HEADER RNA 16-MAR-16 2NC1 TITLE SOLUTION STRUCTURE OF THE DELTA-J-DELTA-K DOMAIN OF EMCV IRES COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRES RNA (67-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS IRES, TRANSLATION INITIATION, VIRAL RNA, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.IMAI,V.D'SOUZA,G.WAGNER REVDAT 3 15-NOV-17 2NC1 1 REMARK REVDAT 2 05-APR-17 2NC1 1 JRNL REVDAT 1 10-AUG-16 2NC1 0 JRNL AUTH S.IMAI,P.KUMAR,C.U.HELLEN,V.M.D'SOUZA,G.WAGNER JRNL TITL AN ACCURATELY PREORGANIZED IRES RNA STRUCTURE ENABLES EIF4G JRNL TITL 2 CAPTURE FOR INITIATION OF VIRAL TRANSLATION. JRNL REF NAT. STRUCT. MOL. BIOL. V. 23 859 2016 JRNL REFN ESSN 1545-9985 JRNL PMID 27525590 JRNL DOI 10.1038/NSMB.3280 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CARA, X-PLOR_NIH REMARK 3 AUTHORS : KELLER AND WUTHRICH (CARA), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR_NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NC1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000104678. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 283; 283 REMARK 210 PH : 6.5; 6.5; 5.5 REMARK 210 IONIC STRENGTH : 20; 20; 20 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM RNA (67-MER), 10 MM REMARK 210 POTASSIUM PHOSPHATE, 10 MM REMARK 210 SODIUM CHLORIDE, 100% D2O; 0.5 REMARK 210 MM RNA (67-MER), 10 MM POTASSIUM REMARK 210 PHOSPHATE, 10 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O; 0.5 MM [U-2H, { REMARK 210 H1',H2',H2,H8}-ADE] RNA (67-MER), REMARK 210 10 MM POTASSIUM PHOSPHATE, 10 REMARK 210 MM SODIUM CHLORIDE, 100% D2O; REMARK 210 0.5 MM [U-2H]-CYT, [U-2H]-URA REMARK 210 RNA (67-MER), 10 MM POTASSIUM REMARK 210 PHOSPHATE, 10 MM SODIUM CHLORIDE, REMARK 210 100% D2O; 0.5 MM [U-2H]-GUA, [U- REMARK 210 2H]-URA RNA (67-MER), 10 MM REMARK 210 POTASSIUM PHOSPHATE, 10 MM REMARK 210 SODIUM CHLORIDE, 100% D2O; 0.5 REMARK 210 MM [U-2H, {H1',H2',H2,H8}-ADE] REMARK 210 RNA (67-MER), 10 MM POTASSIUM REMARK 210 PHOSPHATE, 10 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 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 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 3 G A 731 C2' G A 731 O2' -0.101 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 2 U A 768 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 6 G A 731 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 7 G A 731 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 9 G A 731 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 26000 RELATED DB: BMRB REMARK 900 RELATED ID: 2NBX RELATED DB: PDB REMARK 900 RELATED ID: 2NBY RELATED DB: PDB REMARK 900 RELATED ID: 2NBZ RELATED DB: PDB REMARK 900 RELATED ID: 2NC0 RELATED DB: PDB DBREF 2NC1 A 680 787 PDB 2NC1 2NC1 680 787 SEQRES 1 A 67 G G G G C U G A A G G A U SEQRES 2 A 67 G C C C A G A G A G A U C SEQRES 3 A 67 U G G G G C C U C G G G A SEQRES 4 A 67 G A U C G A G G U U A A A SEQRES 5 A 67 A A A C G U C U A G G C C SEQRES 6 A 67 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 132 0 0 0 0 0 0 6 0 0 0 6 END