HEADER RNA 23-APR-25 9QZJ TITLE SARS-COV-2 OMICRON STEM-LOOP-II-MOTIF (S2M_OMICRON) COMPND MOL_ID: 1; COMPND 2 MOLECULE: S2M_OMICRON; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS; SOURCE 4 ORGANISM_TAXID: 2901879 KEYWDS SARS-COV-2, OMICRON, S2M, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.MATZEL,H.SCHWALBE,A.OXENFARTH,M.A.WIRTZ MARTIN REVDAT 2 26-NOV-25 9QZJ 1 JRNL REVDAT 1 01-OCT-25 9QZJ 0 JRNL AUTH T.MATZEL,J.A.MAKOWSKI,A.H.KENSINGER,A.OXENFARTH,M.W.MARTIN, JRNL AUTH 2 J.D.EVANSECK,H.SCHWALBE JRNL TITL INTEGRATED NMR AND MD STRUCTURE AND DYNAMICS OF THE JRNL TITL 2 STEM-LOOP-II MOTIF (S2M) FROM THE OMICRON VARIANT OF JRNL TITL 3 SARS-COV-2. JRNL REF RNA V. 31 1766 2025 JRNL REFN ESSN 1469-9001 JRNL PMID 40973458 JRNL DOI 10.1261/RNA.080576.125 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9QZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-APR-25. REMARK 100 THE DEPOSITION ID IS D_1292147218. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 125; 125 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 50 UM S2M_OMICRON, 50 MM REMARK 210 POTASSIUM CHLORIDE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 95% H2O/5% REMARK 210 D2O; 700 UM [U-13C; U-15N] S2M_ REMARK 210 OMICRON, 50 MM POTASSIUM REMARK 210 CHLORIDE, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 95% H2O/5% D2O; 680 REMARK 210 UM [U-13C; U-15N] S2M_OMICRON, REMARK 210 50 MM POTASSIUM CHLORIDE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC NH2 ONLY; BEST REMARK 210 -TROSY; 1H-15N CPMG-NOESY; HNN- REMARK 210 COSY; 2D NOESY; 3D 1H-13C NOESY; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; CNC; 2D 1H-1H REMARK 210 TOCSY; HCCNH; 3D HCN; FW-HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III; AVANCE III HD; REMARK 210 AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRFAM-SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34991 RELATED DB: BMRB REMARK 900 SARS-COV-2 OMICRON STEM-LOOP-II-MOTIF (S2M_OMICRON) DBREF 9QZJ A 1 19 PDB 9QZJ 9QZJ 1 19 SEQRES 1 A 19 G G U U C A C C U A C A G SEQRES 2 A 19 U G A A C 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 95 0 0 0 0 0 0 6 403 1 0 2 END