HEADER RNA 05-JUN-24 9FM4 TITLE DYNAMIC STRUCTURE OF THE APICAL STEM LOOP OF THE STEM LOOP 2 MOTIF TITLE 2 (S2M) FROM SCOV-2 DELTA VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (25-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: SEQUENCE NUMBERING CORRESPONDS TO POSITION IN THE RNA COMPND 7 GENOME -29,000 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 4 2; SOURCE 5 ORGANISM_TAXID: 2697049 KEYWDS S2M, COVID-19, NMR ASSIGNMENT, MOLECULAR DYNAMIC SIMULATIONS, NMR KEYWDS 2 DYNAMICS, RNA EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 20 AUTHOR M.A.WIRTZ MARTIN,T.MATZEL,J.MAKOWSKI,A.KENSINGER,A.HERR,A.WACKER, AUTHOR 2 C.RICHTER,H.R.A.JONKER,J.EVANSECK,H.SCHWALBE REVDAT 3 16-JUL-25 9FM4 1 TITLE JRNL REVDAT 2 04-JUN-25 9FM4 1 TITLE REVDAT 1 07-MAY-25 9FM4 0 JRNL AUTH M.A.WIRTZ MARTIN,J.A.MAKOWSKI,T.MATZEL,A.H.KENSINGER,A.HERR, JRNL AUTH 2 C.RICHTER,H.R.A.JONKER,A.WACKER,J.D.EVANSECK,H.SCHWALBE JRNL TITL STRUCTURAL HETEROGENEITY AND DYNAMICS IN THE APICAL STEM JRNL TITL 2 LOOP OF S2M FROM SARS-COV-2 DELTA BY AN INTEGRATIVE NMR JRNL TITL 3 SPECTROSCOPY AND MD SIMULATION APPROACH. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40586311 JRNL DOI 10.1093/NAR/GKAF552 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 (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9FM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292138963. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298; 298 REMARK 210 PH : 6.2; 6.2; 6.2 REMARK 210 IONIC STRENGTH : 75; 75; 75 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 250 UM [U-100% 13C; U-100% 15N] REMARK 210 S2M DELTA_SHORT RNA, 25 MM REMARK 210 DIPOTASSIUM HYDROGEN REMARK 210 ORTHOPHOSPHATE/POTASSIUM REMARK 210 DIHYDROGEN PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 1700 UM [U-100% 13C; U-100% REMARK 210 15N] S2M DELTA_SHORT RNA, 25 MM REMARK 210 DIPOTASSIUM HYDROGEN REMARK 210 ORTHOPHOSPHATE/POTASSIUM REMARK 210 DIHYDROGEN PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 150 UM [U-100% 13C; U-100% REMARK 210 15N] S2M DELTA_SHORT RNA, 25 MM REMARK 210 DIPOTASSIUM HYDROGEN REMARK 210 ORTHOPHOSPHATE/POTASSIUM REMARK 210 DIHYDROGEN PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 150 UM [U-13C; U-15N]-ADE; REMARK 210 U[U-13C; U-15N]-URA S2M DELTA_ REMARK 210 SHORT RNA, 25 MM DIPOTASSIUM REMARK 210 HYDROGEN ORTHOPHOSPHATE/ REMARK 210 POTASSIUM DIHYDROGEN PHOSPHATE, REMARK 210 50 MM POTASSIUM CHLORIDE, 95% REMARK 210 H2O/5% D2O; 200 UM [U-13C; U-15N] REMARK 210 -CYT S2M DELTA_SHORT RNA, 25 MM REMARK 210 DIPOTASSIUM HYDROGEN REMARK 210 ORTHOPHOSPHATE/POTASSIUM REMARK 210 DIHYDROGEN PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 700 UM [U-13C; U-15N]-CYT REMARK 210 S2M DELTA_SHORT RNA, 25 MM REMARK 210 DIPOTASSIUM HYDROGEN REMARK 210 ORTHOPHOSPHATE/POTASSIUM REMARK 210 DIHYDROGEN PHOSPHATE, 50 MM REMARK 210 POTASSIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-15N TROSY; REMARK 210 3D HNN-COSY; 3D HNCO; 2D 1H-13C REMARK 210 HSQC; 2D 1H-15N HSQC NH2 ONLY; REMARK 210 2D 1H-15N HSQC 2J; 2D 1H-13C REMARK 210 HSQC LR; 3D HCN; 2D HCCNH; 3D REMARK 210 TROSY-HCCH-COSY; 3D-NOESY; 4D- REMARK 210 HMQC-NOESY-HMQC; 3D HCCH-TOCSY; REMARK 210 3D FW-HCCH-TOCSY; 2D CN-HSQC; 2D REMARK 210 1H-15N CPMG NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 700 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD; AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY, CNS, TOPSPIN REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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 265 REMARK 265 EXPERIMENTAL DETAILS 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' U A 753 OP1 C A 754 1.59 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 8 A A 749 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 11 A A 749 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 12 A A 749 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES REMARK 500 19 A A 749 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES 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 4 G A 738 0.05 SIDE CHAIN REMARK 500 11 A A 749 0.05 SIDE CHAIN REMARK 500 14 G A 737 0.07 SIDE CHAIN REMARK 500 15 A A 752 0.07 SIDE CHAIN REMARK 500 16 A A 749 0.05 SIDE CHAIN REMARK 500 18 C A 760 0.06 SIDE CHAIN REMARK 500 20 G A 744 0.05 SIDE CHAIN REMARK 500 20 C A 754 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDUD9 RELATED DB: SASBDB REMARK 900 RELATED ID: SASDUD9 RELATED DB: SASBDB REMARK 900 RELATED ID: 34919 RELATED DB: BMRB REMARK 900 DYNAMIC STRUCTURE OF THE APICAL STEM LOOP OF THE STEM LOOP 2 MOTIF REMARK 900 (S2M) FROM SCOV-2 DELTA VARIANT DBREF 9FM4 A 737 761 PDB 9FM4 9FM4 737 761 SEQRES 1 A 25 G G C A C U C G G A G U A SEQRES 2 A 25 C G A U C G A G U G 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 175 0 0 0 0 0 0 6 538 1 0 2 END