HEADER RNA 11-APR-00 1ESY TITLE NMR STRUCTURE OF STEM LOOP SL2 OF THE HIV-1 PSI RNA PACKAGING SIGNAL TITLE 2 REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM CAVEAT 1ESY CHIRALITY ERRORS AT C4' CENTERS OF RESIDUES 12 OF MODEL 4, CAVEAT 2 1ESY 14 OF MODEL 5, 14 OF MODEL 12, 12 OF MODEL 13, 7 OF MODEL CAVEAT 3 1ESY 14, 7 OF MODEL 16, 7 OF MODEL 19, AND 14 OF MODEL 19 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(P*GP*GP*CP*GP*AP*CP*UP*GP*GP*UP*GP*AP*GP*UP*AP*CP*GP*CP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: STEM LOOP 2 OF THE PSI RNA PACKAGING SIGNAL IN HIV-1 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: T7 TRANSCRIPT KEYWDS HIV-1, RNA, SPLICE-DONOR SITE, PLATFORM MOTIF EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.K.AMARASINGHE,R.N.DE GUZMAN,R.B.TURNER,M.F.SUMMERS REVDAT 3 29-DEC-10 1ESY 1 ATOM REVDAT 2 24-FEB-09 1ESY 1 VERSN REVDAT 1 31-MAY-00 1ESY 0 JRNL AUTH G.K.AMARASINGHE,R.N.DE GUZMAN,R.B.TURNER,M.F.SUMMERS JRNL TITL NMR STRUCTURE OF STEM-LOOP SL2 OF THE HIV-1 PSI RNA JRNL TITL 2 PACKAGING SIGNAL REVEALS A NOVEL A-U-A BASE-TRIPLE PLATFORM. JRNL REF J.MOL.BIOL. V. 299 145 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10860728 JRNL DOI 10.1006/JMBI.2000.3710 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1ESY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-00. REMARK 100 THE RCSB ID CODE IS RCSB010866. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 25 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6-1.2 MM SL2 RNA, NATURAL REMARK 210 ABUNDANCE, 25 MM NA-D3-ACETATE REMARK 210 BUFFER; 0.6-1.2 MM SL2 RNA, REMARK 210 NATURAL ABUNDANCE, 25 MM NA-D3- REMARK 210 ACETATE BUFFER; 0.6-1.2 MM SL2 REMARK 210 RNA, U-15N,13C; 25 MM NA-D3- REMARK 210 ACETATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 3D_13C- REMARK 210 SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE 1.0, REMARK 210 NMRVIEW 3.0, DYANA 1.5 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, ENERGY MIMIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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: EXPERIMENTAL TEMPERATURE SET TO EITHER 298 OR 278 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 H1 G A 4 N3 C A 16 1.88 REMARK 500 N3 C A 3 H1 G A 17 1.88 REMARK 500 H1 G A 2 N3 C A 18 1.89 REMARK 500 N3 C A 6 H1 G A 13 1.89 REMARK 500 O4 U A 7 H61 A A 12 1.89 REMARK 500 H41 C A 6 O6 G A 13 1.89 REMARK 500 H1 G A 1 N3 C A 19 1.89 REMARK 500 O2 C A 6 H21 G A 13 1.89 REMARK 500 H21 G A 1 O2 C A 19 1.90 REMARK 500 O6 G A 2 H41 C A 18 1.90 REMARK 500 N1 A A 5 H61 A A 15 1.90 REMARK 500 O2 C A 3 H21 G A 17 1.90 REMARK 500 O6 G A 1 H41 C A 19 1.90 REMARK 500 H41 C A 3 O6 G A 17 1.90 REMARK 500 H21 G A 4 O2 C A 16 1.90 REMARK 500 O6 G A 4 H41 C A 16 1.90 REMARK 500 H21 G A 2 O2 C A 18 1.91 REMARK 500 O2 U A 14 H62 A A 15 1.91 REMARK 500 HO2' U A 7 O4' G A 8 2.00 REMARK 500 H3 U A 7 N1 A A 12 2.00 REMARK 500 O2' U A 14 H42 C A 16 2.00 REMARK 500 HO2' C A 18 O4' C A 19 2.07 REMARK 500 H61 A A 5 O2 U A 14 2.16 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' -0.253 REMARK 500 1 G A 2 O4' G A 2 C4' -0.140 REMARK 500 1 C A 3 O4' C A 3 C4' -0.122 REMARK 500 1 G A 4 O4' G A 4 C4' -0.208 REMARK 500 1 U A 7 O4' U A 7 C4' -0.188 REMARK 500 1 G A 13 O4' G A 13 C4' -0.220 REMARK 500 1 U A 14 O4' U A 14 C4' -0.237 REMARK 500 1 C A 16 O4' C A 16 C4' -0.230 REMARK 500 1 G A 17 O4' G A 17 C4' -0.259 REMARK 500 2 G A 1 O4' G A 1 C4' -0.257 REMARK 500 2 G A 2 O4' G A 2 C4' -0.083 REMARK 500 2 G A 4 O4' G A 4 C4' -0.255 REMARK 500 2 U A 7 O4' U A 7 C4' -0.158 REMARK 500 2 G A 13 O4' G A 13 C4' -0.260 REMARK 500 2 A A 15 O4' A A 15 C4' -0.114 REMARK 500 2 C A 16 O4' C A 16 C4' -0.248 REMARK 500 2 G A 17 O4' G A 17 C4' -0.255 REMARK 500 3 G A 1 O4' G A 1 C4' -0.247 REMARK 500 3 G A 2 O4' G A 2 C4' -0.176 REMARK 500 3 G A 4 O4' G A 4 C4' -0.266 REMARK 500 3 U A 7 O4' U A 7 C4' -0.140 REMARK 500 3 G A 13 O4' G A 13 C4' -0.143 REMARK 500 3 U A 14 O4' U A 14 C4' -0.115 REMARK 500 3 A A 15 