HEADER DNA-RNA HYBRID 20-OCT-98 1BYX TITLE CHIMERIC HYBRID DUPLEX R(GCAGUGGC).R(GCCA)D(CTGC) TITLE 2 COMPRISING THE TRNA-DNA JUNCTION FORMED DURING INITIATION TITLE 3 OF HIV-1 REVERSE TRANSCRIPTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: CHIMERIC HYBRID RNA/RNA-DNA DUPLEX SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE RNA:RNA-DNA CHIMERIC HYBRID DUPLEX WAS SOURCE 4 CHEMICALLY SYNTHESIZED FROM THE HUMAN IMMUNODIFICIENCY SOURCE 5 VIRUS TYPE 1 (HIV-1). THE DUPLEX IS FORMED DURING THE SOURCE 6 INITIATION OF (-)DNA STRAND SYNTHESIS IN HIV-1 SOURCE 7 REPLICATION.; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS RNA:RNA-DNA CHIMERIC HYBRID, RNASE H, REVERSE TRANSCRIPTASE, KEYWDS 2 DNA/RNA COMPLEX, DNA-RNA HYBRID EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.SZYPERSKI,M.GOETTE,M.BILLETER,E.PEROLA,L.CELLAI REVDAT 3 24-FEB-09 1BYX 1 VERSN REVDAT 2 01-APR-03 1BYX 1 JRNL REVDAT 1 20-OCT-99 1BYX 0 JRNL AUTH T.SZYPERSKI,M.GOTTE,M.BILLETER,E.PEROLA,L.CELLAI, JRNL AUTH 2 H.HEUMANN,K.WUTHRICH JRNL TITL NMR STRUCTURE OF THE CHIMERIC HYBRID DUPLEX JRNL TITL 2 R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE TRNA-DNA JRNL TITL 3 JUNCTION FORMED DURING INITIATION OF HIV-1 REVERSE JRNL TITL 4 TRANSCRIPTION. JRNL REF J.BIOMOL.NMR V. 13 343 1999 JRNL REFN ISSN 0925-2738 JRNL PMID 10353196 JRNL DOI 10.1023/A:1008350604637 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA REMARK 3 AUTHORS : GUNTERT,WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS ARE DESCRIBED IN REMARK 3 THE JRNL CITATION ABOVE REMARK 4 REMARK 4 1BYX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB007043. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, DQF-COSY, E H-P REMARK 210 HETCOR, H-C COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : AMX, UNITY+ REMARK 210 SPECTROMETER MANUFACTURER : BRUKER, VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : DYANA TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE 20 STRUCTURES ARE ENERGY-MINIMIZED WITH THE AMBER REMARK 210 FORCE FIELD USING THE PROGRAM OPAL 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 C A 2 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 G A 6 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 G B 101 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C B 102 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 C B 103 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 DC B 105 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DT B 106 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DG B 107 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC B 108 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 C A 2 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 2 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C A 2 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 C B 103 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DC B 105 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DT B 106 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG B 107 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC B 108 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES REMARK 500 3 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 G A 4 N3 - C2 - N2 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 G A 7 O4' - C1' - N9 ANGL. DEV. = 8.1 DEGREES REMARK 500 3 C B 102 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C B 103 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 DC B 105 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 