HEADER RNA 21-NOV-02 1N8X TITLE SOLUTION STRUCTURE OF HIV-1 STEM LOOP SL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 STEM LOOP SL1 MONOMERIC RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HIV-1 STEM LOOP SL1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHESIZED BY IN VITRO SOURCE 4 TRANSCRIPTION USING A SINGLE STRANDED DNA TEMPLATE AND T7 RNA SOURCE 5 POLYMERASE. KEYWDS HIV, SL1, RNA STEM LOOP, BULGE, G-A MISMATCH, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.C.LAWRENCE,C.C.STOVER,J.NOZNITSKY,Z.WU,M.F.SUMMERS REVDAT 5 22-MAY-24 1N8X 1 REMARK REVDAT 4 23-FEB-22 1N8X 1 REMARK REVDAT 3 24-FEB-09 1N8X 1 VERSN REVDAT 2 15-APR-03 1N8X 1 JRNL REVDAT 1 08-APR-03 1N8X 0 JRNL AUTH D.C.LAWRENCE,C.C.STOVER,J.NOZNITSKY,Z.WU,M.F.SUMMERS JRNL TITL STRUCTURE OF THE INTACT STEM AND BULGE OF HIV-1 PSI-RNA JRNL TITL 2 STEM-LOOP SL1 JRNL REF J.MOL.BIOL. V. 326 529 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12559920 JRNL DOI 10.1016/S0022-2836(02)01305-0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, DYANA 1.5 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, MUMENTHALER, WUTHRICH REMARK 3 (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 408 EXPERIMENTAL RESTRAINTS, REMARK 3 INCLUDING 298 NOE-DERIVED DISTANCE RESTRAINTS, 84 HYDROGEN BOND REMARK 3 RESTRAINTS, REMARK 3 AND 26 DIPOLAR COUPLING RESTRAINTS. REMARK 4 REMARK 4 1N8X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000017666. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 308 REMARK 210 PH : 7.0; 8.0 REMARK 210 IONIC STRENGTH : NULL; 10 MM TRIS-CL, 0.1 MM NA REMARK 210 -EDTA REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM SL1 MONOMERIC RNA, U REMARK 210 -15N,13C; 100% D2O; 1 MM SL1 REMARK 210 MONOMERIC RNA, CYT-15N,13C; 100% REMARK 210 D2O; 1 MM SL1 MONOMERIC RNA, GUA- REMARK 210 15N,13C; 100% D2O; 1 MM SL1 REMARK 210 MONOMERIC RNA, GUA-15N,13C; 10 REMARK 210 MM TRIS-D11, PH 8.0, 0.1 MM EDTA; REMARK 210 18 MG/ML PF1 BACTERIOPHAGE REMARK 210 (ASLA); 100% D2O; 1 MM SL1 REMARK 210 MONOMERIC RNA, UNLABELED; 100% REMARK 210 D2O; 1 MM SL1 MONOMERIC RNA, GUA- REMARK 210 15N,13C; 10 MM TRIS-D11, PH 8.0, REMARK 210 0.1 MM EDTA; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 4D_13C REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_ROESY; IPAP H-COUPLED REMARK 210 CT-HSQC; 2D NOESY; 2D ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1, NMRVIEW 5.0.3 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 600 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 EXPERIMENT 8 (IPAP H-COUPLED CT-HSQC) WAS PERFORMED ON SAMPLE 4 REMARK 210 AND SAMPLE 6 (GUA-15N,13C-LABELED SL1 WITH AND WITHOUT PF1 PHAGE). REMARK 210 THE DIFFERENCE BETWEEN THE J-COUPLING VALUES = DIPOLAR COUPLING REMARK 210 VALUE FOR A GIVEN C-H BOND. 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 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 1 G A 1 O4' G A 1 C4' -0.175 REMARK 500 1 G A 12 O4' G A 12 C4' -0.125 REMARK 500 1 G A 26 O4' G A 26 C4' -0.090 REMARK 500 2 G A 1 O4' G A 1 C4' -0.179 REMARK 500 2 G A 2 O4' G A 2 C4' -0.079 REMARK 500 2 G A 12 O4' G A 12 C4' -0.123 REMARK 500 2 G A 26 O4' G A 26 C4' -0.089 REMARK 500 3 G A 1 O4' G A 1 C4' -0.179 REMARK 500 3 G A 12 O4' G A 12 C4' -0.095 REMARK 500 3 G A 18 O4' G A 18 C4' -0.213 REMARK 500 3 G A 26 O4' G A 26 C4' -0.091 REMARK 500 4 G A 1 O4' G A 1 C4' -0.185 REMARK 500 4 G A 12 O4' G A 12 C4' -0.084 REMARK 500 4 G A 18 O4' G A 18 C4' -0.315 REMARK 500 4 G A 26 O4' G A 26 C4' -0.137 REMARK 500 5 G A 1 O4' G A 1 C4' -0.175 REMARK 500 5 G A 2 O4' G A 2 C4' -0.130 REMARK 500 5 G A 12 O4' G A 12 C4' -0.113 REMARK 500 5 G A 18 O4' G A 18 C4' -0.084 REMARK 500 5 G A 26 O4' G A 26 C4' -0.097 REMARK 500 6 G A 1 O4' G A 1 C4' -0.205 REMARK 500 6 G A 12 O4' G A 12 C4' -0.102 REMARK 500 6 G A 26 O4' G A 26 C4' -0.091 REMARK 500 6 G A 29 O4' G A 29 C4' -0.087 REMARK 500 7 G A 1 O4' G A 1 C4' -0.149 REMARK 500 7 G A 12 O4' G A 12 C4' -0.107 REMARK 500 7 G A 29 O4' G A 29 C4' -0.079 REMARK 500 8 G A 1 O4' G A 1 C4' -0.186 REMARK 500 8 G A 12 O4' G A 12 C4' -0.120 REMARK 500 8 C A 36 O4' C A 36 C4' -0.191 REMARK 500 9 G A 1 O4' G A 1 C4' -0.172 REMARK 500 9 G A 12 O4' G A 12 C4' -0.119 REMARK 500 9 G A 18 O4' G A 18 C4' -0.272 REMARK 500 9 G A 26 O4' G A 26 C4' -0.093 REMARK 500 10 G A 1 O4' G A 1 C4' -0.139 REMARK 500 10 G A 12 O4' G A 12 C4' -0.164 REMARK 500 10 G A 18 O4' G A 18 C4' -0.269 REMARK 500 11 G A 1 O4' G A 1 C4' -0.160 REMARK 500 11 G A 12 O4' G A 12 C4' -0.098 REMARK 500 11 G A 18 O4' G A 18 C4' -0.259 REMARK 500 11 G A 26 O4' G A 26 C4' -0.132 REMARK 500 12 G A 1 O4' G A 1 C4' -0.117 REMARK 500 12 G A 12 O4' G A 12 C4' -0.128 REMARK 500 12 G A 26 O4' G A 26 C4' -0.084 REMARK 500 13 G A 1 O4' G A 1 C4' -0.168 REMARK 500 13 G A 12 O4' G A 12 C4' -0.093 REMARK 500 13 G A 29 O4' G A 29 C4' -0.097 REMARK 500 14 G A 1 O4' G A 1 C4' -0.125 REMARK 500 14 G A 12 O4' G A 12 C4' -0.112 REMARK 500 14 A A 27 O4' A A 27 C4' -0.088 REMARK 500 REMARK 500 THIS ENTRY HAS 74 BOND DEVIATIONS. 