O4' A A 15 C4' -0.153 REMARK 500 3 C A 16 O4' C A 16 C4' -0.178 REMARK 500 3 G A 17 O4' G A 17 C4' -0.251 REMARK 500 4 G A 1 O4' G A 1 C4' -0.266 REMARK 500 4 C A 3 O4' C A 3 C4' -0.133 REMARK 500 4 G A 4 O4' G A 4 C4' -0.186 REMARK 500 4 G A 13 O4' G A 13 C4' -0.128 REMARK 500 4 U A 14 O4' U A 14 C4' -0.209 REMARK 500 4 A A 15 O4' A A 15 C4' -0.098 REMARK 500 4 C A 16 O4' C A 16 C4' -0.260 REMARK 500 4 G A 17 O4' G A 17 C4' -0.190 REMARK 500 5 G A 1 O4' G A 1 C4' -0.270 REMARK 500 5 C A 3 O4' C A 3 C4' -0.085 REMARK 500 5 G A 4 O4' G A 4 C4' -0.264 REMARK 500 5 C A 6 O4' C A 6 C4' -0.110 REMARK 500 5 U A 7 O4' U A 7 C4' -0.117 REMARK 500 5 G A 13 O4' G A 13 C4' -0.151 REMARK 500 5 A A 15 O4' A A 15 C4' -0.130 REMARK 500 5 C A 16 O4' C A 16 C4' -0.239 REMARK 500 5 G A 17 O4' G A 17 C4' -0.250 REMARK 500 6 G A 1 O4' G A 1 C4' -0.271 REMARK 500 6 C A 3 O4' C A 3 C4' -0.098 REMARK 500 6 G A 4 O4' G A 4 C4' -0.235 REMARK 500 6 G A 13 O4' G A 13 C4' -0.201 REMARK 500 6 U A 14 O4' U A 14 C4' -0.253 REMARK 500 6 A A 15 O4' A A 15 C4' -0.118 REMARK 500 6 C A 16 O4' C A 16 C4' -0.241 REMARK 500 REMARK 500 THIS ENTRY HAS 178 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. = 22.8 DEGREES REMARK 500 1 G A 1 C1' - O4' - C4' ANGL. DEV. = 10.4 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. = 5.8 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. = 5.5 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 C A 3 O4' - C4' - C3' ANGL. DEV. = -8.4 DEGREES REMARK 500 1 G A 4 C1' - O4' - C4' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 G A 4 C6 - N1 - C2 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 G A 4 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 4 C5 - C6 - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 A A 5 O4' - C4' - C3' ANGL. DEV. = -11.4 DEGREES REMARK 500 1 C A 6 O4' - C4' - C3' ANGL. DEV. = -9.4 DEGREES REMARK 500 1 C A 6 C1' - O4' - C4' ANGL. DEV. = 6.8 DEGREES REMARK 500 1 U A 7 C5' - C4' - O4' ANGL. DEV. = -11.7 DEGREES REMARK 500 1 U A 7 C1' - O4' - C4' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 G A 8 O4' - C4' - C3' ANGL. DEV. = -10.4 DEGREES REMARK 500 1 G A 8 C5' - C4' - O4' ANGL. DEV. = 28.6 DEGREES REMARK 500 1 G A 8 C1' - O4' - C4' ANGL. DEV. = 6.1 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 G A 9 O4' - C4' - C3' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 G A 9 C5' - C4' - O4' ANGL. DEV. = 38.3 DEGREES REMARK 500 1 G A 9 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 G A 9 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 9 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 9 C5 - C6 - N1 ANGL. DEV. = 6.0 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 G A 11 O4' - C4' - C3' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 G A 11 C1' - O4' - C4' ANGL. DEV. = 8.0 DEGREES REMARK 500 1 G A 11 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 11 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 11 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 A A 12 C5' - C4' - O4' ANGL. DEV. = 30.8 DEGREES REMARK 500 1 G A 13 C5' - C4' - O4' ANGL. DEV. = 22.8 DEGREES REMARK 500 1 G A 13 C1' - O4' - C4' ANGL. DEV. = 8.8 DEGREES REMARK 500 1 G A 13 C6 - N1 - C2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 G A 13 N1 - C2 - N3 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 13 C5 - C6 - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U A 14 C5' - C4' - O4' ANGL. DEV. = 30.4 DEGREES REMARK 500 1 U A 14 C1' - O4' - C4' ANGL. DEV. = 8.9 DEGREES REMARK 500 1 C A 16 C5' - C4' - O4' ANGL. DEV. = 35.3 DEGREES REMARK 500 1 C A 16 C1' - O4' - C4' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 G A 17 C5' - C4' - O4' ANGL. DEV. = 22.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1252 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BN0 RELATED DB: PDB DBREF 1ESY A 1 19 PDB 1ESY 1ESY 1 19 SEQRES 1 A 19 G G C G A C U G G U G A G SEQRES 2 A 19 U A C 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 MODEL 1