HEADER DNA-RNA HYBRID 13-DEC-00 1HG9 TITLE SOLUTION STRUCTURE OF DNA:RNA HYBRID COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5- D(*CP*TP*GP*AP*TP*AP*TP*GP*C) -3; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS DNA-RNA HYBRID, DNA RNA HYBRID, DNA/RNA CHIMERIC HYBRID DUPLEX, KEYWDS 2 ANTISENSE, LOCKED NUCLEIC ACID, DNA, RNA, HYBRID, RNASE H EXPDTA SOLUTION NMR NUMMDL 40 AUTHOR M.PETERSEN,K.BONDENSGAARD,J.WENGEL,J.P.JACOBSEN REVDAT 4 09-OCT-19 1HG9 1 SOURCE JRNL REMARK REVDAT 3 24-FEB-09 1HG9 1 VERSN REVDAT 2 30-MAY-02 1HG9 1 REMARK REVDAT 1 02-JAN-02 1HG9 0 JRNL AUTH K.BONDENSGAARD,M.PETERSEN,S.K.SINGH,V.K.RAJWANSHI,R.KUMAR, JRNL AUTH 2 J.WENGEL,J.P.JACOBSEN JRNL TITL STRUCTURAL STUDIES OF LNA:RNA DUPLEXES BY NMR: CONFORMATIONS JRNL TITL 2 AND IMPLICATIONS FOR RNASE H ACTIVITY. JRNL REF CHEMISTRY V. 6 2687 2000 JRNL REFN ISSN 0947-6539 JRNL PMID 10985717 JRNL DOI 10.1002/1521-3765(20000804)6:15<2687::AID-CHEM2687>3.0.CO;2- JRNL DOI 2 U REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.PETERSEN,C.B.NIELSEN,K.E.NIELSEN,G.A.JENSEN, REMARK 1 AUTH 2 K.BONDENSGAARD,S.K.SINGH,V.K.RAJWANSHI,A.A.KOSHKIN,B.M.DAHL, REMARK 1 AUTH 3 J.WENGEL,J.P.JACOBSEN REMARK 1 TITL THE CONFORMATIONS OF LOCKED NUCLEIC ACIDS (LNA) REMARK 1 REF J.MOL.RECOGNIT. V. 13 44 2000 REMARK 1 REFN ISSN 0952-3499 REMARK 1 PMID 10679896 REMARK 1 DOI 10.1002/(SICI)1099-1352(200001/02)13:1<44::AID-JMR486>3.0.CO REMARK 1 REFERENCE 2 REMARK 1 AUTH M.PETERSEN,K.BONDENSGAARD,J.WENGEL,J.P.JACOBSEN REMARK 1 TITL LOCKED NUCLEIC ACID (LNA) RECOGNITION OF RNA: NMR SOLUTION REMARK 1 TITL 2 STRUCTURES OF LNA:RNA HYBRIDS REMARK 1 REF J.AM.CHEM.SOC. V. 124 5974 2002 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 12022830 REMARK 1 DOI 10.1021/JA012288D REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DA, KOLLMAN, PA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 354 NOE DISTANCE RESTRAINTS REMARK 3 WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE REMARK 3 PROGRAM RANDMARDI. 22 WATSON-CRICK BASE PAIRING RESTRAINTS. REMARK 4 REMARK 4 1HG9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-00. REMARK 100 THE DEPOSITION ID IS D_1290005661. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.0E-3M DNA:RNA, 0.1M NACL, 5E REMARK 210 -5M EDTA AND 1E-2M PHOSPHATE REMARK 210 BUFFER IN 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MARDIGRAS, AMBER, FELIX REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 20 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 15 G B 10 C2' G B 10 C1' -0.048 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 2 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 8 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 8 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES REMARK 500 1 DG A 8 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 C B 11 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 A B 12 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES REMARK 500 1 A B 12 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 U B 13 C5' - C4' - O4' ANGL. DEV. = 6.5 DEGREES REMARK 500 1 U B 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 C B 16 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES REMARK 500 1 A B 17 C5' - C4' - O4' ANGL. DEV. = 11.6 DEGREES REMARK 500 1 G B 18 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DT A 2 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES REMARK 500 2 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 2 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 8 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 