A 21 C4' C A 21 C3' 0.070 REMARK 500 4 C A 21 C4' C A 21 C3' 0.068 REMARK 500 6 C A 21 C4' C A 21 C3' 0.067 REMARK 500 10 C A 21 C4' C A 21 C3' 0.074 REMARK 500 12 C A 21 C4' C A 21 C3' 0.072 REMARK 500 13 C A 21 C4' C A 21 C3' 0.070 REMARK 500 14 C A 21 C4' C A 21 C3' 0.076 REMARK 500 17 G A 33 C4' G A 33 C3' 0.066 REMARK 500 18 C A 21 C4' C A 21 C3' 0.076 REMARK 500 19 G A 33 C4' G A 33 C3' 0.067 REMARK 500 20 C A 21 C4' C A 21 C3' 0.069 REMARK 500 REMARK 500 REMARK: NULL DBREF 1TXS A 1 38 PDB 1TXS 1TXS 1 38 SEQRES 1 A 38 G G G C U A G C A C U C U SEQRES 2 A 38 G G U A U U A C G G U A C SEQRES 3 A 38 C U U U G U G C G C C C 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