HEADER RNA 09-MAY-22 7V06 TITLE ENCODED CONFORMATIONAL DYNAMICS OF THE HIV SPLICE SITE A3 REGULATORY TITLE 2 LOCUS: IMPLICATIONS FOR DIFFERENTIAL BINDING OF HNRNP SPLICING TITLE 3 AUXILIARY FACTORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (43-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HIV WHOLE-GENOME VECTOR AA1305#18; SOURCE 4 ORGANISM_TAXID: 672471 KEYWDS HIV, RNA REGULATORY ELEMENT, SPLICE SITE A3, RNA EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 10 AUTHOR B.S.TOLBERT,L.Y.CHIU,A.L.SUGARMAN REVDAT 4 15-MAY-24 7V06 1 REMARK REVDAT 3 14-JUN-23 7V06 1 REMARK REVDAT 2 10-AUG-22 7V06 1 JRNL REVDAT 1 29-JUN-22 7V06 0 JRNL AUTH L.Y.CHIU,A.EMERY,N.JAIN,A.SUGARMAN,N.KENDRICK,L.LUO,W.FORD, JRNL AUTH 2 R.SWANSTROM,B.S.TOLBERT JRNL TITL ENCODED CONFORMATIONAL DYNAMICS OF THE HIV SPLICE SITE A3 JRNL TITL 2 REGULATORY LOCUS: IMPLICATIONS FOR DIFFERENTIAL BINDING OF JRNL TITL 3 HNRNP SPLICING AUXILIARY FACTORS. JRNL REF J.MOL.BIOL. 67728 2022 JRNL REFN ESSN 1089-8638 JRNL PMID 35870649 JRNL DOI 10.1016/J.JMB.2022.167728 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 7V06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000263548. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 283 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 5; 5 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 400 UM ESS2P, 90% H2O/10% D2O; REMARK 210 400 UM [U-100% 13C; U-100% 15N REMARK 210 ON ATP AND GTP ESS2P, 100% D2O; REMARK 210 450 UM SELECTIVE DEUTERATION REMARK 210 ESS2P, 100% D2O; 300 UM UNIFORM_ REMARK 210 15N ON GTP AND UTP ESS2P, 90% REMARK 210 H2O/10% D2O; 300 UM UNIFORM_15N REMARK 210 ON ALL NUCLEOTIDES ESS2P, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-13C HMQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-15N HSQC; REMARK 210 2D 1H-15N HNN-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II; AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, NMRVIEWJ, TOPSPIN, REMARK 210 NMRPIPE, NMRFAM-SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1024 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 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE NEUTRON SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : APS BIOCAT 18ID BEAM REMARK 265 LINE REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : APS REMARK 265 BEAMLINE INSTRUMENT : 18ID REMARK 265 DETECTOR TYPE : NULL REMARK 265 DETECTOR MANUFACTURER DETAILS : NULL REMARK 265 TEMPERATURE (KELVIN) : 298 REMARK 265 PH : 6.2 REMARK 265 NUMBER OF TIME FRAMES USED : NULL REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 6-6.5 REMARK 265 SAMPLE BUFFER : 20 MM BIS-TRIS, 20 MM REMARK 265 NACL, PH 6.2 REMARK 265 DATA REDUCTION SOFTWARE : GNOM REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 2.1 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.1 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 6.9 REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: NMR, SAXS REMARK 265 SOFTWARE USED : NMRPIPE, NMRVIEWJ ,X-PLOR_NIH, AMBER, GNOM REMARK 265 SOFTWARE AUTHORS : FRANK DELAGLIO; AD BAX; BRUCE JOHNSON; CHARLES REMARK 265 SCHWIETERS; MARIUS CLORE; DAVID CASE; DMITRY REMARK 265 SVERGUN REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : 1024 REMARK 265 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 265 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 10 REMARK 265 REMARK 265 OTHER DETAILS: NULL 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 C A 5 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 A A 11 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 11 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 C A 13 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 C A 14 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 A A 15 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 15 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 20 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 20 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 A A 22 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 A A 22 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 22 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 A A 23 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 A A 23 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 C A 32 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 34 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 34 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 34 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 35 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 36 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 36 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 36 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 38 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 38 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 38 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 C A 40 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 41 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 41 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 41 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 42 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 C A 43 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 C A 5 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 C A 5 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 U A 9 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 A A 11 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 A A 11 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 A A 11 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 C A 13 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 C A 14 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 A A 15 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 A A 15 N1 - C6 - N6 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 A A 20 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 20 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 386 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 51310 RELATED DB: BMRB REMARK 900 RELATED ID: SASDPD3 RELATED DB: SASBDB DBREF 7V06 A 1 43 PDB 7V06 7V06 1 43 SEQRES 1 A 43 G G U G C U G U U U A U C SEQRES 2 A 43 C A U U U C A G A A U U G SEQRES 3 A 43 G G U G U C G A C A U A G SEQRES 4 A 43 C A 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