10 20 30 40 50 60 70 80 1JTW - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 22-AUG-01 1JTW
TITLE STRUCTURE OF SL4 RNA FROM THE HIV-1 PACKAGING SIGNAL
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'- COMPND 3 R(*GP*GP*GP*UP*GP*CP*GP*AP*GP*AP*GP*CP*GP*UP*CP*A)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HIV-1 PACKAGING SIGNAL SL4 HAIRPIN
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS IN THE PACKAGING SOURCE 4 SIGNAL OF HIV-1.
KEYWDS HAIRPIN, TANDEM G-U PAIRS, GAGA TETRALOOPS, RNA
EXPDTA SOLUTION NMR
NUMMDL 14
AUTHOR D.J.KERWOOD,M.J.CAVALUZZI,P.N.BORER
REVDAT 2 24-FEB-09 1JTW 1 VERSN REVDAT 1 12-DEC-01 1JTW 0
JRNL AUTH D.J.KERWOOD,M.J.CAVALUZZI,P.N.BORER JRNL TITL STRUCTURE OF SL4 RNA FROM THE HIV-1 PACKAGING JRNL TITL 2 SIGNAL. JRNL REF BIOCHEMISTRY V. 40 14518 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11724565 JRNL DOI 10.1021/BI0111909
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5 REMARK 3 AUTHORS : WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DYANA STRUCTURES WERE FURTHER REMARK 3 REFINED WITH THE MOLECULAR DYNAMICS AND MINIMIZATION PROGRAM, REMARK 3 AMBER.
REMARK 4 REMARK 4 1JTW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-01. REMARK 100 THE RCSB ID CODE IS RCSB014179.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : ~0.7MM SL4 CONCENTRATION IN REMARK 210 BUFFER: 25MM NACL, 5MM NAHPO4 REMARK 210 (PH 7.0), 0.1MM EDTA, 0.01% REMARK 210 NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 5 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 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: SODIUM IONS WHICH WERE DISTANT FROM THE RNA WERE REMARK 210 REMOVED.
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 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 3 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 8 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 10 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 U A 14 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 11 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 12 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 12 U A 14 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 12 C A 15 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 12 A A 16 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 13 G A 2 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 13 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 14 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 14 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 14 A A 16 O4' - C1' - N9 ANGL. DEV. = 4.5 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 1 G A 7 0.07 SIDE_CHAIN REMARK 500 1 G A 11 0.06 SIDE_CHAIN REMARK 500 2 G A 7 0.10 SIDE_CHAIN REMARK 500 2 C A 15 0.06 SIDE_CHAIN REMARK 500 3 G A 7 0.07 SIDE_CHAIN REMARK 500 3 G A 9 0.05 SIDE_CHAIN REMARK 500 4 G A 1 0.06 SIDE_CHAIN REMARK 500 4 G A 7 0.12 SIDE_CHAIN REMARK 500 4 C A 15 0.07 SIDE_CHAIN REMARK 500 5 G A 7 0.08 SIDE_CHAIN REMARK 500 5 G A 9 0.07 SIDE_CHAIN REMARK 500 6 G A 5 0.07 SIDE_CHAIN REMARK 500 6 G A 7 0.05 SIDE_CHAIN REMARK 500 7 G A 2 0.05 SIDE_CHAIN REMARK 500 7 G A 7 0.09 SIDE_CHAIN REMARK 500 7 G A 11 0.06 SIDE_CHAIN REMARK 500 8 G A 5 0.05 SIDE_CHAIN REMARK 500 8 G A 7 0.08 SIDE_CHAIN REMARK 500 9 G A 5 0.06 SIDE_CHAIN REMARK 500 9 G A 7 0.08 SIDE_CHAIN REMARK 500 9 G A 11 0.06 SIDE_CHAIN REMARK 500 9 C A 15 0.08 SIDE_CHAIN REMARK 500 10 G A 2 0.06 SIDE_CHAIN REMARK 500 10 G A 7 0.12 SIDE_CHAIN REMARK 500 11 G A 2 0.06 SIDE_CHAIN REMARK 500 11 U A 4 0.06 SIDE_CHAIN REMARK 500 11 G A 7 0.06 SIDE_CHAIN REMARK 500 11 C A 15 0.09 SIDE_CHAIN REMARK 500 12 G A 7 0.08 SIDE_CHAIN REMARK 500 12 A A 16 0.07 SIDE_CHAIN REMARK 500 13 G A 2 0.06 SIDE_CHAIN REMARK 500 13 G A 7 0.08 SIDE_CHAIN REMARK 500 13 G A 11 0.07 SIDE_CHAIN REMARK 500 13 C A 15 0.09 SIDE_CHAIN REMARK 500 14 G A 5 0.08 SIDE_CHAIN REMARK 500 14 G A 9 0.06 SIDE_CHAIN REMARK 500 14 A A 16 0.09 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 18 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 13 O6 REMARK 620 2 G A 3 O6 87.6 REMARK 620 3 U A 4 O4 79.2 76.5 REMARK 620 4 U A 14 O4 72.3 79.7 143.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 19 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 4 OP2 REMARK 620 2 G A 3 OP1 148.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 24 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 8 OP2 REMARK 620 2 G A 9 OP2 116.