HEADER RNA 03-MAR-23 8CQ1 TITLE STEM-LOOP 4 OF THE 5'-UTR OF THE SARS-COV2 GENOMIC RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5_SL4; 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 SARS-COV2, STEM-LOOP, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.DUCHARDT-FERNER,J.VOEGELE REVDAT 3 22-NOV-23 8CQ1 1 JRNL REVDAT 2 18-OCT-23 8CQ1 1 JRNL REVDAT 1 20-SEP-23 8CQ1 0 JRNL AUTH J.VOGELE,D.HYMON,J.MARTINS,J.FERNER,H.R.A.JONKER, JRNL AUTH 2 A.E.HARGROVE,J.E.WEIGAND,A.WACKER,H.SCHWALBE,J.WOHNERT, JRNL AUTH 3 E.DUCHARDT-FERNER JRNL TITL HIGH-RESOLUTION STRUCTURE OF STEM-LOOP 4 FROM THE 5'-UTR OF JRNL TITL 2 SARS-COV-2 SOLVED BY SOLUTION STATE NMR. JRNL REF NUCLEIC ACIDS RES. V. 51 11318 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37791874 JRNL DOI 10.1093/NAR/GKAD762 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, CYANA, CARA, ARIA REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), GUNTERT, MUMENTHALER AND REMARK 3 WUTHRICH (CYANA), KELLER AND WUTHRICH (CARA), REMARK 3 LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN WATER REMARK 4 REMARK 4 8CQ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292127949. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 1 BAR; 1 BAR REMARK 210 SAMPLE CONTENTS : 500 UM [U-100% 15N] 5_SL4 RNA, REMARK 210 95% H2O/5% D2O; 500 UM [U-13C; U- REMARK 210 15N]-URA,GUA 5_SL4 RNA, 95% H2O/ REMARK 210 5% D2O; 500 UM [U-13C; U-15N]- REMARK 210 ADE,CYT 5_SL4 RNA, 95% H2O/5% REMARK 210 D2O; 350 UM [U-13C; U-15N] 5_ REMARK 210 SL4SH RNA, 95% H2O/5% D2O; 1.8 REMARK 210 MM 5_SL4SH RNA, 95% H2O/5% D2O; REMARK 210 200 UM [U-13C; U-15N]-ADE,CYT 5_ REMARK 210 SL4 RNA, 11.6 MG/ML UNLABELED REMARK 210 PF1 PHAGE, 95% H2O/5% D2O; 200 REMARK 210 UM [U-13C; U-15N]-GUA,URY 5_SL4 REMARK 210 RNA, 11.6 UM UNLABELED PF1 PHAGE, REMARK 210 95% H2O/5% D2O; 200 UM [U-13C; REMARK 210 U-15N]-ADE,CYT 5_SL4 RNA, 95% REMARK 210 H2O/5% D2O; 200 UM [U-13C; U-15N] REMARK 210 -GUA,URA 5_SL4 RNA, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; NOESY[15N]-CPMG; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D REMARK 210 13C,15N-FILTERED 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 13C,15N-FILTERED 1H- REMARK 210 13C NOESY ALIPHATIC; 1H,15N-IPAP- REMARK 210 SOFAST-HMQC; 1H,13C-IPAP-HSQC; REMARK 210 LR HNN-COSY; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 3D (H)CNC; 2D BEST- REMARK 210 TROSY H(N)CO; 2D H5(C5)C4 REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 700 MHZ; 950 REMARK 210 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO; AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 1 C A 106 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 3 C A 106 C1' - O4' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 3 A A 107 C3' - C2' - C1' ANGL. DEV. = -4.2 DEGREES REMARK 500 6 C A 106 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 6 A A 107 C3' - C2' - C1' ANGL. DEV. = -4.5 DEGREES REMARK 500 7 C A 106 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 7 A A 107 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 8 C A 106 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 9 A A 107 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 10 C A 106 C1' - O4' - C4' ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 50760 RELATED DB: BMRB REMARK 900 RELATED ID: 50347 RELATED DB: BMRB DBREF 8CQ1 A 84 127 PDB 8CQ1 8CQ1 84 127 SEQRES 1 A 44 G G G U G U G G C U G U C SEQRES 2 A 44 A C U C G G C U G C A U G SEQRES 3 A 44 C U U A G U G C A C U C A SEQRES 4 A 44 C 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