HEADER RNA 10-FEB-10 2KU0 TITLE INHIBITOR INDUCED STRUCTURAL CHANGE IN THE HCV IRES DOMAIN IIA RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HCV IRES DOMAIN IIA RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 4 ORGANISM_COMMON: HCV; SOURCE 5 ORGANISM_TAXID: 11103; SOURCE 6 OTHER_DETAILS: T7 POLYMERASE KEYWDS HEPATITIS C VIRUS, RNA STRUCTURE, ANTIVIRAL, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.B.PAULSEN,P.P.SETH,E.E.SWAYZE,R.H.GRIFFEY,J.J.SKALICKY,T.E.CHEATHAM AUTHOR 2 III,D.R.DAVIS REVDAT 2 05-MAY-10 2KU0 1 JRNL REVDAT 1 28-APR-10 2KU0 0 JRNL AUTH R.B.PAULSEN,P.P.SETH,E.E.SWAYZE,R.H.GRIFFEY,J.J.SKALICKY, JRNL AUTH 2 T.E.CHEATHAM,D.R.DAVIS JRNL TITL INHIBITOR-INDUCED STRUCTURAL CHANGE IN THE HCV IRES DOMAIN JRNL TITL 2 IIA RNA. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 7263 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20360559 JRNL DOI 10.1073/PNAS.0911896107 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KU0 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB101570. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 304; 283 REMARK 210 PH : 7; 7; 7 REMARK 210 IONIC STRENGTH : 0.150 NACL; 0.150 NACL; 0.150 REMARK 210 NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-13C; U-15N]-ADE, URA REMARK 210 RNA (38-MER)-1, 150 MM SODIUM REMARK 210 CHLORIDE-2, 150 MM POTASSIUM REMARK 210 CHLORIDE-3, 10 MM SODIUM REMARK 210 PHOSPHATE-4, 2 MM SPERMINE-5, 2.8 REMARK 210 MM ISI-6, 100% D2O; 0.4 MM RNA REMARK 210 (38-MER)-7, 150 MM SODIUM REMARK 210 CHLORIDE-8, 150 MM POTASSIUM REMARK 210 CHLORIDE-9, 10 MM SODIUM REMARK 210 PHOSPHATE-10, 2 MM SPERMINE-11, REMARK 210 2.8 MM ISI-12, 100% D2O; 0.4 MM REMARK 210 [U-100% 13C; U-100% 15N] RNA (38- REMARK 210 MER)-13, 150 MM SODIUM CHLORIDE- REMARK 210 14, 150 MM POTASSIUM CHLORIDE-15, REMARK 210 10 MM SODIUM PHOSPHATE-16, 2 MM REMARK 210 SPERMINE-17, 2.8 MM ISI-18, 90% REMARK 210 H2O/10% D2O; 0.4 MM [U-13C; U- REMARK 210 15N]-GUA, CYT RNA (38-MER)-19, REMARK 210 150 MM SODIUM CHLORIDE-20, 150 MM REMARK 210 POTASSIUM CHLORIDE-21, 10 MM REMARK 210 SODIUM PHOSPHATE-22, 2 MM REMARK 210 SPERMINE-23, 2.8 MM ISI-24, 100% REMARK 210 D2O; 0.4 MM [U-100% 13C; U-100% REMARK 210 15N] RNA (38-MER)-25, 150 MM REMARK 210 SODIUM CHLORIDE-26, 150 MM REMARK 210 POTASSIUM CHLORIDE-27, 10 MM REMARK 210 SODIUM PHOSPHATE-28, 2 MM REMARK 210 SPERMINE-29, 2.8 MM ISI-30, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-1H F1FF2F- REMARK 210 NOESY; 1H-1H F1FF2E-NOESY; 2D 1H- REMARK 210 13C HSQC-IPAP; 2D HCCH COSY; 2D REMARK 210 HCCH-COSY-IPAP; 2D 1H-15N HSQC; REMARK 210 2D 1H-1H NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 19 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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 A A 3 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 3 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 G A 4 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 A A 6 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 6 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 U A 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 A A 10 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 10 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 A A 10 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 C A 11 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 U A 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 C A 15 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 18 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 C A 19 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 C A 19 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 G A 23 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 C A 31 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A A 32 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 32 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 