HEADER RNA 18-APR-98 1BAU TITLE NMR STRUCTURE OF THE DIMER INITIATION COMPLEX OF HIV-1 GENOMIC RNA, TITLE 2 MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SL1 RNA DIMER; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HIV-1 PACKAGING SIGNAL, RESIDUE 248-270; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: ENGINEERED SEQUENCE IN THE LOWER STEM REGION SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA SYNTHESIZED USING T7 RNA TRANSCRIPTION KEYWDS RIBONUCLEIC ACID, HIV-1, DIMERIZATION, ENCAPSIDATION, RNA EXPDTA SOLUTION NMR AUTHOR A.MUJEEB,J.L.CLEVER,T.M.BILLECI,T.L.JAMES,T.G.PARSLOW REVDAT 3 16-FEB-22 1BAU 1 REMARK REVDAT 2 24-FEB-09 1BAU 1 VERSN REVDAT 1 27-APR-99 1BAU 0 JRNL AUTH A.MUJEEB,J.L.CLEVER,T.M.BILLECI,T.L.JAMES,T.G.PARSLOW JRNL TITL STRUCTURE OF THE DIMER INITIATION COMPLEX OF HIV-1 GENOMIC JRNL TITL 2 RNA. JRNL REF NAT.STRUCT.BIOL. V. 5 432 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9628479 JRNL DOI 10.1038/NSB0698-432 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : GUNTERT,WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RANDOMLY GENERATED STRUCTURES WERE REMARK 3 FOLDED IN DYANA USING NMR DRIVEN STRUCTURAL RESTRAINTS. 34 REMARK 3 STRUCTURES SHOWING LOWEST TARGET FUNCTION VALUES AND NO REMARK 3 CONSISTENT VIOLATIONS OF NMR RESTRAINTS WERE INDIVIDUALLY REMARK 3 SUBJECTED TO RESTRAINED ENERGY MINIMIZATION IN AMBER 4.1. FOR REMARK 3 DETAILS OF REFINEMENT PROTOCOL, PLEASE REFER TO THE REFERENCE REMARK 3 ABOVE. REMARK 4 REMARK 4 1BAU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171538. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : D2O AND H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOE IN D2O; 2D NOE IN WATER; REMARK 210 DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, AMBER 4.1 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 34 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST NMR CONSTRAINT VIOLATIONS REMARK 210 AND LOWEST AMBER ENERGY. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: INTERPROTON-DISTANCE INFORMATION (IN THE FORM OF NOE CROSS REMARK 210 -PEAKS) WAS COLLECTED FROM 2D NOE EXPERIMENTS IN D2O AS WELL AS REMARK 210 IN 90% H2O FOR NON-EXCHANGEABLE AND EXCHANGEABLE PROTONS, REMARK 210 RESPECTIVELY. 2D NOE EXPERIMENTS WERE CARRIED OUT AT 50, 80, 200 REMARK 210 AND 400 M SEC MIXING TIMES. COUPLING CONSTANTS AND SUGAR REMARK 210 CONFORMATIONS WERE DEDUCED FROM DQF-COSY EXPERIMENTS. 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 H21 G A 12 O2 C B 13 0.32 REMARK 500 O2 C A 13 H21 G B 12 0.74 REMARK 500 H1 G A 12 N3 C B 13 0.80 REMARK 500 C2 C A 13 H21 G B 12 1.08 REMARK 500 O6 G A 12 H41 C B 13 1.13 REMARK 500 N3 C A 13 H1 G B 12 1.14 REMARK 500 N3 C A 11 H1 G B 14 1.19 REMARK 500 O2 C A 11 H21 G B 14 1.23 REMARK 500 C4 C A 11 H1 G B 14 1.26 REMARK 500 H1 G A 14 H41 C B 11 1.27 REMARK 500 N2 G A 12 O2 C B 13 1.27 REMARK 500 H41 C A 11 C6 G B 14 1.30 REMARK 500 C2 C A 11 H21 G B 14 1.31 REMARK 500 H41 C A 13 O6 G B 12 1.33 REMARK 500 H21 G A 12 C2 C B 13 1.34 REMARK 500 N3 C A 11 H21 G B 14 1.38 REMARK 500 N4 C A 11 H1 G B 14 1.39 REMARK 500 O6 G A 14 H41 C B 11 1.40 REMARK 500 H41 C A 11 N1 G B 14 1.41 REMARK 500 H41 C A 11 O6 G B 14 1.44 REMARK 500 O2 C A 13 N2 G B 12 1.47 REMARK 500 H1 G A 14 N3 C B 11 1.50 REMARK 500 H21 G A 10 O2 C B 15 1.54 REMARK 500 C5 C A 17 H61 A B 9 1.58 REMARK 500 OP1 A A 9 OP1 A B 9 1.78 REMARK 500 N1 G A 12 N3 C B 13 1.78 REMARK 500 C5 C A 17 N6 A B 9 1.86 REMARK 500 N4 C A 11 O6 G B 14 1.89 REMARK 500 N3 C A 11 N1 G B 14 1.91 REMARK 500 N6 A A 9 C5 C B 17 1.92 REMARK 500 N3 C A 13 N1 G B 12 1.97 REMARK 500 N4 C A 11 N1 G B 14 1.99 REMARK 500 O2 C A 11 N2 G B 14 2.00 REMARK 500 C6 C A 17 N6 A B 9 2.02 REMARK 500 N3 C A 11 N2 G B 14 2.02 REMARK 500 C2 C A 13 N2 G B 12 2.10 REMARK 500 O6 G A 14 N4 C B 11 2.12 REMARK 500 O6 G A 12 N4 C B 13 2.15 REMARK 500 N4 C A 11 C6 G B 14 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 A A 9 C6 A A 9 N1 -0.052 REMARK 500 A B 9 C6 A B 9 N1 -0.051 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 A A 4 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 