HEADER DNA-RNA HYBRID 20-OCT-98 1BYX TITLE CHIMERIC HYBRID DUPLEX R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE TRNA- TITLE 2 DNA JUNCTION FORMED DURING INITIATION 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 CHEMICALLY SOURCE 4 SYNTHESIZED FROM THE HUMAN IMMUNODIFICIENCY VIRUS TYPE 1 (HIV-1). SOURCE 5 THE DUPLEX IS FORMED DURING THE INITIATION OF (-)DNA STRAND SOURCE 6 SYNTHESIS IN HIV-1 REPLICATION.; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES KEYWDS RNA:RNA-DNA CHIMERIC HYBRID, RNASE H, REVERSE TRANSCRIPTASE, DNA-RNA KEYWDS 2 COMPLEX, DNA-RNA HYBRID EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.SZYPERSKI,M.GOETTE,M.BILLETER,E.PEROLA,L.CELLAI REVDAT 5 27-DEC-23 1BYX 1 REMARK REVDAT 4 16-FEB-22 1BYX 1 REMARK 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,H.HEUMANN, JRNL AUTH 2 K.WUTHRICH JRNL TITL NMR STRUCTURE OF THE CHIMERIC HYBRID DUPLEX JRNL TITL 2 R(GCAGUGGC).R(GCCA)D(CTGC) COMPRISING THE TRNA-DNA JUNCTION JRNL TITL 3 FORMED DURING INITIATION OF HIV-1 REVERSE 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 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 THE REMARK 3 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 DEPOSITION ID IS D_1000007043. 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: REMARK 210 THE 20 STRUCTURES ARE ENERGY-MINIMIZED WITH THE AMBER FORCE FIELD REMARK 210 USING THE REMARK 210 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 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 OP2 G A 7 HO3' C A 8 1.56 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 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. = 6.8 DEGREES REMARK 500 1 C B 103 O4' - C1' - N1 ANGL. DEV. = 4.8 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. = 2.8 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. = 1.9 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. = 3.8 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 REMARK 500 THIS ENTRY HAS 142 PLANE DEVIATIONS. 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 MODEL 1