10 20 30 40 50 60 70 80 1ULL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN/RNA 05-NOV-96 1ULL
TITLE RNA APTAMER COMPLEXED WITH HIV-1 REV PEPTIDE, NMR, 7 TITLE 2 STRUCTURES
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R COMPND 3 (GP*GP*CP*UP*GP*GP*AP*CP*UP*CP*GP*UP*AP*CP*UP*UP*CP*GP* COMPND 4 GP*UP*AP*CP*UP*GP*GP*AP*GP*AP*AP*AP*CP*AP*GP*CP*C)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: REV PEPTIDE; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 34 - 50; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: REV PEPTIDE
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: 17-MER PEPTIDE OF REV PROTEIN FROM HIV-I; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 6 ORGANISM_TAXID: 11676
KEYWDS REV PEPTIDE-RNA RECOGNITION, ALPHA-HELIX IN WIDENED RNA KEYWDS 2 MAJOR GROOVE, PURINE-PURINE MISMATCHES, UAU BASE TRIPLE, KEYWDS 3 ADAPTIVE BINDING OF PEPTIDE AND RNA IN COMPLEX, COMPLEX KEYWDS 4 (RNA APTAMER/REV PEPTIDE), VIRAL PROTEIN/RNA COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 7
AUTHOR X.YE,A.GORIN,A.D.ELLINGTON,D.J.PATEL
REVDAT 2 24-FEB-09 1ULL 1 VERSN REVDAT 1 20-AUG-97 1ULL 0
JRNL AUTH X.YE,A.GORIN,A.D.ELLINGTON,D.J.PATEL JRNL TITL DEEP PENETRATION OF AN ALPHA-HELIX INTO A WIDENED JRNL TITL 2 RNA MAJOR GROOVE IN THE HIV-1 REV PEPTIDE-RNA JRNL TITL 3 APTAMER COMPLEX. JRNL REF NAT.STRUCT.BIOL. V. 3 1026 1996 JRNL REFN ISSN 1072-8368 JRNL PMID 8946856 JRNL DOI 10.1038/NSB1296-1026
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1ULL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 297 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITY PLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VARIAN VNMR (2D) NMRPIPE (3D) REMARK 210 PIPP (3D) (3D) REMARK 210 METHOD USED : DISTANCE GEOMETRY AND REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 14 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 7 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY GAP 400 KCAL/MOLE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-7 REMARK 470 RES CSSEQI ATOMS REMARK 470 G A 1 O5' REMARK 470 ARG B 17 O
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 A A 7 N9 A A 7 C4 0.063 REMARK 500 1 U A 9 N1 U A 9 C2 0.056 REMARK 500 1 A A 13 P A A 13 O5' 0.065 REMARK 500 1 A A 13 N9 A A 13 C4 0.042 REMARK 500 1 C A 17 N1 C A 17 C6 -0.041 REMARK 500 1 G A 18 P G A 18 O5' 0.069 REMARK 500 1 G A 18 N9 G A 18 C4 0.056 REMARK 500 1 G A 19 N9 G A 19 C4 0.070 REMARK 500 1 A A 21 C5' A A 21 C4' 0.072 REMARK 500 1 A A 21 N9 A A 21 C4 0.046 REMARK 500 1 C A 22 P C A 22 O5' 0.065 REMARK 500 1 C A 22 C5' C A 22 C4' 0.088 REMARK 500 1 G A 24 C8 G A 24 N9 -0.051 REMARK 500 1 G A 25 P G A 25 O5' 0.066 REMARK 500 1 A A 26 N9 A A 26 C4 0.036 REMARK 500 1 A A 30 N9 A A 30 C4 0.040 REMARK 500 1 A A 32 C5' A A 32 C4' 0.077 REMARK 500 1 A A 32 N3 A A 32 C4 0.037 REMARK 500 1 A A 32 N9 A A 32 C4 0.065 REMARK 500 2 G A 5 C8 G A 5 N9 -0.050 REMARK 500 2 A A 7 N9 A A 7 C4 0.040 REMARK 500 2 G A 11 N9 G A 11 C4 0.056 REMARK 500 2 A A 13 C5' A A 13 C4' 0.074 REMARK 500 2 U A 16 N1 U A 16 C2 0.054 REMARK 500 2 C A 17 N1 C A 17 C2 0.070 REMARK 500 2 G A 18 N9 G A 18 C4 0.060 REMARK 500 2 U A 20 N1 U A 20 C2 0.057 REMARK 500 2 C A 22 C5' C A 22 C4' 0.086 REMARK 500 2 G A 25 N7 G A 25 C8 0.042 REMARK 500 2 G A 27 C5' G A 27 C4' 0.075 REMARK 500 2 G A 27 C8 G A 27 