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 28 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 13 OP2 REMARK 620 2 C A 12 OP2 148.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 30 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 15 OP2 REMARK 620 2 U A 14 OP2 147.7 REMARK 620 3 U A 14 O5' 96.6 51.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 31 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 16 OP2 REMARK 620 2 C A 15 O5' 102.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 27 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 2 OP2 REMARK 620 2 G A 3 OP2 146.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 20 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 4 OP1 REMARK 620 2 U A 4 O5' 52.6 REMARK 620 3 G A 5 OP2 149.5 97.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 22 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 7 OP1 REMARK 620 2 G A 7 OP2 52.1 REMARK 620 3 A A 8 OP1 134.5 149.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 25 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 9 OP1 REMARK 620 2 G A 9 O5' 50.8 REMARK 620 3 A A 10 OP2 152.9 102.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 26 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 OP1 REMARK 620 2 G A 11 OP2 56.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 NA A 29 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 11 O3' REMARK 620 2 C A 12 OP1 56.3 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 17 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 18 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 19 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 20 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 21 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 22 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 23 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 24 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 25 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 26 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 27 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 28 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 29 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 30 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 31
DBREF 1JTW A 1 16 PDB 1JTW 1JTW 1 16
SEQRES 1 A 16 G G G U G C G A G A G C G SEQRES 2 A 16 U C A
HET NA A 17 1 HET NA A 18 1 HET NA A 19 1 HET NA A 20 1 HET NA A 21 1 HET NA A 22 1 HET NA A 23 1 HET NA A 24 1 HET NA A 25 1 HET NA A 26 1 HET NA A 27 1 HET NA A 28 1 HET NA A 29 1 HET NA A 30 1 HET NA A 31 1
HETNAM NA SODIUM ION
FORMUL 2 NA 15(NA 1+)
LINK NA NA A 17 OP1 G A 2 1555 1555 2.49 LINK NA NA A 18 O6 G A 13 1555 1555 2.59 LINK NA NA A 19 OP2 U A 4 1555 1555 2.54 LINK NA NA A 21 OP1 U A 14 1555 1555 2.58 LINK NA NA A 23 OP1 C A 6 1555 1555 2.50 LINK NA NA A 24 OP2 A A 8 1555 1555 2.60 LINK NA NA A 24 OP2 G A 9 1555 1555 2.56 LINK NA NA A 28 OP2 G A 13 1555 1555 2.56 LINK NA NA A 30 OP2 C A 15 1555 1555 2.54 LINK NA NA A 31 OP2 A A 16 1555 1555 2.59 LINK OP2 G A 2 NA NA A 27 1555 1555 2.73 LINK OP1 G A 3 NA NA A 19 1555 1555 2.63 LINK OP2 G A 3 NA NA A 27 1555 1555 2.62 LINK O6 G A 3 NA NA A 18 1555 1555 2.62 LINK OP1 U A 4 NA NA A 20 1555 1555 2.63 LINK O5' U A 4 NA NA A 20 1555 1555 2.97 LINK O4 U A 4 NA NA A 18 1555 1555 2.74 LINK OP2 G A 5 NA NA A 20 1555 1555 2.68 LINK OP1 G A 7 NA NA A 22 1555 1555 2.95 LINK OP2 G A 7 NA NA A 22 1555 1555 2.85 LINK OP1 A A 8 NA NA A 22 1555 1555 2.70 LINK OP1 G A 9 NA NA A 25 1555 1555 2.85 LINK O5' G A 9 NA NA A 25 1555 1555 2.94 LINK OP2 A A 10 NA NA A 25 1555 1555 2.62 LINK OP1 G A 11 NA NA A 26 1555 1555 2.72 LINK OP2 G A 11 NA NA A 26 1555 1555 2.61 LINK O3' G A 11 NA NA A 29 1555 1555 2.62 LINK OP1 C A 12 NA NA A 29 1555 1555 2.66 LINK OP2 C A 12 NA NA A 28 1555 1555 2.69 LINK OP2 U A 14 NA NA A 30 1555 1555 2.66 LINK O5' U A 14 NA NA A 30 1555 1555 2.99 LINK O4 U A 14 NA NA A 18 1555 1555 2.90 LINK O5' C A 15 NA NA A 31 1555 1555 2.89
SITE 1 AC1 1 G A 2 SITE 1 AC2 4 G A 3 U A 4 G A 13 U A 14 SITE 1 AC3 2 G A 3 U A 4 SITE 1 AC4 2 U A 4 G A 5 SITE 1 AC5 2 G A 13 U A 14 SITE 1 AC6 2 G A 7 A A 8 SITE 1 AC7 1 C A 6 SITE 1 AC8 3 G A 7 A A 8 G A 9 SITE 1 AC9 3 G A 7 G A 9 A A 10 SITE 1 BC1 2 A A 10 G A 11 SITE 1 BC2 2 G A 2 G A 3 SITE 1 BC3 2 C A 12 G A 13 SITE 1 BC4 2 G A 11 C A 12 SITE 1 BC5 2 U A 14 C A 15 SITE 1 BC6 2 C A 15 A A 16
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