HEADER TRANSCRIPTION 31-AUG-18 6MCF TITLE SOLUTION STRUCTURE OF 7SK STEM-LOOP 1 WITH HIV-1 TAT RNA BINDING TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7SK STEM-LOOP 1 RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN TAT; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: RNA BINDING DOMAIN RESIDUES 44-60; COMPND 9 SYNONYM: TRANSACTIVATING REGULATORY PROTEIN; COMPND 10 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: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 9 SUBTYPE B; SOURCE 10 ORGANISM_COMMON: HIV-1; SOURCE 11 ORGANISM_TAXID: 11706 KEYWDS TRANSCRIPTION, RNA BINDING DOMAIN, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR V.V.PHAM,V.M.D'SOUZA REVDAT 3 01-MAY-24 6MCF 1 LINK REVDAT 2 20-NOV-19 6MCF 1 REMARK REVDAT 1 31-OCT-18 6MCF 0 JRNL AUTH V.V.PHAM,C.SALGUERO,S.N.KHAN,J.L.MEAGHER,W.C.BROWN, JRNL AUTH 2 N.HUMBERT,H.DE ROCQUIGNY,J.L.SMITH,V.M.D'SOUZA JRNL TITL HIV-1 TAT INTERACTIONS WITH CELLULAR 7SK AND VIRAL TAR RNAS JRNL TITL 2 IDENTIFIES DUAL STRUCTURAL MIMICRY. JRNL REF NAT COMMUN V. 9 4266 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30323330 JRNL DOI 10.1038/S41467-018-06591-6 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 6MCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1000236625. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.4 REMARK 210 IONIC STRENGTH : 10MM PHOSPHATES, 70MM NACL REMARK 210 PRESSURE : 100000 PA REMARK 210 SAMPLE CONTENTS : 0.5 MM 7SK STEM-LOOP 1 RNA, 0.5 REMARK 210 MM [U-13C; U-15N] HIV-1 TAT RNA REMARK 210 BINDING DOMAIN SELECTIVELY REMARK 210 LABELED WITH THE FOLLOWING REMARK 210 SCHEMA: 1) R49, K50, R57, A58 2) REMARK 210 K51, R52, Q54, R55 3) R53, Q54, REMARK 210 R56, 90% H2O/10% D2O; 0.5 MM [U- REMARK 210 13C; U-15N] 7SK STEM-LOOP 1 RNA, REMARK 210 0.5 MM HIV-1 TAT RNA BINDING REMARK 210 DOMAIN, 90% H2O/10% D2O; 0.5 MM REMARK 210 7SK STEM-LOOP 1 RNA, 0.5 MM [U- REMARK 210 13C; U-15N] HIV-1 TAT RNA REMARK 210 BINDING DOMAIN SELECTIVELY REMARK 210 LABELED WITH THE FOLLOWING REMARK 210 SCHEMA: 1) R49, K50, R57, A58 2) REMARK 210 K51, R52, Q54, R55 3) R53, Q54, REMARK 210 R56, 100% D2O; 0.5 MM [U-13C; U- REMARK 210 15N] 7SK STEM-LOOP 1 RNA, 0.5 MM REMARK 210 HIV-1 TAT RNA BINDING DOMAIN, REMARK 210 100% D2O; 0.5 MM 7SK STEM-LOOP 1 REMARK 210 RNA, 0.5 MM HIV-1 TAT RNA REMARK 210 BINDING DOMAIN, 90% H2O/10% D2O; REMARK 210 0.5 MM 7SK STEM-LOOP 1 RNA, 0.5 REMARK 210 MM HIV-1 TAT RNA BINDING DOMAIN, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC 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 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 A A 27 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 U A 28 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 C A 29 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 33 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A A 34 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 34 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 A A 34 N1 - C6 - N6 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 C A 35 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 C A 36 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C A 36 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 37 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 C A 37 N3 - C2 - O2 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 C A 38 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 A A 39 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 39 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 39 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 43 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 43 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 A A 43 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 U A 44 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 C A 45 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 C A 47 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 48 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 50 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 50 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 50 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 G A 51 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 A A 52 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A A 52 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 C A 62 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 G A 64 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 G A 64 N3 - C2 - N2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 A A 65 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 A A 65 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 C A 67 