DT B 106 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 DG B 107 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 G A 1 N3 - C2 - N2 ANGL. DEV. = -4.9 DEGREES REMARK 500 4 C A 2 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 4 A A 3 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 4 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 G A 6 C5' - C4' - O4' ANGL. DEV. = 5.8 DEGREES REMARK 500 4 C B 102 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 DC B 105 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 DT B 106 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 4 DG B 107 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 4 DC B 108 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 DC B 108 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 C A 2 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 5 A A 3 C5' - C4' - O4' ANGL. DEV. = 5.7 DEGREES REMARK 500 5 G A 4 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 5 G A 6 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 C B 102 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 5 C B 103 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 DC B 105 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 5 DC B 105 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 DT B 106 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 DT B 106 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 DG B 107 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 206 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 G A 4 0.07 SIDE_CHAIN REMARK 500 1 U A 5 0.08 SIDE_CHAIN REMARK 500 1 G A 7 0.08 SIDE_CHAIN REMARK 500 1 G B 101 0.06 SIDE_CHAIN REMARK 500 1 C B 102 0.08 SIDE_CHAIN REMARK 500 1 DG B 107 0.10 SIDE_CHAIN REMARK 500 2 G A 4 0.10 SIDE_CHAIN REMARK 500 2 U A 5 0.11 SIDE_CHAIN REMARK 500 2 G A 7 0.11 SIDE_CHAIN REMARK 500 2 C B 103 0.06 SIDE_CHAIN REMARK 500 2 A B 104 0.09 SIDE_CHAIN REMARK 500 3 A A 3 0.11 SIDE_CHAIN REMARK 500 3 G A 4 0.09 SIDE_CHAIN REMARK 500 3 U A 5 0.09 SIDE_CHAIN REMARK 500 3 C A 8 0.07 SIDE_CHAIN REMARK 500 3 C B 102 0.09 SIDE_CHAIN REMARK 500 3 A B 104 0.09 SIDE_CHAIN REMARK 500 4 C A 2 0.07 SIDE_CHAIN REMARK 500 4 G A 4 0.11 SIDE_CHAIN REMARK 500 4 G B 101 0.05 SIDE_CHAIN REMARK 500 4 C B 102 0.09 SIDE_CHAIN REMARK 500 4 DT B 106 0.10 SIDE_CHAIN REMARK 500 5 G A 1 0.07 SIDE_CHAIN REMARK 500 5 G A 4 0.13 SIDE_CHAIN REMARK 500 5 U A 5 0.08 SIDE_CHAIN REMARK 500 5 C A 8 0.08 SIDE_CHAIN REMARK 500 5 G B 101 0.11 SIDE_CHAIN REMARK 500 5 A B 104 0.07 SIDE_CHAIN REMARK 500 5 DC B 105 0.10 SIDE_CHAIN REMARK 500 5 DT B 106 0.07 SIDE_CHAIN REMARK 500 5 DC B 108 0.10 SIDE_CHAIN REMARK 500 6 G A 1 0.07 SIDE_CHAIN REMARK 500 6 G A 4 0.15 SIDE_CHAIN REMARK 500 6 U A 5 0.11 SIDE_CHAIN REMARK 500 6 G B 101 0.06 SIDE_CHAIN REMARK 500 6 C B 103 0.14 SIDE_CHAIN REMARK 500 6 A B 104 0.07 SIDE_CHAIN REMARK 500 7 C A 2 0.19 SIDE_CHAIN REMARK 500 7 G A 4 0.07 SIDE_CHAIN REMARK 500 7 U A 5 0.08 SIDE_CHAIN REMARK 500 7 G B 101 0.14 SIDE_CHAIN REMARK 500 7 C B 102 0.08 SIDE_CHAIN REMARK 500 7 DC B 105 0.07 SIDE_CHAIN REMARK 500 7 DT B 106 0.10 SIDE_CHAIN REMARK 500 7 DG B 107 0.09 SIDE_CHAIN REMARK 500 8 G A 1 0.07 SIDE_CHAIN REMARK 500 8 C A 2 0.10 SIDE_CHAIN REMARK 500 8 G A 4 0.12 SIDE_CHAIN REMARK 500 8 U A 5 0.08 SIDE_CHAIN REMARK 500 8 A B 104 0.09 SIDE_CHAIN REMARK 500 8 DG B 107 0.06 SIDE_CHAIN REMARK 500 8 DC B 108 0.17 SIDE_CHAIN REMARK 500 9 G A 1 0.09 SIDE_CHAIN REMARK 500 9 G A 4 0.10 SIDE_CHAIN REMARK 500 9 