HEADER RNA 26-JAN-07 2OOM TITLE NMR STRUCTURE OF A KISSING COMPLEX FORMED BETWEEN THE TAR RNA ELEMENT TITLE 2 OF HIV-1 AND A LNA/RNA APTAMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA 16-MER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TAR RNA ELEMENT OF HIV-1; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA SOURCE 4 POLYMERASE; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: PURCHASED FROM EUROGENTEC KEYWDS LNA; LOCKED NUCLEIC ACID; NMR; APTAMER; TAR; HIV-1, RNA EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR I.LEBARS,T.RICHARD,C.DI PRIMO,J.J.TOULME REVDAT 5 27-DEC-23 2OOM 1 REMARK REVDAT 4 16-MAR-22 2OOM 1 REMARK DBREF LINK REVDAT 3 24-FEB-09 2OOM 1 VERSN REVDAT 2 12-FEB-08 2OOM 1 MODRES REVDAT 1 29-JAN-08 2OOM 0 JRNL AUTH I.LEBARS,T.RICHARD,C.DI PRIMO,J.J.TOULME JRNL TITL NMR STRUCTURE OF A KISSING COMPLEX FORMED BETWEEN THE TAR JRNL TITL 2 RNA ELEMENT OF HIV-1 AND A LNA-MODIFIED APTAMER JRNL REF NUCLEIC ACIDS RES. V. 35 6103 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17768146 JRNL DOI 10.1093/NAR/GKM655 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER A. T. ETALL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OOM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041394. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288; 277 REMARK 210 PH : 6.4; 6.4 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM UNLABELED TAR; 10MM REMARK 210 PHOSPHATE BUFFER PH 6.4; 1 MM REMARK 210 UNLABELED APTAMER; 10MM REMARK 210 PHOSPHATE BUFFER PH 6.4; 1 MM REMARK 210 UNLABELED TAR/APTAMER COMPLEX; REMARK 210 10MM PHOSPHATE BUFFER PH 6.4; 1 REMARK 210 MM UNLABELED TAR/APTAMER COMPLEX; REMARK 210 10MM PHOSPHATE BUFFER PH 6.4; 1 REMARK 210 MM 15N,13C TAR/UNLABELED,APTAMER REMARK 210 COMPLEX; 10MM PHOSPHATE BUFFER REMARK 210 PH 6.4; 1 MM 15N,13C TAR/ REMARK 210 UNLABELED,APTAMER COMPLEX; 10MM REMARK 210 PHOSPHATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 HMQC; 3D HMQC-NOESY; 3D HCCH- REMARK 210 TOCSY; 3D NOESY-NOESY; HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED STRUCTURES ARE THE REMARK 210 12 STRUCTURES WITH ZERO REMARK 210 VIOLATION ON NOE DISTANCE, REMARK 210 DIHEDRAL AND WITH THE LOWEST REMARK 210 ENERGY. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD HOMONUCLEAR REMARK 210 AND HETERONUCLEAR METHODS 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N1 A A 3 H3 U A 14 1.51 REMARK 500 H3 U A 7 N1 LCA B 26 1.55 REMARK 500 H21 G A 8 O2 10C B 25 1.57 REMARK 500 H21 G A 9 O2 C B 24 1.57 REMARK 500 H21 G A 4 O2 C A 13 1.58 REMARK 500 H21 G A 10 O2 C B 23 1.58 REMARK 500 O2 C B 19 H21 G B 30 1.58 REMARK 500 O2 C B 17 H21 G B 32 1.58 REMARK 500 H21 G A 2 O2 C A 15 1.59 REMARK 500 H21 G A 1 O2 C A 16 1.60 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 1 C A 15 C5' - C4' - O4' ANGL. DEV. = -7.5 DEGREES REMARK 500 6 C A 15 C5' - C4' - O4' ANGL. DEV. = -7.4 DEGREES REMARK 500 10 C A 15 C5' - C4' - O4' ANGL. DEV. = -7.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2OOM A 1 16 PDB 2OOM 2OOM 1 16 DBREF 2OOM B 17 32 PDB 2OOM 2OOM 17 32 SEQRES 1 A 16 G G A G C C U G G G A G C SEQRES 2 A 16 U C C SEQRES 1 B 16 C A C G G U C C 10C LCA G A C SEQRES 2 B 16 G U G MODRES 2OOM 10C B 25 C MODRES 2OOM LCA B 26 A HET 10C B 25 32 HET LCA B 26 34 HETNAM 10C 4-AMINO-1-{2,5-ANHYDRO-4-[(PHOSPHONOOXY)METHYL]-ALPHA- HETNAM 2 10C L-LYXOFURANOSYL}PYRIMIDIN-2(1H)-ONE HETNAM LCA [(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5- HETNAM 2 LCA DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCA PHOSPHATE FORMUL 2 10C C10 H14 N3 O8 P FORMUL 2 LCA C11 H14 N5 O7 P LINK O3' C B 24 P 10C B 25 1555 1555 1.61 LINK O3' 10C B 25 P LCA B 26 1555 1555 1.61 LINK O3' LCA B 26 P G B 27 1555 1555 1.61 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