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 C5' - C4' - O4' ANGL. DEV. = 9.8 DEGREES REMARK 500 1 G A 1 C1' - O4' - C4' ANGL. DEV. = 10.1 DEGREES REMARK 500 1 G A 1 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 1 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 1 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 2 O4' - C4' - C3' ANGL. DEV. = -8.0 DEGREES REMARK 500 1 G A 2 C1' - O4' - C4' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 G A 2 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 2 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 2 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 A A 3 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 A A 3 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 1 A A 3 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 C A 4 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 C A 4 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 U A 5 O4' - C4' - C3' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 U A 5 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 C A 6 O4' - C4' - C3' ANGL. DEV. = -7.5 DEGREES REMARK 500 1 C A 6 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 G A 7 O4' - C4' - C3' ANGL. DEV. = -8.2 DEGREES REMARK 500 1 G A 7 C5' - C4' - O4' ANGL. DEV. = -7.5 DEGREES REMARK 500 1 G A 7 C1' - O4' - C4' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 G A 7 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 7 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 7 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 8 O4' - C4' - C3' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 G A 8 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 G A 8 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 8 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 8 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 C A 9 O4' - C4' - C3' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 C A 9 C5' - C4' - O4' ANGL. DEV. = 15.7 DEGREES REMARK 500 1 C A 9 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 U A 10 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 U A 10 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 U A 11 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 U A 11 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 G A 12 C5' - C4' - O4' ANGL. DEV. = 22.1 DEGREES REMARK 500 1 G A 12 C1' - O4' - C4' ANGL. DEV. = 8.5 DEGREES REMARK 500 1 G A 12 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 12 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 12 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 C A 13 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 C A 13 C5' - C4' - O4' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 C A 13 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 U A 14 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 U A 14 C5' - C4' - O4' ANGL. DEV. = 9.0 DEGREES REMARK 500 1 U A 14 C1' - O4' - C4' ANGL. DEV. = 7.9 DEGREES REMARK 500 1 G A 15 O4' - C4' - C3' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 G A 15 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 2478 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE AUTHOR STATES THERE ARE THREE ADDITIONAL BASES ON THE 5' REMARK 999 AND 3' ENDS, WHICH FORM WC BASE PAIRS: 5'-GGA ... UCC-3' DIS REMARK 999 LOOP (AAGCGCGCA) REPLACED WITH GAGA TETRALOOP' MONOMERIC RNA REMARK 999 ENGINEERED BY REPLACING THE TERMINAL LOOP WITH A GAGA TETRALOOP. REMARK 999 LOWER STEM HAS AN ADDITIONAL THREE BASE PAIRS: 5'GGA...UCC3'. REMARK 999 RESIDUES ARE NUMBERED 1 THROUGH 36 IN COORDINATE FILE ALTHOUGH REMARK 999 THEY ARE NUMBERED DIFFERENTLY IN ARTICLE. INTERNAL BULGED LOOP REMARK 999 COMPOSED OF G5 (5' STRAND), A24, G25, AND G26 (3' STRAND) IS REMARK 999 STRUCTURED WITH A G5-A24 MISMATCH AND G25, G26 STACKING UNDER REMARK 999 A24. DBREF 1N8X A 1 36 PDB 1N8X 1N8X 1 36 SEQRES 1 A 36 G G A C U C G G C U U G C SEQRES 2 A 36 U G G A G A C G G C A A G SEQRES 3 A 36 A G G C G A G 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