PDB Short entry for 2D18 HEADER RNA 15-AUG-05 2D18 TITLE SOLUTION RNA STRUCTURE OF LOOP REGION OF THE HIV-1 DIMERIZATION TITLE 2 INITIATION SITE IN THE EXTENDED-DUPLEX DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)- COMPND 3 3'; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DIS, HIV-1, RNA EXPDTA SOLUTION NMR NUMMDL 11 MDLTYP MINIMIZED AVERAGE AUTHOR S.BABA,K.TAKAHASHI,S.NOGUCHI,H.TAKAKU,Y.KOYANAGI,N.YAMAMOTO,G.KAWAI REVDAT 3 09-MAR-22 2D18 1 REMARK REVDAT 2 24-FEB-09 2D18 1 VERSN REVDAT 1 01-NOV-05 2D18 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 : XWINNMR 2.6, DISCOVER 97.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), ACCELRYS (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 598 RESTRAINTS, 384 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 138 REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 76 DISTANCE RESTRAINTS FROM HYDROGEN REMARK 3 BONDS. REMARK 4 REMARK 4 2D18 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000024861. 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; 0.4MM [G-13C/ REMARK 210 15N] LABELED 39-MER RNA FRAGMENT; REMARK 210 10MM PHOSPHATE BUFFER, 50MM REMARK 210 NACL; 100% D2O; 0.4MM [G-13C/15N] REMARK 210 LABELED 39-MER RNA FRAGMENT; REMARK 210 10MM PHOSPHATE BUFFER, 50MM NACL; REMARK 210 90% H2O, 10% D2O; 0.2MM [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 : FELIX 97.0, DISCOVER 97.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 CHEMICAL SYNTHESIZED 25-MER RNA CORRESPONDING TO THE HIV-1 REMARK 210 DIMERIZATION INITIATION SITE. REMARK 210 ENZYMATICAL SYNTHESIZED [G-13C/15N] LABELED 39-MER RNA REMARK 210 CORRESPONDING TO THE HIV-1 DIMERIZATION INITIATION SITE. REMARK 210 ENZYMATICAL SYNTHESIZED [A-13C/15N] LABELED 39-MER RNA REMARK 210 CORRESPONDING TO THE HIV-1 DIMERIZATION INITIATION SITE. REMARK 210 ENZYMATICAL SYNTHESIZED 39-MER RNA CORRESPONDING TO THE HIV-1 REMARK 210 DIMERIZATION INITIATION SITE. 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 1 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 U B 3 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 C B 10 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 U B 3 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 2 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 C B 10 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 C B 12 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 C B 14 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES REMARK 500 3 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 U B 3 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 C B 10 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 C B 14 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 U A 3 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 4 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 U B 3 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 4 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 C B 10 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 C B 14 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 C A 2 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 5 U A 3 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 5 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 5 U B 3 O4' - C1' - N1 ANGL. DEV. = 7.2 DEGREES REMARK 500 5 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 C B 10 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 C B 14 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 U A 3 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 6 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 C A 10 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 98 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 C A 2 0.06 SIDE CHAIN REMARK 500 1 G A 4 0.09 SIDE CHAIN REMARK 500 1 A A 11 0.06 SIDE CHAIN REMARK 500 1 G A 15 0.07 SIDE CHAIN REMARK 500 1 A B 5 0.07 SIDE CHAIN REMARK 500 1 A B 11 0.06 SIDE CHAIN REMARK 500 1 G B 15 0.10 SIDE CHAIN REMARK 500 2 C A 2 0.08 SIDE CHAIN REMARK 500 2 A A 11 0.06 SIDE CHAIN REMARK 500 2 G A 15 0.09 SIDE CHAIN REMARK 500 2 C B 2 0.06 SIDE CHAIN REMARK 500 2 G B 15 0.08 SIDE CHAIN REMARK 500 3 G A 4 0.07 SIDE CHAIN REMARK 500 3 A A 11 0.07 SIDE CHAIN REMARK 500 3 G A 15 0.10 SIDE CHAIN REMARK 500 3 C B 2 0.07 SIDE CHAIN REMARK 500 3 G B 9 0.08 SIDE CHAIN REMARK 500 3 A B 11 0.06 SIDE CHAIN REMARK 500 3 G B 15 0.07 SIDE CHAIN REMARK 500 4 G A 4 0.06 SIDE CHAIN REMARK 500 4 A A 6 0.06 SIDE CHAIN REMARK 500 4 A A 11 0.07 SIDE CHAIN REMARK 500 4 G A 15 0.10 SIDE CHAIN REMARK 500 4 G B 4 0.07 SIDE CHAIN REMARK 500 4 A B 11 0.06 SIDE CHAIN REMARK 500 4 G B 15 0.09 SIDE CHAIN REMARK 500 5 C A 2 0.07 SIDE CHAIN REMARK 500 5 G A 15 0.09 SIDE CHAIN REMARK 500 5 G B 4 0.05 SIDE CHAIN REMARK 500 5 A B 13 0.09 SIDE CHAIN REMARK 500 5 G B 15 0.07 SIDE CHAIN REMARK 500 6 G A 4 0.08 SIDE CHAIN REMARK 500 6 A A 11 0.06 SIDE CHAIN REMARK 500 6 G A 15 0.10 SIDE CHAIN REMARK 500 6 G B 4 0.07 SIDE CHAIN REMARK 500 6 A B 6 0.05 SIDE CHAIN REMARK 500 6 G B 9 0.08 SIDE CHAIN REMARK 500 6 A B 13 0.05 SIDE CHAIN REMARK 500 6 G B 15 0.09 SIDE CHAIN REMARK 500 7 G A 4 0.09 SIDE CHAIN REMARK 500 7 G A 15 0.08 SIDE CHAIN REMARK 500 7 A B 11 0.06 SIDE CHAIN REMARK 500 7 G B 15 0.07 SIDE CHAIN REMARK 500 8 G A 4 0.06 SIDE CHAIN REMARK 500 8 G A 9 0.07 SIDE CHAIN REMARK 500 8 A A 11 0.06 SIDE CHAIN REMARK 500 8 G A 15 0.08 SIDE CHAIN REMARK 500 8 G B 4 0.08 SIDE CHAIN REMARK 500 8 G B 7 0.06 SIDE CHAIN REMARK 500 8 G B 9 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 67 PLANE DEVIATIONS. 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: 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 REMARK 900 RELATED ID: 2D1B RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE MODELS OF THE KISSING-LOOP DIMER DBREF 2D18 A 1 17 PDB 2D18 2D18 1 17 DBREF 2D18 B 1 17 PDB 2D18 2D18 1 17 SEQRES 1 A 17 G C U G A A G U G C A C A SEQRES 2 A 17 C G G C SEQRES 1 B 17 G C U G A A G U G C A C A SEQRES 2 B 17 C G G 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