HEADER RNA 07-JUL-99 1QD3 TITLE HIV-1 TAR RNA/NEOMYCIN B COMPLEX CAVEAT 1QD3 RIB B 1 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 TAR RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 17-45; COMPND 5 OTHER_DETAILS: NEOMYCIN B (RESIDUES BDG-CYY-RYB-IDG) COMPLEXED IN THE COMPND 6 RNA MINOR GROOVE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 CELL_LINE: Z2/CDC-Z34 ISOLATE KEYWDS HIV-1, AMINOGLYCOSIDE-RNA-COMPLEX, MINOR GROOVE BINDING, RNA EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR C.FABER,H.STICHT,P.ROESCH REVDAT 5 27-DEC-23 1QD3 1 HETSYN LINK REVDAT 4 29-JUL-20 1QD3 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 24-FEB-09 1QD3 1 VERSN REVDAT 2 01-APR-03 1QD3 1 JRNL REVDAT 1 12-JUL-00 1QD3 0 JRNL AUTH C.FABER,H.STICHT,K.SCHWEIMER,P.ROSCH JRNL TITL STRUCTURAL REARRANGEMENTS OF HIV-1 TAT-RESPONSIVE RNA UPON JRNL TITL 2 BINDING OF NEOMYCIN B. JRNL REF J.BIOL.CHEM. V. 275 20660 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10747964 JRNL DOI 10.1074/JBC.M000920200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.WANG,P.W.HUBER,C.MEI,A.W.CZARNIK,H.Y.MEI REMARK 1 TITL BINDING OF NEOMYCIN TO THE TAR ELEMENT OF HIV-1 RNA INDUCES REMARK 1 TITL 2 DISSOCIATION OF TAT PROTEIN BY AN ALLOSTERIC MECHANISM REMARK 1 REF BIOCHEMISTRY V. 37 5549 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI972808A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 1QD3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000001219. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 110 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; HSQC-NOESY; REMARK 210 HCCH-COSY; HCCH-TOCSY; XFILTERED- REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DRX600; DMX750 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NDEE, XNDEE, XPLOR REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY, AGREEMENT WITH REMARK 210 EXPERIMENTAL DATA REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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, 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 HO2' U A 42 O5' G A 43 1.41 REMARK 500 H61 A A 22 O4 U A 40 1.50 REMARK 500 HO2' U A 25 O3' G A 26 1.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QD3 A 17 45 PDB 1QD3 1QD3 17 45 SEQRES 1 A 29 G C C A G A U U U G A G C SEQRES 2 A 29 C U G G G A G C U C U C U SEQRES 3 A 29 G G C HET RIB B 1 17 HET IDG B 2 24 HET BDG A 46 25 HET CYY A 47 22 HETNAM RIB ALPHA-D-RIBOFURANOSE HETNAM IDG 2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE HETNAM BDG 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM CYY 2-DEOXYSTREPTAMINE HETSYN RIB ALPHA-D-RIBOSE; D-RIBOSE; RIBOSE HETSYN IDG O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSE; 2,6- HETSYN 2 IDG DIAMINO-2,6-DIDEOXY-BETA-L-IDOSE; 2,6-DIAMINO-2,6- HETSYN 3 IDG DIDEOXY-L-IDOSE; 2,6-DIAMINO-2,6-DIDEOXY-IDOSE HETSYN BDG O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE; 2,6- HETSYN 2 BDG DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOSE; 2,6-DIAMINO-2,6- HETSYN 3 BDG DIDEOXY-D-GLUCOSE; 2,6-DIAMINO-2,6-DIDEOXY-GLUCOSE FORMUL 2 RIB C5 H10 O5 FORMUL 2 IDG C6 H14 N2 O4 FORMUL 3 BDG C6 H14 N2 O4 FORMUL 4 CYY C6 H14 N2 O3 LINK O1 BDG A 46 C4 CYY A 47 1555 1555 1.45 LINK O5 CYY A 47 C1 RIB B 1 1555 1555 1.46 LINK O3 RIB B 1 C1 IDG B 2 1555 1555 1.44 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