HEADER TRANSCRIPTION 02-DEC-21 7T1O TITLE SOLUTION STRUCTURE OF 7SK STEM-LOOP 1 WITH HIV-1 TAT SUBTYPE G TITLE 2 ARGININE RICH MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7SK STEM-LOOP 1 RNA (56-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TAT SUBTYPE G ARGININE RICH MOTIF; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HIV-1 06TG.HT008; SOURCE 9 ORGANISM_TAXID: 587638 KEYWDS TRANSCRIPTION EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 10 AUTHOR V.V.PHAM,M.GAO,V.M.D'SOUZA REVDAT 1 14-SEP-22 7T1O 0 JRNL AUTH V.V.PHAM,M.GAO,J.L.MEAGHER,J.L.SMITH,V.M.D'SOUZA JRNL TITL A STRUCTURE-BASED MECHANISM FOR DISPLACEMENT OF THE HEXIM JRNL TITL 2 ADAPTER FROM 7SK SMALL NUCLEAR RNA. JRNL REF COMMUN BIOL V. 5 819 2022 JRNL REFN ESSN 2399-3642 JRNL PMID 35970937 JRNL DOI 10.1038/S42003-022-03734-W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7T1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1000260995. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : 10MM PHOSPHATE, 70MM NACL, 0.1MM REMARK 210 EDTA REMARK 210 PRESSURE : 100000 PA REMARK 210 SAMPLE CONTENTS : 0.5 MM TAT G, 0.5 MM 7SK, 100% REMARK 210 D2O; 0.5 MM TAT G, 0.5 MM 7SK, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRVIEW, CYANA, X-PLOR REMARK 210 NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 : 12.3.1 (SIBYLS) BEAM REMARK 265 LINE REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : 12.3.1 REMARK 265 BEAMLINE INSTRUMENT : SIBYLS REMARK 265 DETECTOR TYPE : PILATUS3 2M PIXEL REMARK 265 ARRAY DETECTOR REMARK 265 DETECTOR MANUFACTURER DETAILS : DECTRIS REMARK 265 TEMPERATURE (KELVIN) : 283 REMARK 265 PH : 5.6 REMARK 265 NUMBER OF TIME FRAMES USED : 10 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : NULL REMARK 265 SAMPLE BUFFER : 10 MM PHOSPHATE, 70 REMARK 265 MM NACL, 0.1 MM EDTA REMARK 265 DATA REDUCTION SOFTWARE : ATSAS REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 2.3 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : NULL 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) : NULL REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: THIS STRUCTURE WAS REMARK 265 CALCULATED WITH XPLOR-NIH REMARK 265 WITH A CYANA INPUT AND REMARK 265 MINIMIZED WITH SAXS. REMARK 265 SOFTWARE USED : NULL REMARK 265 SOFTWARE AUTHORS : NULL REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : NULL REMARK 265 CONFORMERS, NUMBER SUBMITTED : NULL REMARK 265 CONFORMERS, SELECTION CRITERIA : NULL REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 U A 63 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 2 U A 40 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 2 C A 71 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 2 C A 75 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 3 U A 40 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 3 U A 63 C1' - O4' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 4 U A 41 C1' - O4' - C4' ANGL. DEV. = -4.5 DEGREES REMARK 500 5 U A 40 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 6 U A 40 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 8 U A 40 C1' - O4' - C4' ANGL. DEV. = -4.2 DEGREES REMARK 500 8 U A 63 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 9 U A 63 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 10 U A 40 C1' - O4' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 10 U A 63 C1' - O4' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LYS B 50 -56.71 -141.41 REMARK 500 1 LYS B 51 70.44 51.01 REMARK 500 1 HIS B 54 -169.32 -161.37 REMARK 500 1 ARG B 55 108.74 68.56 REMARK 500 1 ARG B 56 76.24 -165.71 REMARK 500 1 ARG B 57 32.30 -157.88 REMARK 500 2 ARG B 52 -31.87 -141.06 REMARK 500 2 HIS B 54 44.90 -150.77 REMARK 500 3 ARG B 52 -12.80 -140.80 REMARK 500 4 LYS B 51 77.33 -111.45 REMARK 500 4 ARG B 53 82.68 57.30 REMARK 500 4 ARG B 56 -51.95 -146.00 REMARK 500 4 ALA B 58 23.18 -140.26 REMARK 500 5 ARG B 53 85.44 62.86 REMARK 500 5 HIS B 54 37.86 -145.05 REMARK 500 5 ARG B 56 -57.97 -146.15 REMARK 500 6 ARG B 55 96.60 66.59 REMARK 500 6 ALA B 58 -35.45 -159.38 REMARK 500 7 LYS B 51 30.93 -164.34 REMARK 500 7 ARG B 55 77.07 65.57 REMARK 500 8 LYS B 51 96.22 -166.47 REMARK 500 9 LYS B 51 -139.79 -115.32 REMARK 500 9 ARG B 52 152.12 71.53 REMARK 500 9 ARG B 56 -39.14 -151.38 REMARK 500 9 ALA B 58 33.89 -148.05 REMARK 500 10 LYS B 50 74.84 48.78 REMARK 500 10 ARG B 52 -34.74 -140.87 REMARK 500 10 HIS B 54 55.28 -168.43 REMARK 500 10 ARG B 56 -177.86 -174.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDMF9 RELATED DB: SASBDB REMARK 900 RELATED ID: 30972 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF 7SK STEM-LOOP 1 WITH HIV-1 TAT SUBTYPE G REMARK 900 ARGININE RICH MOTIF DBREF 7T1O A 24 87 PDB 7T1O 7T1O 24 87 DBREF 7T1O B 44 60 PDB 7T1O 7T1O 44 60 SEQRES 1 A 56 G G G A U C U G U C A C C SEQRES 2 A 56 C C A U U G A U C G C C A SEQRES 3 A 56 G U G G C U G A U C U G G SEQRES 4 A 56 C U G G C U A G G C G G G SEQRES 5 A 56 U C C C SEQRES 1 B 17 GLY ILE SER TYR GLY ARG LYS LYS ARG ARG HIS ARG ARG SEQRES 2 B 17 ARG ALA HIS GLN 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