HEADER RNA 15-MAR-24 9EOW TITLE THE 5-TERMINAL STEM-LOOP RNA ELEMENT OF SARS-COV-2 FEATURES HIGHLY TITLE 2 DYNAMIC STRUCTURAL ELEMENTS THAT ARE SENSITIVE TO DIFFERENCES IN TITLE 3 CELLULAR PH COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (29-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_TAXID: 2697049; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SOLUTION STRUCTURE, CONFORMATIONAL DYNAMICS, PKA SHIFT, ADENOSINE KEYWDS 2 PROTONATION, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.WACKER,H.SCHWALBE REVDAT 1 19-JUN-24 9EOW 0 JRNL AUTH S.TOEWS,A.WACKER,E.M.FAISON,E.DUCHARDT-FERNER,C.RICHTER, JRNL AUTH 2 D.MATHIEU,S.BOTTARO,Q.ZHANG,H.SCHWALBE JRNL TITL THE 5'-TERMINAL STEM-LOOP RNA ELEMENT OF SARS-COV-2 FEATURES JRNL TITL 2 HIGHLY DYNAMIC STRUCTURAL ELEMENTS THAT ARE SENSITIVE TO JRNL TITL 3 DIFFERENCES IN CELLULAR PH. JRNL REF NUCLEIC ACIDS RES. 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38842942 JRNL DOI 10.1093/NAR/GKAE477 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 9EOW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1292137357. 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 : 150 UM [U-15N] 5_SL1 15N, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 50 MM KCL, REMARK 210 93% H2O/7% D2O; 400 UM [U-13C; U- REMARK 210 15N] 5_SL1 15N, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 50 MM KCL, 93% H2O/7% REMARK 210 D2O; 400 UM A,C-13C, U-15N 5_SL1 REMARK 210 15N, 25 MM POTASSIUM PHOSPHATE, REMARK 210 50 MM KCL, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-JR[15N]; NOESY[15N]-IMINO; REMARK 210 HSQC[15N]-AMINO; HSQC[15N]-2J; REMARK 210 TROSY[15N]; NOESY-JR[15N]-AMINO; REMARK 210 TOCSY; HSQC[13C]-AROMATEN REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : BRUKER AVANCE III HD 800 MHZ; REMARK 210 BRUKER AVANCE III HD 700 MHZ; REMARK 210 BRUKER AVANCE I 600 MHZ REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CNS, NMRFAM-SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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 5 G A 6 0.07 SIDE CHAIN REMARK 500 5 C A 33 0.07 SIDE CHAIN REMARK 500 5 C A 34 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDSP7 RELATED DB: SASBDB REMARK 900 RELATED ID: 34909 RELATED DB: BMRB REMARK 900 THE 5-TERMINAL STEM-LOOP RNA ELEMENT OF SARS-COV-2 FEATURES HIGHLY REMARK 900 DYNAMIC STRUCTURAL ELEMENTS THAT ARE SENSITIVE TO DIFFERENCES IN REMARK 900 CELLULAR PH DBREF1 9EOW A 6 34 GB NC_045512.2 DBREF2 9EOW A NC_045512 6 34 SEQADV 9EOW G A 6 GB NC_045512 A 6 ENGINEERED MUTATION SEQADV 9EOW C A 34 GB NC_045512 A 34 ENGINEERED MUTATION SEQRES 1 A 29 G G G U U U A U A C C U U SEQRES 2 A 29 C C C A G G U A A C A A A SEQRES 3 A 29 C 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