N9 -0.046 REMARK 500 2 A A 28 N9 A A 28 C4 0.055 REMARK 500 2 C A 31 P C A 31 O5' 0.071 REMARK 500 2 C A 31 C5' C A 31 C4' 0.089 REMARK 500 2 C A 31 N1 C A 31 C2 0.082 REMARK 500 2 A A 32 N9 A A 32 C4 0.040 REMARK 500 2 G A 33 N9 G A 33 C4 0.055 REMARK 500 3 G A 2 P G A 2 O5' 0.063 REMARK 500 3 G A 2 C5' G A 2 C4' 0.072 REMARK 500 3 G A 5 P G A 5 O5' 0.064 REMARK 500 3 G A 5 N9 G A 5 C4 0.052 REMARK 500 3 A A 7 N9 A A 7 C4 0.042 REMARK 500 3 U A 9 N1 U A 9 C2 0.067 REMARK 500 3 U A 9 C2 U A 9 N3 0.047 REMARK 500 3 A A 13 P A A 13 O5' 0.074 REMARK 500 3 A A 13 C5' A A 13 C4' 0.084 REMARK 500 3 A A 13 N9 A A 13 C4 0.044 REMARK 500 3 G A 18 P G A 18 O5' 0.086 REMARK 500 3 G A 18 C6 G A 18 N1 0.046 REMARK 500 3 G A 18 N9 G A 18 C4 0.062 REMARK 500 REMARK 500 THIS ENTRY HAS 139 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 2 P - O5' - C5' ANGL. DEV. = 19.2 DEGREES REMARK 500 1 G A 2 N3 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 1 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES REMARK 500 1 C A 3 P - O5' - C5' ANGL. DEV. = 15.0 DEGREES REMARK 500 1 C A 3 N1 - C2 - O2 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C A 3 C5 - C4 - N4 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 U A 4 P - O5' - C5' ANGL. DEV. = 10.5 DEGREES REMARK 500 1 G A 5 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 5 C2 - N3 - C4 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 5 N3 - C2 - N2 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 U A 4 C3' - O3' - P ANGL. DEV. = 20.6 DEGREES REMARK 500 1 G A 6 P - O5' - C5' ANGL. DEV. = 24.2 DEGREES REMARK 500 1 G A 6 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 G A 5 C3' - O3' - P ANGL. DEV. = 9.5 DEGREES REMARK 500 1 A A 7 N1 - C6 - N6 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 C A 8 P - O5' - C5' ANGL. DEV. = 12.6 DEGREES REMARK 500 1 C A 8 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 C A 8 N3 - C4 - C5 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 C A 8 N1 - C2 - O2 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 C A 8 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 7 C3' - O3' - P ANGL. DEV. = 16.3 DEGREES REMARK 500 1 U A 9 P - O5' - C5' ANGL. DEV. = 25.5 DEGREES REMARK 500 1 U A 9 C3' - C2' - C1' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 U A 9 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 C A 10 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 C A 10 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 C A 10 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 C A 10 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 U A 9 C3' - O3' - P ANGL. DEV. = 19.1 DEGREES REMARK 500 1 G A 11 P - O5' - C5' ANGL. DEV. = 24.3 DEGREES REMARK 500 1 G A 11 N9 - C1' - C2' ANGL. DEV. = 10.3 DEGREES REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 G A 11 N3 - C2 - N2 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 C A 10 C3' - O3' - P ANGL. DEV. = 14.8 DEGREES REMARK 500 1 U A 12 P - O5' - C5' ANGL. DEV. = 15.4 DEGREES REMARK 500 1 U A 12 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 11 C3' - O3' - P ANGL. DEV. = 20.0 DEGREES REMARK 500 1 A A 13 P - O5' - C5' ANGL. DEV. = 10.9 DEGREES REMARK 500 1 A A 13 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 C A 14 P - O5' - C5' ANGL. DEV. = 12.1 DEGREES REMARK 500 1 C A 14 