HEADER RNA 05-JUN-20 6XB7 TITLE IRES-TARGETING SMALL MOLECULE INHIBITS ENTEROVIRUS 71 REPLICATION VIA TITLE 2 ALLOSTERIC STABILIZATION OF A TERNARY COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (41-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ENTEROVIRUS A71; SOURCE 4 ORGANISM_TAXID: 39054 KEYWDS RNA-SMALL MOLECULE COMPLEX, RNA BINDING PROTEIN, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR B.S.TOLBERT,J.DAVILA,A.L.SUGARMAN,L.Y.CHIU REVDAT 3 01-MAY-24 6XB7 1 REMARK REVDAT 2 07-OCT-20 6XB7 1 JRNL REVDAT 1 02-SEP-20 6XB7 0 JRNL AUTH J.DAVILA-CALDERON,N.N.PATWARDHAN,L.Y.CHIU,A.SUGARMAN,Z.CAI, JRNL AUTH 2 S.R.PENUTMUTCHU,M.L.LI,G.BREWER,A.E.HARGROVE,B.S.TOLBERT JRNL TITL IRES-TARGETING SMALL MOLECULE INHIBITS ENTEROVIRUS 71 JRNL TITL 2 REPLICATION VIA ALLOSTERIC STABILIZATION OF A TERNARY JRNL TITL 3 COMPLEX. JRNL REF NAT COMMUN V. 11 4775 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32963221 JRNL DOI 10.1038/S41467-020-18594-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XB7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249267. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 200 UM SELECTIVE DEUTERATION; REMARK 210 FULLY DEUTERATION FOR U AND C; REMARK 210 SELECTIVE DEUTERATION FOR A AND REMARK 210 G RNTP, 800 UM DMA135, 100% D2O; REMARK 210 200 UM SELECTIVE DEUTERATION; REMARK 210 EQUIMOLAR MIX:ATP, GTP, CTP, UTP REMARK 210 RNTP, 800 UM DMA135, 100% D2O; REMARK 210 200 UM SELECTIVE DEUTERATION; REMARK 210 FULLY DEUTERATION FOR U AND C; REMARK 210 SELECTIVE DEUTERATION FOR A AND REMARK 210 G RNTP, 100% D2O; 200 UM REMARK 210 SELECTIVE DEUTERATION; EQUIMOLAR REMARK 210 MIX:ATP, GTP, CTP, UTP RNTP, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, SPARKY, TOPSPIN, REMARK 210 NMRPIPE, NMRDRAW REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 16 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 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: 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 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 3 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 C A 5 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 C A 5 N3 - C2 - O2 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 A A 6 C1' - O4' - C4' ANGL. DEV. = -9.1 DEGREES REMARK 500 1 A A 6 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 1 A A 6 C4 - C5 - C6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 A A 6 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 A A 6 N1 - C6 - N6 ANGL. DEV. = -6.1 DEGREES REMARK 500 1 A A 7 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 7 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 A A 9 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 9 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 C A 11 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 C A 20 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 21 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 21 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 21 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 22 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 23 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 23 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 C A 24 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 C A 25 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 26 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 26 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 26 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 C A 29 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 C A 29 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 A A 30 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 30 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 30 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 A A 32 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 32 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 A A 32 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 33 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 34 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 A A 38 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 38 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 40 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 41 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 A A 3 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 C A 5 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 2 A A 6 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 A A 6 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 A A 7 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 433 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UYS A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 50268 RELATED DB: BMRB DBREF 6XB7 A 1 41 PDB 6XB7 6XB7 1 41 SEQRES 1 A 41 G G A U C A A U A G C A G SEQRES 2 A 41 G U G U G G C A C A C C A SEQRES 3 A 41 G U C A U A C C U U G A U SEQRES 4 A 41 C C HET UYS A 101 42 HETNAM UYS 3-AMINO-N-(DIAMINOMETHYLIDENE)-5-(DIMETHYLAMINO)-6- HETNAM 2 UYS (PHENYLETHYNYL)PYRAZINE-2-CARBOXAMIDE FORMUL 2 UYS C16 H17 N7 O SITE 1 AC1 7 A A 6 A A 7 A A 9 G A 13 SITE 2 AC1 7 U A 35 U A 36 G A 37 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