HEADER RNA 03-MAY-06 2GVO TITLE SOLUTION STRUCTURE OF A PURINE RICH HEXALOOP HAIRPIN BELONGING TO TITLE 2 PGY/MDR1 MRNA AND TARGETED BY ANTISENSE OLIGONUCLEOTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANOSINE-5'-MONOPHOSPHATE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PGY/MDR1 MRNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS SOURCE 4 (HUMANS) KEYWDS RNA STRUCTURE, HAIRPIN STRUCTURE, G.U WOBBLE PAIR, HEXALOOP, 13C/15N- KEYWDS 2 LABELED RNA, RNA EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR F.JOLI,N.BOUCHEMAL,A.LAIGLE,B.HARTMANN,E.HANTZ REVDAT 4 29-MAY-24 2GVO 1 REMARK REVDAT 3 09-MAR-22 2GVO 1 REMARK REVDAT 2 24-FEB-09 2GVO 1 VERSN REVDAT 1 08-MAY-07 2GVO 0 JRNL AUTH F.JOLI,N.BOUCHEMAL,A.LAIGLE,B.HARTMANN,E.HANTZ JRNL TITL SOLUTION STRUCTURE OF A PURINE RICH HEXALOOP HAIRPIN JRNL TITL 2 BELONGING TO PGY/MDR1 MRNA AND TARGETED BY ANTISENSE JRNL TITL 3 OLIGONUCLEOTIDES. JRNL REF NUCLEIC ACIDS RES. V. 34 5740 2006 JRNL REFN ISSN 0305-1048 JRNL PMID 17041234 JRNL DOI 10.1093/NAR/GKL617 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.2, AMBER 7 REMARK 3 AUTHORS : DELAGLIO, F. ET AL. (NMRPIPE), CASE, D.A. ET AL. REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 187 RESTRAINTS, 84 ARE SEQUENTIAL AND LONG RANGE INTERNUCLEOTIDE REMARK 3 DISTANCES, 85 DIHEDRAL ANGLE RESTRAINTS, 18 SUGAR PUCKERS REMARK 3 RESTRAINTS AND 15 DISTANCE RESTAINTS FROM HYDROGEN BONDS. REMARK 4 REMARK 4 2GVO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037604. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 274 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : 10MM; 10MM REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM 18MER MRNA UNIFORMLY 13C/15N REMARK 210 LABELED, 10 MM SODIUM PHOSPHATE REMARK 210 BUFFER, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D HCCH-COSY; 2D 1H REMARK 210 -13C HSQC; DQF-COSY; HNN COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.110, FELIX 97.0, AMBER REMARK 210 7.0, JUMNA 12 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED, BACK CALCULATED DATA REMARK 210 AGREE WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM, STRUCTURES WITH REMARK 210 ACCEPTABLE COVALENT GEOMETRY, REMARK 210 STRUCTURES WITH FAVORABLE NON- REMARK 210 BOND ENERGY,STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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: 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 O5' G A 1 C5' -0.608 REMARK 500 1 G A 1 C2 G A 1 N2 -0.064 REMARK 500 1 A A 2 O5' A A 2 C5' -0.122 REMARK 500 1 C A 6 C2' C A 6 O2' -0.083 REMARK 500 1 C A 6 C4 C A 6 N4 -0.057 REMARK 500 1 C A 6 N3 C A 6 C4 -0.044 REMARK 500 1 G A 7 C6 G A 7 N1 -0.047 REMARK 500 1 G A 7 C2 G A 7 N2 -0.079 REMARK 500 1 G A 8 C2' G A 8 C1' -0.057 REMARK 500 1 G A 8 N1 G A 8 C2 -0.070 REMARK 500 1 G A 8 N3 G A 8 C4 -0.048 REMARK 500 1 G A 8 C4 G A 8 C5 -0.051 REMARK 500 1 G A 8 C6 G A 8 N1 -0.079 REMARK 500 1 G A 8 C5 G A 8 N7 -0.059 REMARK 500 1 G A 8 N7 G A 8 C8 -0.045 REMARK 500 1 G A 8 C8 G A 8 N9 -0.062 REMARK 500 1 G A 8 N9 G A 8 C4 -0.057 REMARK 500 1 G A 8 C2 G A 8 N2 -0.110 REMARK 500 1 G A 8 C6 G A 8 O6 -0.054 REMARK 500 1 G A 8 O3' G A 9 P -0.078 REMARK 500 1 G A 9 O5' G A 