HEADER RNA 10-OCT-25 9SY8 TITLE BEYOND SINGLE-STATE RNA STRUCTURAL BIOLOGY: MD/NMR DESCRIPTION OF TITLE 2 TEMPERATURE-SENSITIVE DYNAMIC RNA ENSEMBLES - GAAG ARIA STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA HAIRPIN WITH GAAG TETRALOOP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC RNA; SOURCE 4 ORGANISM_TAXID: 2086595; SOURCE 5 OTHER_DETAILS: 14MER RNA HAIRPIN WITH GAAG TETRALOOP KEYWDS MODEL HAIRPIN, RNA, GAAG, TETRALOOP, HIGH RESOLUTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.LEOPOLD,A.OXENFARTH,F.E.THOMASEN,F.KUEMMERER,R.SCHNIEDERS,G.PINTER, AUTHOR 2 A.WACKER,H.R.A.JONKER,B.FUERTIG,C.RICHTER,K.LINDORFF-LARSEN, AUTHOR 3 H.SCHWALBE REVDAT 2 29-JUL-26 9SY8 1 JRNL REVDAT 1 24-JUN-26 9SY8 0 JRNL AUTH D.LEOPOLD,A.OXENFARTH,F.E.THOMASEN,F.KUMMERER,R.SCHNIEDERS, JRNL AUTH 2 G.PINTER,A.WACKER,H.R.A.JONKER,B.FURTIG,C.RICHTER, JRNL AUTH 3 K.LINDORFF-LARSEN,H.SCHWALBE JRNL TITL INTEGRATED NMR/MD INVESTIGATION REVEALS DIFFERENCES AFTER JRNL TITL 2 REWEIGHTING IN CONFORMATIONAL ENSEMBLES OF THE GAAG AND GCAA JRNL TITL 3 TETRALOOPS. JRNL REF RNA V. 32 1199 2026 JRNL REFN ESSN 1469-9001 JRNL PMID 42215280 JRNL DOI 10.1261/RNA.081067.126 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9SY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1292151345. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.24 MM [U-13C; U-15N] RNA REMARK 210 HAIRPIN WITH GAAG TETRALOOP, 50 REMARK 210 MM POTASSIUM PHOSPHATE, 50 UM REMARK 210 DSS, 95% H2O/5% D2O; 0.64 MM [U- REMARK 210 13C; U-15N] RNA HAIRPIN WITH REMARK 210 GAAG TETRALOOP, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 50 UM DSS, 100% D2O; REMARK 210 1.3 MM RNA HAIRPIN WITH GAAG REMARK 210 TETRALOOP, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 50 UM DSS, 100% D2O; REMARK 210 1.26 MM RNA HAIRPIN WITH GAAG REMARK 210 TETRALOOP, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 50 UM DSS, 95% H2O/5% REMARK 210 D2O; 0.2 MM [U-13C; U-15N] RNA REMARK 210 HAIRPIN WITH GAAG TETRALOOP, 50 REMARK 210 MM POTASSIUM PHOSPHATE, 50 UM REMARK 210 DSS, 100% D2O; 0.2 MM [U-13C; U- REMARK 210 15N] RNA HAIRPIN WITH GAAG REMARK 210 TETRALOOP, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 50 UM DSS, 20 MG/ML REMARK 210 PF1 PHAGE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D 1H-15N HSQC; 3D QHCP; 2D QHCP; REMARK 210 2D P-FIDS; 3D HCC-TOCSY-CCH- REMARK 210 E.COSY; 2D HNN-COSY; 2D GAMMA REMARK 210 HCCH; 2D GAMMA HCNCH; 2D GAMMA REMARK 210 HCP; 2D HCN; 3D FORWARD DIRECTED REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ; 900 REMARK 210 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE III HD; AVANCE REMARK 210 NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 4.2.0, TOPSPIN 4.20, REMARK 210 NMRFAM-SPARKY 1.470, PALES, ARIA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 HO2' A A 8 O5' G A 9 1.52 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 7 0.07 SIDE CHAIN REMARK 500 2 A A 7 0.09 SIDE CHAIN REMARK 500 3 A A 7 0.08 SIDE CHAIN REMARK 500 4 C A 5 0.06 SIDE CHAIN REMARK 500 4 A A 7 0.08 SIDE CHAIN REMARK 500 5 A A 7 0.07 SIDE CHAIN REMARK 500 6 A A 7 0.08 SIDE CHAIN REMARK 500 7 A A 7 0.08 SIDE CHAIN REMARK 500 8 A A 7 0.07 SIDE CHAIN REMARK 500 9 A A 7 0.07 SIDE CHAIN REMARK 500 10 A A 7 0.08 SIDE CHAIN REMARK 500 11 A A 7 0.08 SIDE CHAIN REMARK 500 12 A A 7 0.07 SIDE CHAIN REMARK 500 13 A A 7 0.08 SIDE CHAIN REMARK 500 14 A A 7 0.08 SIDE CHAIN REMARK 500 15 A A 7 0.08 SIDE CHAIN REMARK 500 16 A A 7 0.08 SIDE CHAIN REMARK 500 17 A A 7 0.08 SIDE CHAIN REMARK 500 18 A A 7 0.08 SIDE CHAIN REMARK 500 19 A A 7 0.08 SIDE CHAIN REMARK 500 20 A A 7 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 35020 RELATED DB: BMRB REMARK 900 BEYOND SINGLE-STATE RNA STRUCTURAL BIOLOGY: MD/NMR DESCRIPTION OF REMARK 900 TEMPERATURE-SENSITIVE DYNAMIC RNA ENSEMBLES - GAAG ARIA STRUCTURE DBREF 9SY8 A 1 14 PDB 9SY8 9SY8 1 14 SEQRES 1 A 14 G G C A C G A A G G U G C SEQRES 2 A 14 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MASTER 146 0 0 0 0 0 0 6 305 1 0 2 END