2 DG A 8 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 G B 10 O4' - C4' - C3' ANGL. DEV. = 6.2 DEGREES REMARK 500 2 G B 10 C5' - C4' - C3' ANGL. DEV. = -10.3 DEGREES REMARK 500 2 G B 10 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 2 C B 11 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 A B 12 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES REMARK 500 2 A B 12 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 U B 13 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES REMARK 500 2 U B 15 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 C B 16 O4' - C1' - N1 ANGL. DEV. = 8.2 DEGREES REMARK 500 2 A B 17 C5' - C4' - O4' ANGL. DEV. = 11.2 DEGREES REMARK 500 2 G B 18 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 3 DT A 2 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 3 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DG A 8 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES REMARK 500 3 DG A 8 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 3 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 C B 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 A B 12 C3' - C2' - C1' ANGL. DEV. = -6.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 850 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 DT A 2 0.08 SIDE CHAIN REMARK 500 1 DC A 9 0.13 SIDE CHAIN REMARK 500 1 G B 10 0.08 SIDE CHAIN REMARK 500 1 A B 12 0.08 SIDE CHAIN REMARK 500 1 A B 14 0.11 SIDE CHAIN REMARK 500 1 U B 15 0.11 SIDE CHAIN REMARK 500 1 A B 17 0.09 SIDE CHAIN REMARK 500 1 G B 18 0.08 SIDE CHAIN REMARK 500 2 DT A 2 0.07 SIDE CHAIN REMARK 500 2 DC A 9 0.14 SIDE CHAIN REMARK 500 2 G B 10 0.08 SIDE CHAIN REMARK 500 2 A B 12 0.09 SIDE CHAIN REMARK 500 2 A B 14 0.13 SIDE CHAIN REMARK 500 2 U B 15 0.11 SIDE CHAIN REMARK 500 2 A B 17 0.10 SIDE CHAIN REMARK 500 2 G B 18 0.07 SIDE CHAIN REMARK 500 3 DT A 2 0.08 SIDE CHAIN REMARK 500 3 DC A 9 0.14 SIDE CHAIN REMARK 500 3 G B 10 0.08 SIDE CHAIN REMARK 500 3 C B 11 0.09 SIDE CHAIN REMARK 500 3 A B 12 0.07 SIDE CHAIN REMARK 500 3 U B 13 0.06 SIDE CHAIN REMARK 500 3 A B 14 0.11 SIDE CHAIN REMARK 500 3 U B 15 0.11 SIDE CHAIN REMARK 500 3 A B 17 0.08 SIDE CHAIN REMARK 500 3 G B 18 0.08 SIDE CHAIN REMARK 500 4 DT A 2 0.07 SIDE CHAIN REMARK 500 4 DC A 9 0.14 SIDE CHAIN REMARK 500 4 G B 10 0.08 SIDE CHAIN REMARK 500 4 A B 12 0.08 SIDE CHAIN REMARK 500 4 A B 14 0.11 SIDE CHAIN REMARK 500 4 U B 15 0.10 SIDE CHAIN REMARK 500 4 A B 17 0.09 SIDE CHAIN REMARK 500 4 G B 18 0.07 SIDE CHAIN REMARK 500 5 DT A 2 0.07 SIDE CHAIN REMARK 500 5 DC A 9 0.14 SIDE CHAIN REMARK 500 5 G B 10 0.09 SIDE CHAIN REMARK 500 5 C B 11 0.07 SIDE CHAIN REMARK 500 5 A B 12 0.09 SIDE CHAIN REMARK 500 5 A B 14 0.12 SIDE CHAIN REMARK 500 5 U B 15 0.11 SIDE CHAIN REMARK 500 5 A B 17 0.10 SIDE CHAIN REMARK 500 5 G B 18 0.07 SIDE CHAIN REMARK 500 6 DT A 2 0.07 SIDE CHAIN REMARK 500 6 DC A 9 0.14 SIDE CHAIN REMARK 500 6 G B 10 0.08 SIDE CHAIN REMARK 500 6 A B 12 0.09 SIDE CHAIN REMARK 500 6 A B 14 0.12 SIDE CHAIN REMARK 500 6 U B 15 0.10 SIDE CHAIN REMARK 500 6 A B 17 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 296 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HHW RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF LNA1:RNA HYBRID REMARK 900 RELATED ID: 1HHX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF LNA3:RNA HYBRID DBREF 1HG9 A 1 9 PDB 1HG9 1HG9 1 9 DBREF 1HG9 B 10 18 PDB 1HG9 1HG9 10 18 SEQRES 1 A 9 DC DT DG DA DT DA DT DG DC SEQRES 1 B 9 G C A U A U C A G 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