A A 8 C4' - C3' - C2' ANGL. DEV. = -9.3 DEGREES REMARK 500 A A 8 C3' - C2' - C1' ANGL. DEV. = 5.9 DEGREES REMARK 500 A A 8 N9 - C1' - C2' ANGL. DEV. = 8.2 DEGREES REMARK 500 A A 8 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 A A 8 N1 - C6 - N6 ANGL. DEV. = -6.8 DEGREES REMARK 500 A A 9 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 A A 9 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 9 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 A A 9 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 G A 10 O4' - C1' - N9 ANGL. DEV. = 9.4 DEGREES REMARK 500 C A 11 C5' - C4' - O4' ANGL. DEV. = 10.0 DEGREES REMARK 500 C A 11 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 C A 11 N1 - C2 - O2 ANGL. DEV. = 4.8 DEGREES REMARK 500 C A 11 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 C A 13 C5' - C4' - O4' ANGL. DEV. = 9.1 DEGREES REMARK 500 C A 13 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 C A 13 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 C A 15 O4' - C1' - N1 ANGL. DEV. = 7.4 DEGREES REMARK 500 A A 16 C3' - C2' - C1' ANGL. DEV. = 7.0 DEGREES REMARK 500 A A 16 C2 - N3 - C4 ANGL. DEV. = 3.1 DEGREES REMARK 500 A A 16 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 A A 16 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 A A 16 N7 - C8 - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 A A 16 C8 - N9 - C4 ANGL. DEV. = -5.2 DEGREES REMARK 500 A A 16 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 C A 17 C6 - N1 - C2 ANGL. DEV. = -3.5 DEGREES REMARK 500 U A 19 O4' - C1' - N1 ANGL. DEV. = 7.4 DEGREES REMARK 500 U A 20 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 G A 21 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 A B 4 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 U B 6 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 G B 7 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 A B 8 C4' - C3' - C2' ANGL. DEV. = -9.3 DEGREES REMARK 500 A B 8 C3' - C2' - C1' ANGL. DEV. = 5.9 DEGREES REMARK 500 A B 8 N9 - C1' - C2' ANGL. DEV. = 8.2 DEGREES REMARK 500 A B 8 C2 - N3 - C4 ANGL. DEV. = 3.2 DEGREES REMARK 500 A B 8 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 A B 8 N1 - C6 - N6 ANGL. DEV. = -6.8 DEGREES REMARK 500 A B 9 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 A B 9 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES REMARK 500 A B 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 A B 9 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 A B 9 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 G B 10 O4' - C1' - N9 ANGL. DEV. = 9.3 DEGREES REMARK 500 C B 11 C5' - C4' - O4' ANGL. DEV. = 10.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 68 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 A A 4 0.07 SIDE CHAIN REMARK 500 U A 6 0.07 SIDE CHAIN REMARK 500 G A 7 0.14 SIDE CHAIN REMARK 500 A A 8 0.09 SIDE CHAIN REMARK 500 A A 9 0.14 SIDE CHAIN REMARK 500 C A 11 0.10 SIDE CHAIN REMARK 500 G A 12 0.09 SIDE CHAIN REMARK 500 C A 13 0.07 SIDE CHAIN REMARK 500 G A 14 0.09 SIDE CHAIN REMARK 500 C A 17 0.14 SIDE CHAIN REMARK 500 G A 18 0.09 SIDE CHAIN REMARK 500 U A 19 0.11 SIDE CHAIN REMARK 500 U A 20 0.11 SIDE CHAIN REMARK 500 C A 22 0.09 SIDE CHAIN REMARK 500 C A 23 0.09 SIDE CHAIN REMARK 500 A B 4 0.07 SIDE CHAIN REMARK 500 U B 6 0.07 SIDE CHAIN REMARK 500 G B 7 0.14 SIDE CHAIN REMARK 500 A B 8 0.09 SIDE CHAIN REMARK 500 A B 9 0.14 SIDE CHAIN REMARK 500 C B 11 0.10 SIDE CHAIN REMARK 500 G B 12 0.09 SIDE CHAIN REMARK 500 C B 13 0.07 SIDE CHAIN REMARK 500 G B 14 0.09 SIDE CHAIN REMARK 500 C B 17 0.14 SIDE CHAIN REMARK 500 G B 18 0.09 SIDE CHAIN REMARK 500 U B 19 0.11 SIDE CHAIN REMARK 500 U B 20 0.11 SIDE CHAIN REMARK 500 C B 22 0.09 SIDE CHAIN REMARK 500 C B 23 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1BAU A 1 23 PDB 1BAU 1BAU 1 23 DBREF 1BAU B 1 23 PDB 1BAU 1BAU 1 23 SEQRES 1 A 23 G G C A A U G A A G C G C SEQRES 2 A 23 G C A C G U U G C C SEQRES 1 B 23 G G C A A U G A A G C G C SEQRES 2 B 23 G C A C G U U G C C 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