9 C5' -0.076 REMARK 500 1 G A 9 C2' G A 9 C1' -0.051 REMARK 500 1 G A 9 N1 G A 9 C2 -0.068 REMARK 500 1 G A 9 N3 G A 9 C4 -0.042 REMARK 500 1 G A 9 C4 G A 9 C5 -0.050 REMARK 500 1 G A 9 C6 G A 9 N1 -0.074 REMARK 500 1 G A 9 C5 G A 9 N7 -0.051 REMARK 500 1 G A 9 N7 G A 9 C8 -0.038 REMARK 500 1 G A 9 C8 G A 9 N9 -0.057 REMARK 500 1 G A 9 C2 G A 9 N2 -0.098 REMARK 500 1 A A 10 N1 A A 10 C2 -0.054 REMARK 500 1 A A 10 C4 A A 10 C5 -0.058 REMARK 500 1 A A 10 C6 A A 10 N1 -0.063 REMARK 500 1 A A 10 C8 A A 10 N9 -0.050 REMARK 500 1 A A 10 C6 A A 10 N6 -0.061 REMARK 500 1 U A 11 O4' U A 11 C4' -0.081 REMARK 500 1 U A 11 C2 U A 11 O2 -0.057 REMARK 500 1 U A 11 C4 U A 11 O4 -0.076 REMARK 500 1 U A 11 N1 U A 11 C2 -0.055 REMARK 500 1 U A 11 N1 U A 11 C6 -0.070 REMARK 500 1 U A 11 C2 U A 11 N3 -0.069 REMARK 500 1 U A 11 N3 U A 11 C4 -0.086 REMARK 500 1 U A 11 C4 U A 11 C5 -0.068 REMARK 500 1 U A 11 O3' G A 12 P -0.076 REMARK 500 1 G A 12 N1 G A 12 C2 -0.055 REMARK 500 1 G A 12 C6 G A 12 N1 -0.054 REMARK 500 1 G A 12 C2 G A 12 N2 -0.080 REMARK 500 1 C A 18 C4 C A 18 N4 -0.060 REMARK 500 1 C A 18 N3 C A 18 C4 -0.043 REMARK 500 2 G A 1 C5 G A 1 C6 0.061 REMARK 500 REMARK 500 THIS ENTRY HAS 653 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 O5' - C5' - C4' ANGL. DEV. = 19.1 DEGREES REMARK 500 1 A A 2 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 2 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 C A 6 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 1 C A 6 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 G A 8 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 A A 10 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 10 N1 - C6 - N6 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 G A 12 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 13 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 14 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 U A 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 C A 16 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 G A 1 C6 - N1 - C2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 G A 1 C5 - C6 - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 G A 1 C4 - C5 - N7 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 G A 1 N9 - C4 - C5 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 G A 1 N3 - C4 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 1 N3 - C2 - N2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 G A 1 N1 - C6 - O6 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 A A 2 O4' - C1' - N9 ANGL. DEV. = 10.4 DEGREES REMARK 500 2 A A 2 C2 - N3 - C4 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 A A 2 N3 - C4 - C5 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A A 2 C4 - C5 - N7 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 A A 2 C8 - N9 - C4 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 A A 2 N9 - C4 - C5 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 G A 3 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 2 G A 3 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 2 G A 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 3 C4 - C5 - N7 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 