HEADER RNA 18-JUL-23 8THV TITLE FARFAR-NMR ENSEMBLE OF HIV-1 TAR WITH APICAL LOOP CAPTURING GROUND AND TITLE 2 EXCITED CONFORMATIONAL STATES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (29-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_TAXID: 11676 KEYWDS VIRAL RNA, HIV-1 TAR, EXCITED CONFORMATIONAL STATES, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.ROY,A.GENG,H.SHI,D.K.MERRIMAN,E.A.DETHOFF,L.SALMON,H.M.AL-HASHIMI REVDAT 4 15-MAY-24 8THV 1 REMARK REVDAT 3 01-NOV-23 8THV 1 JRNL REVDAT 2 25-OCT-23 8THV 1 JRNL REVDAT 1 02-AUG-23 8THV 0 JRNL AUTH R.ROY,A.GENG,H.SHI,D.K.MERRIMAN,E.A.DETHOFF,L.SALMON, JRNL AUTH 2 H.M.AL-HASHIMI JRNL TITL KINETIC RESOLUTION OF THE ATOMIC 3D STRUCTURES FORMED BY JRNL TITL 2 GROUND AND EXCITED CONFORMATIONAL STATES IN AN RNA DYNAMIC JRNL TITL 3 ENSEMBLE. JRNL REF J.AM.CHEM.SOC. V. 145 22964 2023 JRNL REFN ESSN 1520-5126 JRNL PMID 37831584 JRNL DOI 10.1021/JACS.3C04614 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ROSETTA REMARK 3 AUTHORS : SHI ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FARFAR-NMR REMARK 4 REMARK 4 8THV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1000275897. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM 13C, 15N E0_WT_TAR RNA REMARK 210 (29-MER), 90% H2O/10% D2O; 1.0 REMARK 210 MM 13C, 15N EI22_WT_TAR RNA (29- REMARK 210 MER), 90% H2O/10% D2O; 1.0 MM REMARK 210 13C, 15N EII3_WT_TAR RNA (29-MER) REMARK 210 , 90% H2O/10% D2O; 1.0 MM 13C, REMARK 210 15N EII13_WT_TAR RNA (29-MER), REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 13C-1H S3CT HSQC; 2D 13C-1H REMARK 210 TROSY HSQC; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; VARIAN REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 G A 17 O5' 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 9 A A 20 C6 A A 20 N1 -0.043 REMARK 500 9 A A 22 C6 A A 22 N1 -0.042 REMARK 500 9 A A 35 C6 A A 35 N1 -0.043 REMARK 500 18 G A 34 O3' A A 35 P -0.083 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 A A 22 C3' - O3' - P ANGL. DEV. = 11.5 DEGREES REMARK 500 8 A A 22 C5' - C4' - O4' ANGL. DEV. = 5.4 DEGREES REMARK 500 9 C A 19 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 9 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 A A 20 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 9 G A 21 OP1 - P - OP2 ANGL. DEV. = -9.4 DEGREES REMARK 500 9 G A 21 C2 - N3 - C4 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 A A 22 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 9 C A 24 OP1 - P - OP2 ANGL. DEV. = -12.2 DEGREES REMARK 500 9 U A 25 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 G A 26 OP1 - P - OP2 ANGL. DEV. = -9.4 DEGREES REMARK 500 9 A A 27 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 9 G A 28 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 9 C A 29 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 9 C A 30 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 9 U A 31 OP1 - P - OP2 ANGL. DEV. = -9.8 DEGREES REMARK 500 9 G A 34 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 9 A A 35 OP1 - P - OP2 ANGL. DEV. = -11.3 DEGREES REMARK 500 9 G A 36 OP1 - P - OP2 ANGL. DEV. = -10.0 DEGREES REMARK 500 9 C A 37 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 9 U A 38 OP1 - P - OP2 ANGL. DEV. = -9.1 DEGREES REMARK 500 9 C A 39 OP1 - P - OP2 ANGL. DEV. = -9.2 DEGREES REMARK 500 9 C A 39 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 U A 40 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 9 U A 40 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 C A 41 OP1 - P - OP2 ANGL. DEV. = -10.8 DEGREES REMARK 500 9 U A 42 OP1 - P - OP2 ANGL. DEV. = -9.3 DEGREES REMARK 500 9 G A 43 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 9 C A 44 OP1 - P - OP2 ANGL. DEV. = -9.5 DEGREES REMARK 500 9 C A 44 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 C A 45 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31099 RELATED DB: BMRB REMARK 900 FARFAR-NMR ENSEMBLE OF HIV-1 TAR WITH APICAL LOOP CAPTURING GROUND REMARK 900 AND EXCITED CONFORMATIONAL STATES DBREF 8THV A 17 45 PDB 8THV 8THV 17 45 SEQRES 1 A 29 G G C A G A U C U G A G C SEQRES 2 A 29 C U G G G A G C U C U C U SEQRES 3 A 29 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