HEADER RNA 22-OCT-03 1R7Z TITLE NMR STRUCTURE OF THE R(GGAGGACAUUCCUCACGGGUGACCGUGGUCCUCC), DOMAIN IV TITLE 2 STEM-LOOP B OF ENTEROVIRAL IRES WITH AUUCCU BULGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 34-MER; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN IV, LOOP B; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: RNA FRAGMENT OF ENTEROVIRAL IRES 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 STEM-AND-LOOP STRUCTURE, SIX-NUCLEOTIDE BULGE, GUGA TETRALOOP, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Z.DU,N.B.ULYANOV,J.YU,T.L.JAMES REVDAT 4 22-MAY-24 1R7Z 1 REMARK REVDAT 3 02-MAR-22 1R7Z 1 REMARK REVDAT 2 24-FEB-09 1R7Z 1 VERSN REVDAT 1 25-MAY-04 1R7Z 0 JRNL AUTH Z.DU,N.B.ULYANOV,J.YU,R.ANDINO,T.L.JAMES JRNL TITL NMR STRUCTURES OF LOOP B RNAS FROM THE STEM-LOOP IV DOMAIN JRNL TITL 2 OF THE ENTEROVIRUS INTERNAL RIBOSOME ENTRY SITE: A SINGLE C JRNL TITL 3 TO U SUBSTITUTION DRASTICALLY CHANGES THE SHAPE AND JRNL TITL 4 FLEXIBILITY OF RNA(,). JRNL REF BIOCHEMISTRY V. 43 5757 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15134450 JRNL DOI 10.1021/BI0363228 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, DYANA 1.5, AMBER 7 REMARK 3 AUTHORS : VARIAN ASSOCIATES, INC. (VNMR), P.GUNTERT (DYANA), REMARK 3 D.A.CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE REFINED BASED ON 614 NOE REMARK 3 -DERIVED DISTANCES AND 26 RESIDUAL DIPOLAR COUPLINGS REMARK 4 REMARK 4 1R7Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020549. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 50 MM NA+ IONS; 50 MM NA+ IONS REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM UNLABELED RNA, 25MM NACL, REMARK 210 25MM SODIUM PHOSPHATE BUFFER (PH REMARK 210 6.5), 90% H2O; 10% D2O; 1MM REMARK 210 UNLABELED RNA, 25MM NACL, 25MM REMARK 210 SODIUM PHOSPHATE BUFFER (PH 6.5), REMARK 210 D2O; 1MM OF RNA LABELED IN REMARK 210 RESIDUES A AND U WITH 13C, 15N, REMARK 210 25MM NACL, 25MM SODIUM PHOSPHATE REMARK 210 BUFFER (PH 6.5), 5% (WEIGHT/ REMARK 210 VOLUME) OF C12E6/N-HEXANOL REMARK 210 MIXTURE (MOLAR RATIO 0.64), D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 1H-13C REMARK 210 CONSTANT TIME 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, MARDIGRAS 3.2 REMARK 210 METHOD USED : FULL MATRIX RELAXATION ANALYSIS REMARK 210 OF NOE, RANDOM ERROR ANALYSIS OF REMARK 210 NOE, SIMULATED ANNEALING USING REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TOTAL ENERGY (A WEIGHTED REMARK 210 SUM OF CONFORMATIONAL ENERGY AND REMARK 210 RESTRAINT ENERGY) 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 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 13 U A 13 P U A 13 O5' 0.060 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1R7W RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE R(GGAGGACAUCCCUCACGGGUGACCGUGGUCCUCC), DOMAIN REMARK 900 IV STEM-LOOP B OF ENTEROVIRAL IRES WITH AUCCCU BULGE DBREF 1R7Z A 1 34 PDB 1R7Z 1R7Z 1 34 SEQRES 1 A 34 G G A G G A C A U U C C U SEQRES 2 A 34 C A C G G G U G A C C G U SEQRES 3 A 34 G G U C C U 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