262D - Header Asymmetric Unit

HEADER RNA/TRANSCRIPTION REGULATION PROTEIN 05-APR-94 262D

TITLE A THREE-DIMENSIONAL MODEL OF THE REV BINDING ELEMENT OF HIV- TITLE 2 1 DERIVED FROM ANALYSES OF IN VITRO SELECTED VARIANTS

COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (30-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE:; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2

KEYWDS RNA/TRANSCRIPTION REGULATION PROTEIN

EXPDTA THEORETICAL MODEL

AUTHOR F.LECLERC,R.J.CEDERGREN,A.D.ELLINGTON

REVDAT 2 01-APR-03 262D 1 JRNL REVDAT 1 15-OCT-94 262D 0

JRNL AUTH F.LECLERC,R.CEDERGREN,A.D.ELLINGTON JRNL TITL A THREE-DIMENSIONAL MODEL OF THE REV-BINDING JRNL TITL 2 ELEMENT OF HIV-1 DERIVED FROM ANALYSES OF APTAMERS. JRNL REF NAT.STRUCT.BIOL. V. 1 293 1994 JRNL REFN ASTM NSBIEW US ISSN 1072-8368

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.L.BATTISTE,R.TAN,A.D.FRANKEL,J.R.WILLIAMSON REMARK 1 TITL BINDING OF AN HIV REV PEPTIDE TO RRE RNA INDUCES REMARK 1 TITL 2 FORMATION OF PURINE-PURINE BASE PAIRS REMARK 1 REF BIOCHEMISTRY V. 33 2741 1994 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.GIVER,D.BARTEL,M.ZAPP,A.PAWUL,M.GREEN, REMARK 1 AUTH 2 A.D.ELLINGTON REMARK 1 TITL SELECTION AND DESIGN OF HIGH-AFFINITY RNA LIGANDS REMARK 1 TITL 2 FOR HIV-1 REV. GENE REMARK 1 REF GENE V. 137 19 1994 REMARK 1 REFN ASTM GENED6 NE ISSN 0378-1119 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.B.JENSEN,L.GREEN,S.MACDOUGAL-WAUGH,C.TUERK REMARK 1 TITL CHARACTERIZATION OF AN IN VITRO-SELECTED RNA REMARK 1 TITL 2 LIGAND TO THE HIV-1 REV PROTEIN REMARK 1 REF J.MOL.BIOL. V. 235 237 1994 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH R.TAN,L.CHEN,J.A.BUETTNER,D.HUDSON,A.D.FRANKEL REMARK 1 TITL RNA RECOGNITION BY AN ISOLATED "A"(ALPHA)-HELIX REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 73 1031 1993 REMARK 1 REFN ASTM CELLB5 US ISSN 0092-8674 REMARK 1 REFERENCE 5 REMARK 1 AUTH L.GIVER,D.BARTEL,M.ZAPP,A.PAWUL,M.GREEN, REMARK 1 AUTH 2 A.D.ELLINGTON REMARK 1 TITL SELECTIVE OPTIMIZATION OF THE REV-BINDING ELEMENT REMARK 1 TITL 2 OF HIV-1 REMARK 1 REF NUCLEIC ACIDS RES. V. 21 5509 1993 REMARK 1 REFN ASTM NARHAD UK ISSN 0305-1048 REMARK 1 REFERENCE 6 REMARK 1 AUTH M.L.ZAPP,S.STERN,M.R.GREEN REMARK 1 TITL SMALL MOLECULES THAT SELECTIVELY BLOCK RNA BINDING REMARK 1 TITL 2 OF HIV-1 REV PROTEIN INHIBIT REV FUNCTION AND REMARK 1 TITL 3 VIRAL PRODUCTION REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 74 969 1993 REMARK 1 REFN ASTM CELLB5 US ISSN 0092-8674 REMARK 1 REFERENCE 7 REMARK 1 AUTH D.P.BARTEL,M.L.ZAPP,M.R.GREEN,J.W.SZOSTAK REMARK 1 TITL HIV-1 REV REGULATION INVOLVES RECOGNITION OF REMARK 1 TITL 2 NON-WATSON-CRICK BASE-PAIRS IN VIRAL RNA REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 67 529 1991 REMARK 1 REFN ASTM CELLB5 US ISSN 0092-8674

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 262D COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 5 REMARK 5 THE RNA MOLECULE (30 NUCLEOTIDES) IS DERIVED FROM THE REV REMARK 5 RESPONSE ELEMENT (RRE) RNA (234 NUCLEOTIDES) WHICH IS A REMARK 5 STEM-LOOP STRUCTURE PRESENT WITHIN THE THE ENVELOPE-CODING REMARK 5 REGION OF THE HIV-1 ENVELOPE GLYCOPROTEIN GENE. THE RNA REMARK 5 SEQUENCE CORRESPONDS TO THE SEQUENCE OF RBE3 IN REFERENCE REMARK 5 8 GIVEN ABOVE.

REMARK 6 REMARK 6 IN THIS ENTRY NUCLEOTIDE ADENINE 68 FORMS A BASE PAIR WITH REMARK 6 GUANINE 50 AND CYTOSINE 69 BULGES OUT FROM THE STRUCTURE. REMARK 6 IN PDB ENTRY 163D CYTOSINE 69 FORMS A BASE PAIR WITH REMARK 6 GUANINE 50 AND ADENINE 68 BULGES OUT FROM THE STRUCTURE.

REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL

REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.

DBREF 262D B 1 17 UNP P05872 REV_HV1SC 34 50

SEQRES 1 A 30 G G U G G G C G C A G C U SEQRES 2 A 30 U C G G C U G A C G G U A SEQRES 3 A 30 C A C C SEQRES 1 B 17 THR ARG GLN ALA ARG ARG ASN ARG ARG ARG ARG TRP ARG SEQRES 2 B 17 GLU ARG GLN ARG

HELIX 1 H1 THR B 1 ARG B 17 1 17

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