HEADER RNA 10-NOV-03 1RFR TITLE NMR STRUCTURE OF THE 30MER STEMLOOP-D OF COXSACKIEVIRAL RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEMLOOP-D RNA OF THE 5'-CLOVERLEAF OF COXSACKIEVIRUS B3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PROTEINASE 3C BINDING DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN COXSACKIEVIRUS B3; SOURCE 3 ORGANISM_TAXID: 12072; SOURCE 4 GENE: 5'-NONTRANSLATED REGION; SOURCE 5 EXPRESSION_SYSTEM: IN VITRO; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PUC-19; SOURCE 8 OTHER_DETAILS: TWO NUCLEOTIDES (GG) AT 5'-END AND TWO NUCLEOTIDES SOURCE 9 (UC) AT THE 3'-END WERE ADDED FOR IN VITRO PRODUCTION KEYWDS LOOP WITH CONFORMATION SIMILAR TO STABLE UNCG-TETRALOOPS AND U:G KEYWDS 2 CLOSING BASE PAIR, BASE-PAIRED U:U-C:U-U:U MISMATCH, A-FORM HELIX KEYWDS 3 STEMS, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR O.OHLENSCHLAGER,J.WOHNERT,E.BUCCI,S.SEITZ,S.HAFNER,R.RAMACHANDRAN, AUTHOR 2 R.ZELL,M.GORLACH REVDAT 3 02-MAR-22 1RFR 1 REMARK REVDAT 2 24-FEB-09 1RFR 1 VERSN REVDAT 1 23-MAR-04 1RFR 0 JRNL AUTH O.OHLENSCHLAGER,J.WOHNERT,E.BUCCI,S.SEITZ,S.HAFNER, JRNL AUTH 2 R.RAMACHANDRAN,R.ZELL,M.GORLACH JRNL TITL THE STRUCTURE OF THE STEMLOOP D SUBDOMAIN OF COXSACKIEVIRUS JRNL TITL 2 B3 CLOVERLEAF RNA AND ITS INTERACTION WITH THE PROTEINASE JRNL TITL 3 3C. JRNL REF STRUCTURE V. 12 237 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 14962384 JRNL DOI 10.1016/S0969-2126(04)00008-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, REV. C, OPAL 2.6 REMARK 3 AUTHORS : VARIAN INC. (VNMR), LUGINBUHL (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 1001 EXPERIMENTAL DISTANCES DERIVED FROM NOE CROSS PEAKS, REMARK 3 280 TORSION ANGLE CONSTRAINTS DESCRIBING 258 TORSION ANGLES, REMARK 3 52 HYDROGEN BOND CONSTRAINTS REMARK 4 REMARK 4 1RFR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020708. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 283 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 10MM KH2PO4/K2HPO4, 40MM KCL, REMARK 210 0.2MM EDTA; 10MM KH2PO4/K2HPO4, REMARK 210 40MM KCL, 0.2MM EDTA REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.9MM SLD-RNA U-15N,13C; 10MM REMARK 210 KH2PO4/K2HPO4, 40MM KCL, 0.2MM REMARK 210 EDTA; 1.2MM SLD-RNA G,C-15N,13C; REMARK 210 10MM KH2PO4/K2HPO4, 40MM KCL, REMARK 210 0.2MM EDTA; 1.2MM SLD-RNA A,U- REMARK 210 15N,13C; 10MM KH2PO4/K2HPO4, REMARK 210 40MM KCL, 0.2MM EDTA; 1.4MM SLD- REMARK 210 RNA U-15N; 10MM KH2PO4/K2HPO4, REMARK 210 40MM KCL, 0.2MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : SEE BELOW REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, REV. C, XEASY 1.3.9, REMARK 210 FOUND IMPLEMENTED IN CYANA-1.0.6, REMARK 210 CYANA 1.0.6 REMARK 210 METHOD USED : DISTANCE GEOMETRY/SIMULATED REMARK 210 ANNEALING, ENERGY MINIMISATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY,TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR 2D AND 3D NMR REMARK 210 EXPERIMENTS, E.G. REMARK 210 3D HCCH-COSY, REMARK 210 RELAY-COSY, REMARK 210 TOCSY, REMARK 210 H6/H5(C4N)H, REMARK 210 C6/C5(C4N)H, REMARK 210 H(CCN)H-TOCSY, REMARK 210 HCCH-TOCSY, REMARK 210 2D H(N)CO, REMARK 210 2D CPMG-HSQC-NOESY, REMARK 210 2D NOESY, REMARK 210 3D 1H,1H,15N-NOESY-HSQC, REMARK 210 3D 1H,1H,13C-NOESY-HSQC, REMARK 210 CLEAN-TOCSY, REMARK 210 31P-SPINECHO-DIFFERENCE-CT-HMQC, REMARK 210 HNN-COSY, REMARK 210 2D 1H,13C-HSQC, REMARK 210 2D 1H,15N-HSQC, REMARK 210 HCN, REMARK 210 H5(C5C4N)H, REMARK 210 H8(C8C2)H2, REMARK 210 3D 13C-F1-FILTERED,13C-F3-EDITED-NOESY-HSQC 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 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 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 C A 5 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 17 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 C A 22 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 