HEADER RNA 07-SEP-00 1FQZ TITLE NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL TITLE 2 RIBOSOME ENTRY SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPATITIS C VIRUS IRES DOMAIN IIID; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: TRANSCRIBED USING T7 RNA POLYMERASE KEYWDS TRANS WOBBLE G.U PAIR, S-TURN, SARCIN-RICIN LOOP, LOOP E MOTIF, KEYWDS 2 SHEARED G.A PAIR, REVERSE HOOGSTEEN A.U PAIR, RNA EXPDTA SOLUTION NMR AUTHOR R.KLINCK,E.WESTHOF,S.WALKER,M.AFSHAR,A.COLLIER,F.ABOUL-ELA REVDAT 5 22-MAY-24 1FQZ 1 REMARK REVDAT 4 23-FEB-22 1FQZ 1 REMARK REVDAT 3 24-FEB-09 1FQZ 1 VERSN REVDAT 2 01-APR-03 1FQZ 1 JRNL REVDAT 1 17-JAN-01 1FQZ 0 JRNL AUTH R.KLINCK,E.WESTHOF,S.WALKER,M.AFSHAR,A.COLLIER,F.ABOUL-ELA JRNL TITL A POTENTIAL RNA DRUG TARGET IN THE HEPATITIS C VIRUS JRNL TITL 2 INTERNAL RIBOSOMAL ENTRY SITE. JRNL REF RNA V. 6 1423 2000 JRNL REFN ISSN 1355-8382 JRNL PMID 11073218 JRNL DOI 10.1017/S1355838200000935 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.5, CHARMM 25.2, INSIGHT II 97.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), BROOKS ET AL. (CHARMM), MSI REMARK 3 (INSIGHT II) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MOTIFS (I) TO (VI) WERE OBTAINED FROM REMARK 3 THE FOLLOWING SOURCES: (I) IDEALIZED A-FORM COORDINATES REMARK 3 (INSIGHTII, MSI); (II)&(III) PDB 430D.PDB; (IV) PDB 1ETG.PDB; REMARK 3 (VI) PDB 1QA6.PDB; MOTIF (V) WAS CONSTRUCTED MANUALLY. REMARK 4 REMARK 4 1FQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1000011837. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298; 303 REMARK 210 PH : 6.6; 6.6; 6.6 REMARK 210 IONIC STRENGTH : 8MM NA PHOSPHATE; 8MM NA REMARK 210 PHOSPHATE; 8MM NA PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM RNA, 8MM SODIUM PHOSPHATE REMARK 210 BUFFER PH 6.6; 1.2 MM RNA, 8MM REMARK 210 SODIUM PHOSPHATE BUFFER PH 6.6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.7, SPARKY 3.66 REMARK 210 METHOD USED : USING A MOTIF-BASED APPROACH, A REMARK 210 MODEL WAS CONSTRUCTED FROM X-RAY REMARK 210 AND NMR STRUCTURES OF 6 KNOWN REMARK 210 RNA MOTIFS: (I) DOUBLE HELIX, REMARK 210 (II) SHEARED G.A BASE PAIR, (III) REMARK 210 EUKARYOTIC LOOP E MOTIF, (IV) S- REMARK 210 TURN, (V) TRANS WOBBLE G.U PAIR, REMARK 210 (VI) U-TURN. THE RESULTING REMARK 210 ENERGY MINIMIZED MODEL WAS THEN REMARK 210 VALIDATED BY COMPARING IT WITH REMARK 210 THE NOESY DATA. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 U A 7 C2 U A 7 N3 0.042 REMARK 500 U A 10 C2 U A 10 N3 0.045 REMARK 500 U A 13 C2 U A 13 N3 0.046 REMARK 500 U A 17 C2 U A 17 N3 0.046 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 G A 1 N3 - C2 - N2 ANGL. DEV. = 6.4 DEGREES REMARK 500 G A 1 N1 - C6 - O6 ANGL. DEV. = 3.7 DEGREES REMARK 500 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 4 N3 - C2 - N2 ANGL. DEV. = 6.7 DEGREES REMARK 500 A A 5 N1 - C6 - N6 ANGL. DEV. = 6.7 DEGREES REMARK 500 G A 6 N3 - C2 - N2 ANGL. DEV. = 5.5 DEGREES REMARK 500 A A 8 N1 - C6 - N6 ANGL. DEV. = 6.6 DEGREES REMARK 500 G A 9 N3 - C2 - N2 ANGL. DEV. = 6.4 DEGREES REMARK 500 G A 11 N3 - C2 - N2 ANGL. DEV. = 6.8 DEGREES REMARK 500 G A 11 N1 - C6 - O6 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 11 C5 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 U A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 14 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 G A 15 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 G A 15 N1 - C6 - O6 ANGL. DEV. = 3.6 DEGREES REMARK 500 G A 16 N3 - C2 - N2 ANGL. DEV. = 6.5 DEGREES REMARK 500 G A 16 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 G A 16 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 G A 19 N3 - C2 - N2 ANGL. DEV. = 6.5 DEGREES REMARK 500 G A 19 N1 - C6 - O6 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 19 C5 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 C A 20 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 21 N3 - C2 - N2 ANGL. DEV. = 7.0 DEGREES REMARK 500 G A 21 N1 - C6 - O6 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 22 N1 - C6 - N6 ANGL. DEV. = 6.6 DEGREES REMARK 500 A A 23 N1 - C6 - N6 ANGL. DEV. = 6.9 DEGREES REMARK 500 A A 24 N1 - C6 - N6 ANGL. DEV. = 6.9 DEGREES REMARK 500 G A 25 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES REMARK 500 G A 25 N1 - C6 - O6 ANGL. DEV. = 3.7 DEGREES REMARK 500 G A 26 N3 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 G A 26 N1 - C6 - O6 ANGL. DEV. = 3.6 DEGREES 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 U A 12 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1FQZ A 1 27 PDB 1FQZ 1FQZ 1 27 SEQRES 1 A 27 G C C G A G U A G U G U U SEQRES 2 A 27 G G G U C G C G A A A G G SEQRES 3 A 27 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