HEADER RNA 15-AUG-05 2D1B TITLE SOLUTION RNA STRUCTURE MODEL OF THE HIV-1 DIMERIZATION INITIATION SITE TITLE 2 IN THE KISSING-LOOP DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DIS, HIV-1, RNA EXPDTA SOLUTION NMR AUTHOR S.BABA,K.TAKAHASHI,S.NOGUCHI,H.TAKAKU,Y.KOYANAGI,N.YAMAMOTO,G.KAWAI REVDAT 3 09-MAR-22 2D1B 1 REMARK REVDAT 2 24-FEB-09 2D1B 1 VERSN REVDAT 1 01-NOV-05 2D1B 0 JRNL AUTH S.BABA,K.TAKAHASHI,S.NOGUCHI,H.TAKAKU,Y.KOYANAGI,N.YAMAMOTO, JRNL AUTH 2 G.KAWAI JRNL TITL SOLUTION RNA STRUCTURES OF THE HIV-1 DIMERIZATION INITIATION JRNL TITL 2 SITE IN THE KISSING-LOOP AND EXTENDED-DUPLEX DIMERS. JRNL REF J.BIOCHEM.(TOKYO) V. 138 583 2005 JRNL REFN ISSN 0021-924X JRNL PMID 16272570 JRNL DOI 10.1093/JB/MVI158 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 97.0 REMARK 3 AUTHORS : ACCELRYS REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SOLUTION STRUCTURES OF DIS39 REMARK 3 WERE CONSTRUCTED BY COMBINING THE STRUCTURE PARTS. REMARK 3 STRUCTURES OF THE LOOP REGION OF THE KISSING-LOOP DIMER (2D19) AND REMARK 3 STEM-BULGE-STEM REGION (2D17) WERE COMBINED BY SUPERIMPOSING THE REMARK 3 TWO BASE PAIRS, C12:G26 AND U13:G25. REMARK 4 REMARK 4 2D1B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000024864. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 50MM NACL; 50MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.8MM 25-MER RNA FRAGMENT; 10MM REMARK 210 PHOSPHATE BUFFER, 50MM NACL; 100% REMARK 210 D2O; 1.8MM 25-MER RNA FRAGMENT; REMARK 210 10MM PHOSPHATE BUFFER, 50MM NACL; REMARK 210 90% H2O, 10% D2O; 0.3MM [G-13C/ REMARK 210 15N] LABELED 39-MER RNA FRAGMENT; REMARK 210 10MM PHOSPHATE BUFFER, 50MM REMARK 210 NACL; 100% D2O; 0.3MM [G-13C/15N] REMARK 210 LABELED 39-MER RNA FRAGMENT; REMARK 210 10MM PHOSPHATE BUFFER, 50MM NACL; REMARK 210 90% H2O, 10% D2O; 0.1MM [A-13C/ REMARK 210 15N] LABELED 39-MER RNA FRAGMENT; REMARK 210 10MM PHOSPHATE BUFFER, 50MM REMARK 210 NACL; 100% D2O; 1.0MM 39-MER RNA REMARK 210 FRAGMENT; 10MM PHOSPHATE BUFFER, REMARK 210 50MM NACL; 100% D2O; 1.0MM 39- REMARK 210 MER RNA FRAGMENT; 10MM PHOSPHATE REMARK 210 BUFFER, 50MM NACL; 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 1D-HSQC-SELECTED REMARK 210 SPECTRUM; 1D-HSQC-FILTERED REMARK 210 SPECTRUM; 2D TOCSY; 2D-W2- REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MINIMIZATION OF MODEL RNA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: MODEL STRUCTURE WAS CONSTRUCTED BY COMBINING THE STRUCTURE REMARK 210 PARTS 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: 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 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 C A 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 U A 9 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 U A 10 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 20 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 C A 24 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 G A 30 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 C A 37 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 C A 38 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 U B 4 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 C B 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 U B 9 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 U B 10 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 U B 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 C B 20 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 C B 22 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 C B 24 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 G B 30 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 C B 37 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 C B 38 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES 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 G A 14 0.08 SIDE CHAIN REMARK 500 A A 15 0.16 SIDE CHAIN REMARK 500 G A 25 0.06 SIDE CHAIN REMARK 500 G A 35 0.07 SIDE CHAIN REMARK 500 G B 14 0.07 SIDE CHAIN REMARK 500 G B 25 0.06 SIDE CHAIN REMARK 500 G B 35 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D17 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF STEM-BULGE-STEM REGION OF DIS REMARK 900 RELATED ID: 2D18 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF LOOP REGION OF THE EXTENDED-DUPLEX DIMER REMARK 900 RELATED ID: 2D19 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF LOOP REGION OF THE KISSING-LOOP DIMER REMARK 900 RELATED ID: 2D1A RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE MODEL OF THE EXTENDED-DUPLEX DIMER DBREF 2D1B A 1 39 PDB 2D1B 2D1B 1 39 DBREF 2D1B B 1 39 PDB 2D1B 2D1B 1 39 SEQRES 1 A 39 G G G U C G G C U U G C U SEQRES 2 A 39 G A A G U G C A C A C G G SEQRES 3 A 39 C A A G A G G C G A C C C SEQRES 1 B 39 G G G U C G G C U U G C U SEQRES 2 B 39 G A A G U G C A C A C G G SEQRES 3 B 39 C A A G A G G C G A C 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