HEADER RNA 04-AUG-07 2JTP TITLE SOLUTION STRUCTURE OF THE FRAMESHIFT-INDUCING RNA STEM-LOOP IN SIV COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIV17-50 RNA (34-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO TRANSCRIPTION USING PURIFIED T7 RNA SOURCE 4 POLYMERASE AND SYNTHETIC DNA OLIGONUCLEOTIDES KEYWDS SIV, RNA STEM-LOOP, TRILOOP, FRAMESHIFTING, HIV-2, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.J.MARCHESCHI,D.W.STAPLE,S.E.BUTCHER REVDAT 4 16-MAR-22 2JTP 1 REMARK REVDAT 3 24-FEB-09 2JTP 1 VERSN REVDAT 2 16-OCT-07 2JTP 1 JRNL REVDAT 1 02-OCT-07 2JTP 0 JRNL AUTH R.J.MARCHESCHI,D.W.STAPLE,S.E.BUTCHER JRNL TITL PROGRAMMED RIBOSOMAL FRAMESHIFTING IN SIV IS INDUCED BY A JRNL TITL 2 HIGHLY STRUCTURED RNA STEM-LOOP JRNL REF J.MOL.BIOL. V. 373 652 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17868691 JRNL DOI 10.1016/J.JMB.2007.08.033 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JTP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000100277. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM SIV17-50 RNA (34-MER), 90% REMARK 210 H2O/10% D2O; 1 MM SIV17-50 RNA REMARK 210 (34-MER), 100% D2O; 1 MM [U-100% REMARK 210 13C; U-100% 15N] SIV17-50 RNA REMARK 210 (34-MER), 90% H2O/10% D2O; 1 MM REMARK 210 [U-100% 13C; U-100% 15N] SIV17- REMARK 210 50 RNA (34-MER), 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H COSY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC; 3D 1H-13C-1H REMARK 210 HCCH-TOCSY; 3D NOESY-HMQC; J- REMARK 210 MODULATED 1H-13C CT-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 800 MHZ; 500 REMARK 210 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, SPARKY 3.111, CNS REMARK 210 1.1, X-PLOR NIH, VNMR, NMRDRAW REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS, MOLECULAR REMARK 210 DYNAMICS, RESIDUAL DIPOLAR REMARK 210 COUPLINGS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HO2' G A 20 OP2 C A 21 1.51 REMARK 500 HO2' A A 22 O5' A A 23 1.58 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 20 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 31 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 5 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 5 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 11 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 12 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 14 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 540 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2JTP A 1 34 PDB 2JTP 2JTP 1 34 SEQRES 1 A 34 G G A U G G G G A A A G A SEQRES 2 A 34 A G C C C C G C A A U U U SEQRES 3 A 34 C C C C A U 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 MODEL 1