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C A 67 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 G A 74 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 A A 77 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 A A 77 C5 - C6 - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 A A 77 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 G A 79 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 C A 80 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 C A 85 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 C A 86 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 87 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 ARG B 53 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 27 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 A A 27 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 C A 29 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 470 ANGLE DEVIATIONS. 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 GLN B 54 -56.14 -144.29 REMARK 500 1 ARG B 56 -33.82 -146.44 REMARK 500 2 GLN B 54 -58.02 -149.39 REMARK 500 2 HIS B 59 -39.14 -146.92 REMARK 500 3 ARG B 53 16.27 56.83 REMARK 500 3 GLN B 54 -64.23 -157.89 REMARK 500 4 GLN B 54 -54.60 -158.38 REMARK 500 4 ARG B 56 -66.19 -146.99 REMARK 500 4 ARG B 57 -8.04 -59.67 REMARK 500 4 HIS B 59 -39.05 -143.64 REMARK 500 5 GLN B 54 -56.68 -157.37 REMARK 500 5 ARG B 57 14.75 58.49 REMARK 500 6 ARG B 53 9.39 56.54 REMARK 500 6 GLN B 54 -66.72 -148.58 REMARK 500 6 ARG B 57 -5.09 87.46 REMARK 500 6 HIS B 59 -32.68 -145.99 REMARK 500 7 LYS B 50 115.28 -164.89 REMARK 500 7 ARG B 53 -1.96 60.68 REMARK 500 7 GLN B 54 -55.54 -147.13 REMARK 500 7 ARG B 57 -4.37 67.02 REMARK 500 8 ARG B 53 12.20 56.25 REMARK 500 8 GLN B 54 -63.78 -155.52 REMARK 500 9 ARG B 49 38.08 -151.44 REMARK 500 9 GLN B 54 -64.87 -150.78 REMARK 500 10 GLN B 54 -59.02 -146.09 REMARK 500 10 ARG B 57 33.09 70.04 REMARK 500 10 HIS B 59 -8.18 -154.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 G A 25 0.07 SIDE CHAIN REMARK 500 1 U A 28 0.08 SIDE CHAIN REMARK 500 1 C A 33 0.10 SIDE CHAIN REMARK 500 1 A A 34 0.10 SIDE CHAIN REMARK 500 1 C A 36 0.11 SIDE CHAIN REMARK 500 1 G A 46 0.10 SIDE CHAIN REMARK 500 1 C A 47 0.07 SIDE CHAIN REMARK 500 1 A A 50 0.07 SIDE CHAIN REMARK 500 1 U A 63 0.11 SIDE CHAIN REMARK 500 1 G A 69 0.08 SIDE CHAIN REMARK 500 1 G A 70 0.07 SIDE CHAIN REMARK 500 2 U A 28 0.07 SIDE CHAIN REMARK 500 2 C A 33 0.12 SIDE CHAIN REMARK 500 2 C A 35 0.06 SIDE CHAIN REMARK 500 2 G A 46 0.09 SIDE CHAIN REMARK 500 2 C A 47 0.07 SIDE CHAIN REMARK 500 2 A A 50 0.07 SIDE CHAIN REMARK 500 2 U A 63 0.11 SIDE CHAIN REMARK 500 2 U A 66 0.06 SIDE CHAIN REMARK 500 2 U A 68 0.06 SIDE CHAIN REMARK 500 2 G A 74 0.09 SIDE CHAIN REMARK 500 3 G A 24 0.06 SIDE CHAIN REMARK 500 3 G A 25 0.07 SIDE CHAIN REMARK 500 3 U A 28 0.07 SIDE CHAIN REMARK 500 3 C A 33 0.11 SIDE CHAIN REMARK 500 3 A A 34 0.09 SIDE CHAIN REMARK 500 3 U A 40 0.09 SIDE CHAIN REMARK 500 3 G A 46 0.10 SIDE CHAIN REMARK 500 3 C A 47 0.06 SIDE CHAIN REMARK 500 3 A A 50 0.07 SIDE CHAIN REMARK 500 3 U A 63 0.14 SIDE CHAIN REMARK 500 3 C A 67 0.06 SIDE CHAIN REMARK 500 3 G A 69 0.07 SIDE CHAIN REMARK 500 3 G A 74 0.07 SIDE CHAIN REMARK 500 3 C A 87 0.07 SIDE CHAIN REMARK 500 4 G A 24 0.06 SIDE CHAIN REMARK 500 4 G A 25 0.07 SIDE CHAIN REMARK 500 4 U A 28 0.07 SIDE CHAIN REMARK 500 4 C A 33 0.10 SIDE CHAIN REMARK 500 4 A A 34 0.09 SIDE CHAIN REMARK 500 4 U A 40 0.06 SIDE CHAIN REMARK 500 4 G A 46 0.10 SIDE CHAIN REMARK 500 4 C A 47 0.08 SIDE CHAIN REMARK 500 4 A A 50 0.09 SIDE CHAIN REMARK 500 4 U A 63 0.12 SIDE CHAIN REMARK 500 4 U A 66 0.07 SIDE CHAIN REMARK 500 4 G A 73 0.06 SIDE CHAIN REMARK 500 5 G A 24 0.05 SIDE CHAIN REMARK 500 5 G A 25 0.07 SIDE CHAIN REMARK 500 5 U A 28 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 122 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30511 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF 7SK STEM-LOOP 1 WITH HIV-1 TAT RNA BINDING REMARK 900 DOMAIN DBREF 6MCF A 24 87 PDB 6MCF 6MCF 24 87 DBREF 6MCF B 44 60 UNP P04608 TAT_HV1H2 44 60 SEQRES 1 A 57 G G G A U C U G U C A C C SEQRES 2 A 57 C C A U U G A U C G C C G SEQRES 3 A 57 A G A G G C U G A U C U G SEQRES 4 A 57 G RY U G G RY U A G G C G G SEQRES 5 A 57 G U C C C SEQRES 1 B 17 GLY ILE SER TYR GLY ARG LYS LYS ARG ARG GLN ARG ARG SEQRES 2 B 17 ARG ALA HIS GLN HET RY A 71 32 HET RY A 75 32 HETNAM RY 5'-3,6-DIHYDROCYTIDYLIC ACID FORMUL 1 RY 2(C9 H16 N3 O8 P) LINK O3' G A 70 P RY A 71 1555 1555 1.62 LINK O3' RY A 71 P U A 72 1555 1555 1.60 LINK O3' G A 74 P RY A 75 1555 1555 1.61 LINK O3' RY A 75 P U A 76 1555 1555 1.61 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