HEADER RNA 05-AUG-21 7RQ5 TITLE HAIRPIN NEAR 3'-SPLICE SITE OF INFLUENZA A SEGMENT 7 BOUND TO 5-NT TITLE 2 OLIGONUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS; SOURCE 4 ORGANISM_TAXID: 11320; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS SPLICE-SITE, HAIRPIN, BOUND MODIFIED-OLIGONUCLEOTIDE, RNA EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR A.D.KAUFFMANN,S.D.KENNEDY,D.H.TURNER REVDAT 2 30-MAR-22 7RQ5 1 JRNL REVDAT 1 19-JAN-22 7RQ5 0 JRNL AUTH A.D.KAUFFMANN,S.D.KENNEDY,W.N.MOSS,E.KIERZEK,R.KIERZEK, JRNL AUTH 2 D.H.TURNER JRNL TITL NUCLEAR MAGNETIC RESONANCE REVEALS A TWO HAIRPIN EQUILIBRIUM JRNL TITL 2 NEAR THE 3'-SPLICE SITE OF INFLUENZA A SEGMENT 7 MRNA THAT JRNL TITL 3 CAN BE SHIFTED BY OLIGONUCLEOTIDES. JRNL REF RNA V. 28 508 2022 JRNL REFN ESSN 1469-9001 JRNL PMID 34983822 JRNL DOI 10.1261/RNA.078951.121 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 102 NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 89 DIHEDRAL ANGLE RESTRAINTS, 25 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS, 216 TOTAL RESTRAINTS REMARK 4 REMARK 4 7RQ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000258748. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 274 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 11; 11 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM RNA (5' REMARK 210 -R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP*A)-3'), REMARK 210 0.49 MM RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))-3'), REMARK 210 10 MM POTASSIUM PHOSPHATE, 0.05 MM SODIUM EDTA, 100% D2O; 0.5 MM REMARK 210 RNA (5'-R(*AP*UP*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*AP*UP* REMARK 210 A)-3'), 0.49 MM RNA (5'-D(*(MU5)P*(MLC)P*(MRC))-R(P*(LG)P*(MU3))- REMARK 210 3'), 10 MM POTASSIUM PHOSPHATE, 0.05 MM SODIUM EDTA, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-31P COSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, NMRPIPE, VNMR REMARK 210 METHOD USED : MD SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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 A A 1 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 1 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 3 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 4 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 5 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 A A 5 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 8 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 A A 9 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 9 N1 - C6 - N6 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 C A 10 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A A 13 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 13 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 13 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A A 17 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 17 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 A A 19 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 A A 19 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 19 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 A A 1 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 1 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 1 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 C A 3 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 C A 4 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 2 A A 5 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 5 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 A A 7 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 A A 8 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 8 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 8 N1 - C6 - N6 ANGL. DEV. = -5.5 DEGREES REMARK 500 2 A A 9 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 9 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 A A 9 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 2 C A 10 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 A A 13 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 13 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 A A 13 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 A A 17 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 A A 17 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 A A 19 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 A A 19 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 3 A A 1 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 A A 1 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 422 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 2 G A 6 0.06 SIDE CHAIN REMARK 500 2 A A 8 0.05 SIDE CHAIN REMARK 500 3 A A 8 0.08 SIDE CHAIN REMARK 500 6 A A 9 0.05 SIDE CHAIN REMARK 500 8 G A 6 0.09 SIDE CHAIN REMARK 500 9 A A 9 0.05 SIDE CHAIN REMARK 500 10 G A 6 0.06 SIDE CHAIN REMARK 500 11 A A 5 0.05 SIDE CHAIN REMARK 500 12 A A 7 0.05 SIDE CHAIN REMARK 500 13 G A 6 0.09 SIDE CHAIN REMARK 500 13 A A 9 0.05 SIDE CHAIN REMARK 500 14 A A 13 0.07 SIDE CHAIN REMARK 500 15 A A 9 0.05 SIDE CHAIN REMARK 500 17 G A 6 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30940 RELATED DB: BMRB REMARK 900 HAIRPIN NEAR 3'-SPLICE SITE OF INFLUENZA A SEGMENT 7 BOUND TO 5-NT REMARK 900 OLIGONUCLEOTIDE DBREF 7RQ5 A 1 19 PDB 7RQ5 7RQ5 1 19 DBREF 7RQ5 B 20 24 PDB 7RQ5 7RQ5 20 24 SEQRES 1 A 19 A U C C A G A A A C G G A SEQRES 2 A 19 U G G A U A SEQRES 1 B 5 OMU LCC OMC LCG OMU HET OMU B 20 31 HET LCC B 21 35 HET OMC B 22 34 HET LCG B 23 35 HET OMU B 24 34 HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM LCC [(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5- HETNAM 2 LCC DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCC PHOSPHATE HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM LCG [(1R,3R,4R,7S)-7-HYDROXY-3-(GUANIN-9-YL)-2,5- HETNAM 2 LCG DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCG PHOSPHATE FORMUL 2 OMU 2(C10 H15 N2 O9 P) FORMUL 2 LCC C11 H16 N3 O8 P FORMUL 2 OMC C10 H16 N3 O8 P FORMUL 2 LCG C11 H14 N5 O8 P LINK O3' OMU B 20 P LCC B 21 1555 1555 1.60 LINK O3' LCC B 21 P OMC B 22 1555 1555 1.60 LINK O3' OMC B 22 P LCG B 23 1555 1555 1.60 LINK O3' LCG B 23 P OMU B 24 1555 1555 1.60 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