HEADER RNA 27-APR-03 1P5O TITLE SOLUTION STRUCTURE OF HCV IRES DOMAIN II COMPND MOL_ID: 1; COMPND 2 MOLECULE: 77-MER; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HCV IRES DOMAIN II (RESIDUES 45-117); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHESIZED BY IN VITRO TRANSCRIPTION FROM LINEARIZED SOURCE 4 PLASMID DNA USING T7 RNA POLYMERASE KEYWDS RIBONUCLEIC ACID, HEPATITIS C VIRUS, INTERNAL RIBOSOME ENTRY SITE, KEYWDS 2 TRNA, LOOP E MOTIF, HAIRPIN LOOP, RNA EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR P.J.LUKAVSKY,I.KIM,G.A.OTTO,J.D.PUGLISI REVDAT 4 23-FEB-22 1P5O 1 REMARK REVDAT 3 24-FEB-09 1P5O 1 VERSN REVDAT 2 30-MAR-04 1P5O 1 JRNL REVDAT 1 04-NOV-03 1P5O 0 JRNL AUTH P.J.LUKAVSKY,I.KIM,G.A.OTTO,J.D.PUGLISI JRNL TITL STRUCTURE OF HCV IRES DOMAIN II DETERMINED BY NMR. JRNL REF NAT.STRUCT.BIOL. V. 10 1033 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 14578934 JRNL DOI 10.1038/NSB1004 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, X-PLOR 3.1, CNS 1.1, PALES 1 REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER, A.T. (X-PLOR), BRUNGER, REMARK 3 A.T. ET AL (CNS), ZWECKSTETTER, M. & BAX, A. REMARK 3 (PALES) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SEE REFERENCE ABOVE REMARK 4 REMARK 4 1P5O COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019038. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 298; 303 REMARK 210 PH : 6.40; 6.40; 6.40 REMARK 210 IONIC STRENGTH : 100MM NACL, 5MM MGCL2; 100MM REMARK 210 NACL, 5MM MGCL2; 100MM NACL, 5MM REMARK 210 MGCL2 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1.5MM HCV IRES DOMAIN II RNA REMARK 210 10MM PHOSPHATE BUFFER 100MM REMARK 210 SODIUM CHLORIDE 5MM MAGNESIUM REMARK 210 CHLORIDE; 0.5-1.5MM HCV IRES REMARK 210 DOMAIN II RNA 10MM PHOSPHATE REMARK 210 BUFFER 100MM SODIUM CHLORIDE 5MM REMARK 210 MAGNESIUM CHLORIDE; 0.5-1.5MM REMARK 210 HCV IRES DOMAIN II RNA U-15N,13C REMARK 210 10MM PHOSPHATE BUFFER 100MM REMARK 210 SODIUM CHLORIDE 5MM MAGNESIUM REMARK 210 CHLORIDE; 0.5-1.5MM HCV IRES REMARK 210 DOMAIN II RNA U-15N,13C 10MM REMARK 210 PHOSPHATE BUFFER 100MM SODIUM REMARK 210 CHLORIDE 5MM MAGNESIUM CHLORIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D S-NOESY; 2D NOESY; DQF-COSY; REMARK 210 2D HP-COSY; 3D_13C-SEPARATED_ REMARK 210 NOESY; 3D HCP; 3D HMQC TOCSY 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 REMARK 210 METHOD USED : SEE REFERENCE ABOVE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST RESTRAINT VIOLATION AND REMARK 210 TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS SOLVED USING TRIPLE RESONANCE, REMARK 210 MULTIDIMENSIONAL NMR SPECTROSCOPY AND TROSY-TYPE EXPERIMENTS TO REMARK 210 MEASURE RESIDUAL DIPOLAR COUPLINGS 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: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 C A 76 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1P5O A 1 77 PDB 1P5O 1P5O 1 77 SEQRES 1 A 77 G G C U G U G A G G A A C SEQRES 2 A 77 U A C U G U C U U C A C G SEQRES 3 A 77 C A G A A A G C G U C U A SEQRES 4 A 77 G C C A U G G C G U U A G SEQRES 5 A 77 U A U G A G U G U C G U G SEQRES 6 A 77 C A G C C U C C A 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 MODEL 1