3 C5 - N7 - C8 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 G A 3 N3 - C4 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 4 C5' - C4' - O4' ANGL. DEV. = 6.2 DEGREES REMARK 500 2 G A 4 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 4 C2 - N3 - C4 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 4 N3 - C4 - C5 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 G A 4 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 2 G A 4 N3 - C4 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 U A 5 C1' - O4' - C4' ANGL. DEV. = 4.9 DEGREES REMARK 500 2 U A 5 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES REMARK 500 2 U A 5 O4' - C1' - N1 ANGL. DEV. = 8.1 DEGREES REMARK 500 2 C A 6 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 G A 7 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 G A 7 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 G A 7 N1 - C6 - O6 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 G A 8 C4 - C5 - N7 ANGL. DEV. = 2.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1572 ANGLE DEVIATIONS. 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 U A 5 0.07 SIDE CHAIN REMARK 500 2 A A 2 0.12 SIDE CHAIN REMARK 500 2 G A 4 0.10 SIDE CHAIN REMARK 500 2 U A 5 0.14 SIDE CHAIN REMARK 500 2 C A 6 0.10 SIDE CHAIN REMARK 500 2 G A 7 0.08 SIDE CHAIN REMARK 500 2 G A 8 0.07 SIDE CHAIN REMARK 500 2 G A 9 0.09 SIDE CHAIN REMARK 500 2 U A 11 0.11 SIDE CHAIN REMARK 500 2 G A 12 0.07 SIDE CHAIN REMARK 500 2 G A 13 0.09 SIDE CHAIN REMARK 500 2 A A 14 0.14 SIDE CHAIN REMARK 500 2 U A 17 0.15 SIDE CHAIN REMARK 500 3 G A 1 0.08 SIDE CHAIN REMARK 500 3 A A 2 0.06 SIDE CHAIN REMARK 500 3 G A 4 0.07 SIDE CHAIN REMARK 500 3 U A 5 0.10 SIDE CHAIN REMARK 500 3 G A 7 0.08 SIDE CHAIN REMARK 500 3 U A 11 0.14 SIDE CHAIN REMARK 500 3 G A 12 0.07 SIDE CHAIN REMARK 500 3 G A 13 0.09 SIDE CHAIN REMARK 500 3 U A 15 0.10 SIDE CHAIN REMARK 500 3 C A 16 0.08 SIDE CHAIN REMARK 500 3 U A 17 0.06 SIDE CHAIN REMARK 500 4 A A 2 0.07 SIDE CHAIN REMARK 500 4 G A 3 0.08 SIDE CHAIN REMARK 500 4 G A 4 0.07 SIDE CHAIN REMARK 500 4 C A 6 0.13 SIDE CHAIN REMARK 500 4 G A 7 0.08 SIDE CHAIN REMARK 500 4 G A 8 0.08 SIDE CHAIN REMARK 500 4 G A 9 0.09 SIDE CHAIN REMARK 500 4 A A 10 0.06 SIDE CHAIN REMARK 500 4 U A 11 0.10 SIDE CHAIN REMARK 500 4 G A 12 0.08 SIDE CHAIN REMARK 500 4 G A 13 0.09 SIDE CHAIN REMARK 500 4 U A 15 0.09 SIDE CHAIN REMARK 500 4 U A 17 0.07 SIDE CHAIN REMARK 500 5 G A 3 0.07 SIDE CHAIN REMARK 500 5 U A 5 0.16 SIDE CHAIN REMARK 500 5 C A 6 0.12 SIDE CHAIN REMARK 500 5 G A 7 0.09 SIDE CHAIN REMARK 500 5 G A 8 0.15 SIDE CHAIN REMARK 500 5 G A 9 0.15 SIDE CHAIN REMARK 500 5 U A 11 0.16 SIDE CHAIN REMARK 500 5 G A 12 0.09 SIDE CHAIN REMARK 500 5 G A 13 0.07 SIDE CHAIN REMARK 500 5 U A 17 0.10 SIDE CHAIN REMARK 500 6 G A 1 0.07 SIDE CHAIN REMARK 500 6 A A 2 0.10 SIDE CHAIN REMARK 500 6 G A 3 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 224 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7090 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT DATA DBREF 2GVO A 1 18 PDB 2GVO 2GVO 1 18 SEQRES 1 A 18 G A G G U C G G G A U G G SEQRES 2 A 18 A U C U 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