2RN1 - Header Asymmetric Unit

HEADER RNA 05-DEC-07 2RN1

TITLE LIQUID CRYSTAL SOLUTION STRUCTURE OF THE KISSING COMPLEX TITLE 2 FORMED BY THE APICAL LOOP OF THE HIV TAR RNA AND A HIGH TITLE 3 AFFINITY RNA APTAMER 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 KEYWDS 2 SELECTED BY SELEX, LIQUID CRYSTAL NMR, GA BASE PAIR

EXPDTA SOLUTION NMR

NUMMDL 17

AUTHOR H.VAN MELCKEBEKE,M.DEVANY,C.DI PRIMO,F.BEAURAIN,J.TOULME, AUTHOR 2 D.L.BRYCE,J.BOISBOUVIER

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, JRNL AUTH 2 D.L.BRYCE,J.BOISBOUVIER JRNL TITL LIQUID-CRYSTAL NMR STRUCTURE OF HIV TAR RNA BOUND JRNL TITL 2 TO ITS SELEX RNA APTAMER REVEALS THE ORIGINS OF JRNL TITL 3 THE HIGH STABILITY 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 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE 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 RCSB ID CODE IS RCSB150051.

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 REMARK 210 CHLORIDE, 0.01MM EDTA, 0.4G/L REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O; REMARK 210 0.37MM [U-98% 13C; U-98% 15N] REMARK 210 TAR, 0.74MM 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 0.74MM TAR, 0.37MM [U-98% 13C; REMARK 210 U-98% 15N] TAR*GA, 10MM SODIUM REMARK 210 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 REMARK 210 CHLORIDE, 0.01MM EDTA, 0.4G/L REMARK 210 SODIUM AZIDE, 100% D2O; 0.5MM REMARK 210 [U-98% 13C; U-98% 15N] TAR, REMARK 210 1.0MM TAR*GA, 10MM SODIUM REMARK 210 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% REMARK 210 15N] TAR*GA, 10MM SODIUM REMARK 210 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% REMARK 210 15N] TAR*GA, 10MM SODIUM REMARK 210 PHOSPHATE, 50MM SODIUM REMARK 210 CHLORIDE, 0.01MM EDTA, 0.4G/L REMARK 210 SODIUM AZIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY, 3D 1H-13C REMARK 210 TROSY NOESY, 2D JNN-COSY, 3D REMARK 210 HCCH-COSY, 3D HCN, 2D INTRA REMARK 210 BASE TOCSY, 13C-1H SPIN STATE REMARK 210 SELECTIVE 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 : X-PLOR_NIH, FELIX 2000, REMARK 210 INSIGHTII, NMRPIPE, NMRDRAW, REMARK 210 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 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