1F84 - Header Asymmetric Unit

HEADER RNA 28-JUN-00 1F84

TITLE SOLUTION STRUCTURE OF HCV IRES RNA DOMAIN IIID

COMPND MOL_ID: 1; COMPND 2 MOLECULE: HCV-1B IRES RNA DOMAIN IIID; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HCV IRES RNA DOMAIN IIID (NUCLEOTIDES 252-290 OF COMPND 5 GENOMIC HEPATITIS C VIRAL RNA); COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED ENZYMATICALLY IN-VITRO USING T7 SOURCE 4 RNA POLYMERASE

KEYWDS RIBONUCLEIC ACID, HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY KEYWDS 2 SITE, SARCIN/RICIN LOOP, LOOP E MOTIF, HAIRPIN LOOP, RNA KEYWDS 3 STRUCTURE

EXPDTA SOLUTION NMR

NUMMDL 25

AUTHOR P.J.LUKAVSKY,G.A.OTTO,A.M.LANCASTER,P.SARNOW,J.D.PUGLISI

REVDAT 4 24-FEB-09 1F84 1 VERSN REVDAT 3 08-MAR-05 1F84 3 ATOM HETATM REMARK MASTER REVDAT 2 01-APR-03 1F84 1 JRNL REVDAT 1 17-NOV-00 1F84 0

JRNL AUTH P.J.LUKAVSKY,G.A.OTTO,A.M.LANCASTER,P.SARNOW, JRNL AUTH 2 J.D.PUGLISI JRNL TITL STRUCTURES OF TWO RNA DOMAINS ESSENTIAL FOR JRNL TITL 2 HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE JRNL TITL 3 FUNCTION. JRNL REF NAT.STRUCT.BIOL. V. 7 1105 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 11101890 JRNL DOI 10.1038/81951

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SEE REFERENCE ABOVE

REMARK 4 REMARK 4 1F84 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-00. REMARK 100 THE RCSB ID CODE IS RCSB011359.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298 REMARK 210 PH : 6.40; 6.40 REMARK 210 IONIC STRENGTH : 10MM; 10MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM RNA, NON-ISOTOPICALLY REMARK 210 LABELLED; 1MM RNA, U-15N,13C REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : P31-DECOUPLED DQF COSY, HP REMARK 210 COSY, D2O NOESY, H2O NOESY, 3D REMARK 210 HCP, 3D HMQC-TOCSY, 3D C13- REMARK 210 EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.8 REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 21 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE REMARK 210 RESONANCE HCN AND HCP EXPERIMENTS ON N15,C13-LABELLED RNA

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 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 15 G A 1 O5' G A 1 C5' -0.699 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 15 G A 1 O5' - C5' - C4' ANGL. DEV. = 24.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL

DBREF 1F84 A 1 29 PDB 1F84 1F84 1 29

SEQRES 1 A 29 G G C C G A G U A G U G U SEQRES 2 A 29 U G G G U C G C G A A A G SEQRES 3 A 29 G 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