HEADER RNA 05-DEC-07 2RN1 TITLE LIQUID CRYSTAL SOLUTION STRUCTURE OF THE KISSING COMPLEX FORMED BY THE TITLE 2 APICAL LOOP OF THE HIV TAR RNA AND A HIGH AFFINITY RNA APTAMER TITLE 3 OPTIMIZED BY SELEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(P*GP*AP*GP*CP*CP*CP*UP*GP*GP*GP*AP*GP*GP*CP*UP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 SYNONYM: TAR; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'- COMPND 9 R(P*GP*CP*UP*GP*GP*UP*CP*CP*CP*AP*GP*AP*CP*AP*GP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 SYNONYM: TAR*GA; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: NUCLEOTIDE SYNTHESIS; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: NUCLEOTIDE SYNTHESIS KEYWDS RNA KISSING COMPLEX, HIV TAR, HIGH AFFINITY RNA APTAMER SELECTED BY KEYWDS 2 SELEX, LIQUID CRYSTAL NMR, GA BASE PAIR, RNA EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR H.VAN MELCKEBEKE,M.DEVANY,C.DI PRIMO,F.BEAURAIN,J.TOULME,D.L.BRYCE, AUTHOR 2 J.BOISBOUVIER REVDAT 4 01-MAY-24 2RN1 1 REMARK REVDAT 3 26-FEB-20 2RN1 1 REMARK REVDAT 2 24-FEB-09 2RN1 1 VERSN REVDAT 1 23-SEP-08 2RN1 0 JRNL AUTH H.VAN MELCKEBEKE,M.DEVANY,C.DI PRIMO,F.BEAURAIN,D.L.BRYCE, JRNL AUTH 2 J.BOISBOUVIER JRNL TITL LIQUID-CRYSTAL NMR STRUCTURE OF HIV TAR RNA BOUND TO ITS JRNL TITL 2 SELEX RNA APTAMER REVEALS THE ORIGINS OF THE HIGH STABILITY JRNL TITL 3 OF THE COMPLEX JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 9210 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18607001 JRNL DOI 10.1073/PNAS.0712121105 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: XPLOR-NIH (WIMBERLY, 1992) REMARK 4 REMARK 4 2RN1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000150051. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 283; 278 REMARK 210 PH : 6.6; 6.6; 6.6 REMARK 210 IONIC STRENGTH : 60; 60; 60 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.3MM TAR, 1.3MM TAR*GA, 10MM REMARK 210 SODIUM PHOSPHATE, 50MM SODIUM REMARK 210 CHLORIDE, 0.01MM EDTA, 0.4G/L REMARK 210 SODIUM AZIDE, 100% D2O; 1.1MM REMARK 210 TAR, 1.1MM TAR*GA, 10MM SODIUM REMARK 210 PHOSPHATE, 50MM SODIUM CHLORIDE, REMARK 210 0.01MM EDTA, 0.4G/L SODIUM AZIDE, REMARK 210 90% H2O/10% D2O; 0.37MM [U-98% REMARK 210 13C; U-98% 15N] TAR, 0.74MM TAR* REMARK 210 GA, 10MM SODIUM PHOSPHATE, 50MM REMARK 210 SODIUM CHLORIDE, 0.01MM EDTA, REMARK 210 0.4G/L SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O; 0.74MM TAR, 0.37MM [U-98% REMARK 210 13C; U-98% 15N] TAR*GA, 10MM REMARK 210 SODIUM PHOSPHATE, 50MM SODIUM REMARK 210 CHLORIDE, 0.01MM EDTA, 0.4G/L REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O; REMARK 210 1.6MM TAR, 0.8MM [U-98% 13C; U- REMARK 210 98% 15N] TAR*GA, 10MM SODIUM REMARK 210 PHOSPHATE, 50MM SODIUM CHLORIDE, REMARK 210 0.01MM EDTA, 0.4G/L SODIUM AZIDE, REMARK 210 100% D2O; 0.5MM [U-98% 13C; U- REMARK 210 98% 15N] TAR, 1.0MM TAR*GA, 10MM REMARK 210 SODIUM PHOSPHATE, 50MM SODIUM REMARK 210 CHLORIDE, 0.01MM EDTA, 0.4G/L REMARK 210 SODIUM AZIDE, 100% D2O; 1.8MM REMARK 210 TAR, 0.9MM [U-98% 13C; U-98% 15N] REMARK 210 TAR*GA, 10MM SODIUM PHOSPHATE, REMARK 210 50MM SODIUM CHLORIDE, 0.01MM REMARK 210 EDTA, 0.4G/L SODIUM AZIDE, 100% REMARK 210 D2O; 1.8MM TAR, 0.9MM [U-98% 13C; REMARK 210 U-98% 15N] TAR*GA, 10MM SODIUM REMARK 210 PHOSPHATE, 50MM SODIUM CHLORIDE, REMARK 210 0.01MM EDTA, 0.4G/L SODIUM AZIDE, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-13C TROSY REMARK 210 NOESY; 2D JNN-COSY; 3D HCCH-COSY; REMARK 210 3D HCN; 2D INTRA BASE TOCSY; REMARK 210 13C-1H SPIN STATE SELECTIVE REMARK 210 EXPERIMENTS REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, INSIGHT II, NMRPIPE, REMARK 210 NMRDRAW, CURVES 5.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 800 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES REMARK 500 2 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.6 DEGREES REMARK 500 3 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.1 DEGREES REMARK 500 4 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.6 DEGREES REMARK 500 5 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.2 DEGREES REMARK 500 6 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 7 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.3 DEGREES REMARK 500 8 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 9 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.4 DEGREES REMARK 500 10 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.2 DEGREES REMARK 500 11 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 12 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES REMARK 500 13 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 14 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 15 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.5 DEGREES REMARK 500 16 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES REMARK 500 17 A A 11 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KIS RELATED DB: PDB REMARK 900 LOWER AFFINITY APTAMER - HIV TAR KISSING COMPLEX REMARK 900 RELATED ID: 11014 RELATED DB: BMRB DBREF 2RN1 A 1 16 PDB 2RN1 2RN1 1 16 DBREF 2RN1 B 17 32 PDB 2RN1 2RN1 17 32 SEQRES 1 A 16 G A G C C C U G G G A G G SEQRES 2 A 16 C U C SEQRES 1 B 16 G C U G G U C C C A G A C SEQRES 2 B 16 A G 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