32 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 C A 34 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 C A 34 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 C A 35 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 U A 36 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 C A 37 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 38 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 A A 3 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 A A 3 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 2 G A 4 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 A A 6 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 A A 6 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 A A 6 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 U A 9 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 A A 10 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 A A 10 C5 - C6 - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 A A 10 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 C A 11 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 C A 11 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 U A 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 C A 15 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 C A 18 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 346 ANGLE DEVIATIONS. 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 1 G A 4 0.07 SIDE CHAIN REMARK 500 1 A A 6 0.13 SIDE CHAIN REMARK 500 1 C A 8 0.10 SIDE CHAIN REMARK 500 1 U A 9 0.07 SIDE CHAIN REMARK 500 1 G A 13 0.06 SIDE CHAIN REMARK 500 2 G A 4 0.08 SIDE CHAIN REMARK 500 2 G A 5 0.06 SIDE CHAIN REMARK 500 2 A A 6 0.08 SIDE CHAIN REMARK 500 2 U A 9 0.07 SIDE CHAIN REMARK 500 2 G A 13 0.06 SIDE CHAIN REMARK 500 2 U A 14 0.07 SIDE CHAIN REMARK 500 2 U A 21 0.06 SIDE CHAIN REMARK 500 2 C A 22 0.11 SIDE CHAIN REMARK 500 2 U A 29 0.07 SIDE CHAIN REMARK 500 3 G A 28 0.07 SIDE CHAIN REMARK 500 4 G A 4 0.07 SIDE CHAIN REMARK 500 4 A A 6 0.15 SIDE CHAIN REMARK 500 4 G A 13 0.06 SIDE CHAIN REMARK 500 4 U A 14 0.06 SIDE CHAIN REMARK 500 4 U A 29 0.08 SIDE CHAIN REMARK 500 5 G A 4 0.08 SIDE CHAIN REMARK 500 5 G A 5 0.06 SIDE CHAIN REMARK 500 5 C A 8 0.10 SIDE CHAIN REMARK 500 5 G A 13 0.06 SIDE CHAIN REMARK 500 5 U A 14 0.07 SIDE CHAIN REMARK 500 6 G A 4 0.07 SIDE CHAIN REMARK 500 6 G A 5 0.09 SIDE CHAIN REMARK 500 6 A A 6 0.12 SIDE CHAIN REMARK 500 6 U A 9 0.07 SIDE CHAIN REMARK 500 6 A A 10 0.06 SIDE CHAIN REMARK 500 6 G A 13 0.06 SIDE CHAIN REMARK 500 6 U A 14 0.07 SIDE CHAIN REMARK 500 6 U A 21 0.09 SIDE CHAIN REMARK 500 6 C A 22 0.10 SIDE CHAIN REMARK 500 6 G A 24 0.06 SIDE CHAIN REMARK 500 6 C A 27 0.06 SIDE CHAIN REMARK 500 6 U A 29 0.07 SIDE CHAIN REMARK 500 7 G A 4 0.09 SIDE CHAIN REMARK 500 7 G A 5 0.06 SIDE CHAIN REMARK 500 7 G A 13 0.07 SIDE CHAIN REMARK 500 7 U A 14 0.08 SIDE CHAIN REMARK 500 7 U A 29 0.09 SIDE CHAIN REMARK 500 8 G A 4 0.07 SIDE CHAIN REMARK 500 8 A A 6 0.13 SIDE CHAIN REMARK 500 8 C A 8 0.06 SIDE CHAIN REMARK 500 8 U A 9 0.07 SIDE CHAIN REMARK 500 8 A A 10 0.07 SIDE CHAIN REMARK 500 8 G A 13 0.06 SIDE CHAIN REMARK 500 8 U A 14 0.06 SIDE CHAIN REMARK 500 8 U A 21 0.10 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 65 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ISI A 39 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KTZ RELATED DB: PDB DBREF 2KU0 A 1 38 PDB 2KU0 2KU0 1 38 SEQRES 1 A 38 G G A G G A A C U A C U G SEQRES 2 A 38 U C U U C C U U C G G G U SEQRES 3 A 38 C G U G C A G C C U C C HET ISI A 39 53 HETNAM ISI (7S)-7-[(DIMETHYLAMINO)METHYL]-1-[3-(DIMETHYLAMINO) HETNAM 2 ISI PROPYL]-7,8-DIHYDRO-1H-FURO[3,2-E]BENZIMIDAZOL-2-AMINE FORMUL 2 ISI C17 H27 N5 O SITE 1 AC1 8 G A 4 G A 5 A A 6 A A 7 SITE 2 AC1 8 A A 10 C A 11 G A 33 C A 34 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 223 0 1 0 0 0 2 6 0 0 0 3 END