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 14 O4' - C1' - N1 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 C A 14 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 C A 14 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 C A 14 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 C A 14 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 C A 14 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 14 N3 - C4 - N4 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 C A 14 C5 - C4 - N4 ANGL. DEV. = 10.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 962 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ARG B 6 18.12 -69.04 REMARK 500 1 ASN B 7 -37.04 -143.92 REMARK 500 2 ARG B 8 -73.30 -57.48 REMARK 500 2 ARG B 10 38.54 -64.71 REMARK 500 2 ARG B 11 -74.91 -159.84 REMARK 500 3 ARG B 9 29.40 -75.49 REMARK 500 3 ARG B 10 -77.46 -125.15 REMARK 500 3 GLN B 16 -61.42 -105.71 REMARK 500 5 ALA B 4 -75.76 -76.77 REMARK 500 5 ARG B 5 -51.12 -26.64 REMARK 500 7 ARG B 2 -52.72 59.48 REMARK 500 7 ARG B 10 45.88 -64.23 REMARK 500 7 ARG B 11 -77.66 -175.52 REMARK 500 7 GLN B 16 -38.30 -134.44 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 A A 28 0.07 SIDE_CHAIN REMARK 500 1 ARG B 8 0.07 SIDE_CHAIN REMARK 500 1 ARG B 9 0.11 SIDE_CHAIN REMARK 500 1 ARG B 11 0.12 SIDE_CHAIN REMARK 500 1 ARG B 13 0.11 SIDE_CHAIN REMARK 500 1 ARG B 15 0.07 SIDE_CHAIN REMARK 500 2 U A 4 0.06 SIDE_CHAIN REMARK 500 2 A A 28 0.06 SIDE_CHAIN REMARK 500 2 ARG B 2 0.18 SIDE_CHAIN REMARK 500 2 ARG B 6 0.11 SIDE_CHAIN REMARK 500 2 ARG B 8 0.11 SIDE_CHAIN REMARK 500 2 ARG B 10 0.17 SIDE_CHAIN REMARK 500 2 ARG B 15 0.19 SIDE_CHAIN REMARK 500 2 ARG B 17 0.10 SIDE_CHAIN REMARK 500 3 A A 28 0.08 SIDE_CHAIN REMARK 500 3 ARG B 5 0.18 SIDE_CHAIN REMARK 500 3 ARG B 6 0.12 SIDE_CHAIN REMARK 500 3 ARG B 8 0.09 SIDE_CHAIN REMARK 500 3 ARG B 11 0.21 SIDE_CHAIN REMARK 500 3 ARG B 13 0.23 SIDE_CHAIN REMARK 500 3 ARG B 15 0.08 SIDE_CHAIN REMARK 500 3 ARG B 17 0.15 SIDE_CHAIN REMARK 500 4 A A 30 0.06 SIDE_CHAIN REMARK 500 4 ARG B 2 0.19 SIDE_CHAIN REMARK 500 4 ARG B 5 0.14 SIDE_CHAIN REMARK 500 4 ARG B 6 0.27 SIDE_CHAIN REMARK 500 4 ARG B 10 0.15 SIDE_CHAIN REMARK 500 4 ARG B 11 0.09 SIDE_CHAIN REMARK 500 4 ARG B 13 0.17 SIDE_CHAIN REMARK 500 4 ARG B 15 0.09 SIDE_CHAIN REMARK 500 5 A A 28 0.06 SIDE_CHAIN REMARK 500 5 ARG B 2 0.10 SIDE_CHAIN REMARK 500 5 ARG B 5 0.16 SIDE_CHAIN REMARK 500 5 ARG B 9 0.35 SIDE_CHAIN REMARK 500 5 ARG B 13 0.15 SIDE_CHAIN REMARK 500 5 ARG B 15 0.07 SIDE_CHAIN REMARK 500 5 ARG B 17 0.14 SIDE_CHAIN REMARK 500 6 ARG B 6 0.17 SIDE_CHAIN REMARK 500 6 ARG B 10 0.10 SIDE_CHAIN REMARK 500 6 ARG B 11 0.16 SIDE_CHAIN REMARK 500 6 ARG B 13 0.07 SIDE_CHAIN REMARK 500 7 ARG B 2 0.13 SIDE_CHAIN REMARK 500 7 ARG B 5 0.14 SIDE_CHAIN REMARK 500 7 ARG B 8 0.12 SIDE_CHAIN REMARK 500 7 ARG B 9 0.19 SIDE_CHAIN REMARK 500 7 ARG B 13 0.08 SIDE_CHAIN REMARK 500 7 ARG B 17 0.11 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1ULL A 1 35 PDB 1ULL 1ULL 1 35 DBREF 1ULL B 1 17 UNP P05866 REV_HV1W2 8 24
SEQRES 1 A 35 G G C U G G A C U C G U A SEQRES 2 A 35 C U U C G G U A C U G G A SEQRES 3 A 35 G A A A C A G C C SEQRES 1 B 17 THR ARG GLN ALA ARG ARG ASN ARG ARG ARG ARG TRP ARG SEQRES 2 B 17 GLU ARG GLN ARG
HELIX 1 1 ARG B 2 TRP B 12 1 11
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