U A 23 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 U A 24 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 U A 27 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C A 5 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 9 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 17 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 2 G A 17 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 C A 22 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 U A 23 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 U A 24 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 U A 27 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 C A 5 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 3 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 C A 22 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 3 U A 23 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 U A 27 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 4 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 4 C A 5 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 G A 17 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 4 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 4 C A 22 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 4 U A 23 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 U A 24 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 U A 25 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 G A 26 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 U A 27 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 C A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 5 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 C A 22 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 202 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 C A 3 0.07 SIDE CHAIN REMARK 500 1 U A 8 0.07 SIDE CHAIN REMARK 500 1 A A 12 0.06 SIDE CHAIN REMARK 500 1 U A 13 0.10 SIDE CHAIN REMARK 500 1 U A 19 0.06 SIDE CHAIN REMARK 500 1 C A 21 0.06 SIDE CHAIN REMARK 500 1 U A 24 0.08 SIDE CHAIN REMARK 500 2 A A 4 0.05 SIDE CHAIN REMARK 500 2 U A 6 0.06 SIDE CHAIN REMARK 500 2 A A 12 0.06 SIDE CHAIN REMARK 500 2 U A 13 0.10 SIDE CHAIN REMARK 500 2 U A 24 0.09 SIDE CHAIN REMARK 500 3 C A 3 0.07 SIDE CHAIN REMARK 500 3 U A 6 0.06 SIDE CHAIN REMARK 500 3 U A 8 0.06 SIDE CHAIN REMARK 500 3 A A 12 0.06 SIDE CHAIN REMARK 500 3 U A 13 0.10 SIDE CHAIN REMARK 500 3 C A 21 0.06 SIDE CHAIN REMARK 500 3 U A 24 0.08 SIDE CHAIN REMARK 500 4 C A 3 0.07 SIDE CHAIN REMARK 500 4 U A 6 0.06 SIDE CHAIN REMARK 500 4 U A 8 0.07 SIDE CHAIN REMARK 500 4 A A 12 0.06 SIDE CHAIN REMARK 500 4 U A 13 0.10 SIDE CHAIN REMARK 500 4 C A 21 0.06 SIDE CHAIN REMARK 500 4 U A 24 0.09 SIDE CHAIN REMARK 500 5 A A 4 0.05 SIDE CHAIN REMARK 500 5 A A 12 0.06 SIDE CHAIN REMARK 500 5 U A 13 0.09 SIDE CHAIN REMARK 500 5 U A 24 0.07 SIDE CHAIN REMARK 500 6 C A 3 0.06 SIDE CHAIN REMARK 500 6 A A 4 0.06 SIDE CHAIN REMARK 500 6 U A 8 0.07 SIDE CHAIN REMARK 500 6 U A 13 0.09 SIDE CHAIN REMARK 500 6 U A 24 0.08 SIDE CHAIN REMARK 500 7 A A 4 0.06 SIDE CHAIN REMARK 500 7 U A 8 0.06 SIDE CHAIN REMARK 500 7 A A 12 0.06 SIDE CHAIN REMARK 500 7 U A 13 0.10 SIDE CHAIN REMARK 500 7 U A 19 0.07 SIDE CHAIN REMARK 500 7 A A 20 0.05 SIDE CHAIN REMARK 500 7 C A 21 0.06 SIDE CHAIN REMARK 500 7 U A 24 0.09 SIDE CHAIN REMARK 500 8 A A 12 0.06 SIDE CHAIN REMARK 500 8 U A 13 0.10 SIDE CHAIN REMARK 500 8 C A 21 0.06 SIDE CHAIN REMARK 500 8 U A 24 0.08 SIDE CHAIN REMARK 500 9 U A 6 0.06 SIDE CHAIN REMARK 500 9 U A 8 0.07 SIDE CHAIN REMARK 500 9 A A 12 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 115 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1RFR A 1 30 PDB 1RFR 1RFR 1 30 SEQRES 1 A 30 G G C A C U C U G G U A U SEQRES 2 A 30 C A C G G U A C C U U U G SEQRES 3 A 30 U G U 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