U A 5 0.13 SIDE_CHAIN REMARK 500 9 G A 7 0.08 SIDE_CHAIN REMARK 500 9 C B 103 0.06 SIDE_CHAIN REMARK 500 9 DT B 106 0.09 SIDE_CHAIN REMARK 500 9 DG B 107 0.08 SIDE_CHAIN REMARK 500 9 DC B 108 0.11 SIDE_CHAIN REMARK 500 10 G A 1 0.07 SIDE_CHAIN REMARK 500 10 A A 3 0.08 SIDE_CHAIN REMARK 500 10 G A 7 0.06 SIDE_CHAIN REMARK 500 10 G B 101 0.09 SIDE_CHAIN REMARK 500 10 A B 104 0.06 SIDE_CHAIN REMARK 500 10 DC B 108 0.11 SIDE_CHAIN REMARK 500 11 G A 1 0.08 SIDE_CHAIN REMARK 500 11 A A 3 0.11 SIDE_CHAIN REMARK 500 11 G A 7 0.14 SIDE_CHAIN REMARK 500 11 G B 101 0.09 SIDE_CHAIN REMARK 500 11 C B 102 0.09 SIDE_CHAIN REMARK 500 11 DT B 106 0.09 SIDE_CHAIN REMARK 500 11 DC B 108 0.07 SIDE_CHAIN REMARK 500 12 G A 1 0.15 SIDE_CHAIN REMARK 500 12 A A 3 0.10 SIDE_CHAIN REMARK 500 12 G A 4 0.10 SIDE_CHAIN REMARK 500 12 U A 5 0.11 SIDE_CHAIN REMARK 500 12 G A 6 0.06 SIDE_CHAIN REMARK 500 12 C A 8 0.13 SIDE_CHAIN REMARK 500 12 G B 101 0.10 SIDE_CHAIN REMARK 500 12 A B 104 0.08 SIDE_CHAIN REMARK 500 12 DC B 108 0.14 SIDE_CHAIN REMARK 500 13 G A 1 0.20 SIDE_CHAIN REMARK 500 13 A A 3 0.10 SIDE_CHAIN REMARK 500 13 G A 4 0.12 SIDE_CHAIN REMARK 500 13 U A 5 0.10 SIDE_CHAIN REMARK 500 13 G A 7 0.06 SIDE_CHAIN REMARK 500 13 C A 8 0.15 SIDE_CHAIN REMARK 500 13 G B 101 0.09 SIDE_CHAIN REMARK 500 13 C B 102 0.06 SIDE_CHAIN REMARK 500 13 A B 104 0.06 SIDE_CHAIN REMARK 500 13 DC B 105 0.08 SIDE_CHAIN REMARK 500 13 DT B 106 0.10 SIDE_CHAIN REMARK 500 13 DG B 107 0.05 SIDE_CHAIN REMARK 500 13 DC B 108 0.07 SIDE_CHAIN REMARK 500 14 G A 4 0.13 SIDE_CHAIN REMARK 500 14 U A 5 0.10 SIDE_CHAIN REMARK 500 14 C B 102 0.10 SIDE_CHAIN REMARK 500 14 A B 104 0.08 SIDE_CHAIN REMARK 500 14 DT B 106 0.09 SIDE_CHAIN REMARK 500 15 G A 4 0.12 SIDE_CHAIN REMARK 500 15 U A 5 0.11 SIDE_CHAIN REMARK 500 15 G B 101 0.11 SIDE_CHAIN REMARK 500 15 DC B 105 0.07 SIDE_CHAIN REMARK 500 16 G A 1 0.08 SIDE_CHAIN REMARK 500 16 A A 3 0.06 SIDE_CHAIN REMARK 500 16 G A 4 0.13 SIDE_CHAIN REMARK 500 16 U A 5 0.08 SIDE_CHAIN REMARK 500 16 G A 7 0.06 SIDE_CHAIN REMARK 500 16 G B 101 0.14 SIDE_CHAIN REMARK 500 16 C B 102 0.07 SIDE_CHAIN REMARK 500 16 C B 103 0.07 SIDE_CHAIN REMARK 500 16 DG B 107 0.06 SIDE_CHAIN REMARK 500 16 DC B 108 0.07 SIDE_CHAIN REMARK 500 17 C A 2 0.07 SIDE_CHAIN REMARK 500 17 G A 4 0.12 SIDE_CHAIN REMARK 500 17 G A 6 0.06 SIDE_CHAIN REMARK 500 17 G A 7 0.08 SIDE_CHAIN REMARK 500 17 A B 104 0.09 SIDE_CHAIN REMARK 500 17 DT B 106 0.09 SIDE_CHAIN REMARK 500 18 G A 1 0.08 SIDE_CHAIN REMARK 500 18 A A 3 0.11 SIDE_CHAIN REMARK 500 18 G A 4 0.13 SIDE_CHAIN REMARK 500 18 U A 5 0.13 SIDE_CHAIN REMARK 500 18 G A 7 0.07 SIDE_CHAIN REMARK 500 18 G B 101 0.06 SIDE_CHAIN REMARK 500 18 A B 104 0.07 SIDE_CHAIN REMARK 500 18 DC B 108 0.08 SIDE_CHAIN REMARK 500 19 G A 1 0.08 SIDE_CHAIN REMARK 500 19 G A 4 0.12 SIDE_CHAIN REMARK 500 19 G A 7 0.11 SIDE_CHAIN REMARK 500 19 A B 104 0.07 SIDE_CHAIN REMARK 500 19 DT B 106 0.08 SIDE_CHAIN REMARK 500 19 DG B 107 0.06 SIDE_CHAIN REMARK 500 19 DC B 108 0.13 SIDE_CHAIN REMARK 500 20 G A 1 0.12 SIDE_CHAIN REMARK 500 20 G A 4 0.09 SIDE_CHAIN REMARK 500 20 U A 5 0.10 SIDE_CHAIN REMARK 500 20 G A 7 0.06 SIDE_CHAIN REMARK 500 20 G B 101 0.14 SIDE_CHAIN REMARK 500 20 DT B 106 0.08 SIDE_CHAIN REMARK 500 20 DC B 108 0.11 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1BYX A 1 8 PDB 1BYX 1BYX 1 8 DBREF 1BYX B 101 108 PDB 1BYX 1BYX 101 108 SEQRES 1 A 8 G C A G U G G C SEQRES 1 B 8 G C C A DC DT DG DC 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 275 0 0 0 0 0 0 6 0 0 0 2 END