HEADER RNA 11-JUN-24 9FO9 TITLE 5_SL5A OF S_SL5 OF SARS-COV-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (33-MER); 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 5_SL5, 5_SL5A, SARS-COV-2, UUUCGU, REPETETIVE STRUCTURE MOTIFS, U KEYWDS 2 RICH BULGES, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.R.MERTINKUS,A.OXENFARTH,H.J.SCHWALBE REVDAT 2 13-NOV-24 9FO9 1 JRNL REVDAT 1 06-NOV-24 9FO9 0 JRNL AUTH K.R.MERTINKUS,A.OXENFARTH,C.RICHTER,A.WACKER,C.P.MATA, JRNL AUTH 2 J.M.CARAZO,A.SCHLUNDT,H.SCHWALBE JRNL TITL DISSECTING THE CONFORMATIONAL HETEROGENEITY OF STEM-LOOP JRNL TITL 2 SUBSTRUCTURES OF THE FIFTH ELEMENT IN THE 5'-UNTRANSLATED JRNL TITL 3 REGION OF SARS-COV-2. JRNL REF J.AM.CHEM.SOC. V. 146 30139 2024 JRNL REFN ESSN 1520-5126 JRNL PMID 39442924 JRNL DOI 10.1021/JACS.4C08406 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, ARIA REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WATER REFINEMENT REMARK 4 REMARK 4 9FO9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1292139093. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : 1 PA REMARK 210 SAMPLE CONTENTS : 280 MM [U-10% 13C; U-100% 15N] REMARK 210 RNA (33-MER), 50 MM POTASSIUM REMARK 210 CHLORIDE, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 95% H2O/5% D2O; 400 REMARK 210 MM [U-10% 13C; U-100% 15N] RNA REMARK 210 (33-MER), 50 MM POTASSIUM REMARK 210 CHLORIDE, 25 MM POTASSIUM REMARK 210 PHOSPHATE, 100% D2O; 200 MM [U- REMARK 210 10% 13C; U-100% 15N] RNA (33-MER) REMARK 210 , 50 MM POTASSIUM CHLORIDE, 25 REMARK 210 MM POTASSIUM PHOSPHATE, 95% H2O/ REMARK 210 5% D2O; 200 MM [U-10% 13C; U-100% REMARK 210 15N] RNA (33-MER), 50 MM REMARK 210 POTASSIUM CHLORIDE, 25 MM REMARK 210 POTASSIUM PHOSPHATE, 21 MG/ML REMARK 210 PF1 PHAGE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HSQC AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 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 3.190, TOPSPIN REMARK 210 3.6.3, TOPSPIN 4.1.4 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 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: 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: 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 7 U A 15 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES REMARK 500 9 U A 19 C3' - O3' - P ANGL. DEV. = 7.5 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 1 U A 14 0.06 SIDE CHAIN REMARK 500 1 C A 32 0.08 SIDE CHAIN REMARK 500 2 U A 14 0.07 SIDE CHAIN REMARK 500 2 C A 32 0.07 SIDE CHAIN REMARK 500 3 G A 1 0.06 SIDE CHAIN REMARK 500 4 C A 32 0.08 SIDE CHAIN REMARK 500 5 U A 14 0.08 SIDE CHAIN REMARK 500 5 G A 18 0.05 SIDE CHAIN REMARK 500 5 C A 32 0.07 SIDE CHAIN REMARK 500 6 U A 14 0.07 SIDE CHAIN REMARK 500 6 C A 32 0.07 SIDE CHAIN REMARK 500 7 G A 18 0.05 SIDE CHAIN REMARK 500 7 C A 32 0.08 SIDE CHAIN REMARK 500 9 U A 14 0.09 SIDE CHAIN REMARK 500 9 G A 18 0.06 SIDE CHAIN REMARK 500 10 G A 1 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 50346 RELATED DB: BMRB DBREF 9FO9 A 1 33 PDB 9FO9 9FO9 1 33 SEQRES 1 A 33 G G G C U G C U U A C G G SEQRES 2 A 33 U U U C G U C C G U G U U SEQRES 3 A 33 G C A G 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