HEADER PEPTIDE/RNA 13-APR-18 6D2U TITLE SOLUTION STRUCTURE OF A ULTRA-HIGH AFFINITY MACROCYCLE BOUND TO HIV-1 TITLE 2 TAR RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA (29-MER); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS MACROCYCLE INHIBITOR, COMPLEX, HIV-1 TAR, TAT, P-TEFB, RNA, PEPTIDE- KEYWDS 2 RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.D.SHORTRIDGE,G.VARANI REVDAT 5 15-NOV-23 6D2U 1 REMARK REVDAT 4 14-JUN-23 6D2U 1 LINK REVDAT 3 01-JAN-20 6D2U 1 REMARK REVDAT 2 03-JUL-19 6D2U 1 JRNL REMARK REVDAT 1 12-DEC-18 6D2U 0 JRNL AUTH M.D.SHORTRIDGE,P.T.WILLE,A.N.JONES,A.DAVIDSON,J.BOGDANOVIC, JRNL AUTH 2 E.ARTS,J.KARN,J.A.ROBINSON,G.VARANI JRNL TITL AN ULTRA-HIGH AFFINITY LIGAND OF HIV-1 TAR REVEALS THE RNA JRNL TITL 2 STRUCTURE RECOGNIZED BY P-TEFB. JRNL REF NUCLEIC ACIDS RES. V. 47 1523 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30481318 JRNL DOI 10.1093/NAR/GKY1197 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 6D2U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233920. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277; 303 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 10 MM NACL, 20MM NA PHOSPHATE; REMARK 210 10 MM NACL, 20MM NA PHOSPHATE REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.7 MM DAB-VAL-ARG-THR-ARG-LYS REMARK 210 -GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO, 1.2 MM RNA (29-MER), 0.01 MM REMARK 210 EDTA, 20 MM POTASSIUM PHOSPHATE, 10 MM SODIUM CHLORIDE, 95% H2O/ REMARK 210 5% D2O; 1.7 MM DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE- REMARK 210 DPR-PRO, 1.2 MM RNA (29-MER), 0.01 MM EDTA, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 10 MM SODIUM CHLORIDE, 100% D2O; 1.5 MM DAB-VAL-ARG- REMARK 210 THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO, 1.0 MM [U-99% 13C; REMARK 210 U-99% 15N] RNA (29-MER), 0.01 MM EDTA, 20 MM POTASSIUM PHOSPHATE, REMARK 210 10 MM SODIUM CHLORIDE, 95% H2O/5% D2O; 1.5 MM DAB-VAL-ARG-THR- REMARK 210 ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO, 1.0 MM [U-99% 13C; U-99% REMARK 210 15N] RNA (29-MER), 0.01 MM EDTA, 20 MM POTASSIUM PHOSPHATE, 10 REMARK 210 MM SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE II; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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: 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 O2' U B 23 H1' U B 25 1.52 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 8 DPR A 13 C - N - CD ANGL. DEV. = -14.3 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 A 6 59.96 9.23 REMARK 500 1 DPR A 13 -97.78 47.41 REMARK 500 2 LYS A 6 55.50 39.00 REMARK 500 2 DPR A 13 -108.00 49.71 REMARK 500 3 LYS A 6 71.12 1.95 REMARK 500 3 DPR A 13 -107.46 48.86 REMARK 500 4 LYS A 6 78.03 -39.89 REMARK 500 4 ILE A 12 78.76 -109.54 REMARK 500 4 DPR A 13 -106.79 51.39 REMARK 500 5 LYS A 6 76.92 -48.48 REMARK 500 5 ILE A 10 -168.63 -129.94 REMARK 500 5 DPR A 13 -83.75 25.33 REMARK 500 6 LYS A 6 73.81 13.03 REMARK 500 6 DPR A 13 -105.16 46.19 REMARK 500 7 LYS A 6 75.95 -49.17 REMARK 500 7 DPR A 13 -104.09 45.20 REMARK 500 8 LYS A 6 78.76 29.29 REMARK 500 8 DPR A 13 -107.31 49.13 REMARK 500 9 LYS A 6 81.51 -43.24 REMARK 500 9 DPR A 13 -106.23 46.55 REMARK 500 10 LYS A 6 73.03 33.79 REMARK 500 10 ILE A 12 79.61 -109.54 REMARK 500 10 DPR A 13 -106.02 49.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30452 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF A ULTRA-HIGH AFFINITY MACROCYCLE BOUND TO HIV- REMARK 900 1 TAR RNA DBREF 6D2U A 1 14 PDB 6D2U 6D2U 1 14 DBREF 6D2U B 17 45 PDB 6D2U 6D2U 17 45 SEQRES 1 A 14 DAB VAL ARG THR ARG LYS GLY ARG ARG ILE 4J5 ILE DPR SEQRES 2 A 14 PRO SEQRES 1 B 29 G G C A G A U C U G A G C SEQRES 2 B 29 C U G G G A G C U C U C U SEQRES 3 B 29 G C C HET DAB A 1 16 HET 4J5 A 11 21 HET DPR A 13 14 HETNAM DAB 2,4-DIAMINOBUTYRIC ACID HETNAM 4J5 AMINO{[(3S)-3-AMINO-3-CARBOXYPROPYL]AMINO}METHANIMINIUM HETNAM DPR D-PROLINE FORMUL 1 DAB C4 H10 N2 O2 FORMUL 1 4J5 C5 H13 N4 O2 1+ FORMUL 1 DPR C5 H9 N O2 SHEET 1 AA1 2 VAL A 2 ARG A 5 0 SHEET 2 AA1 2 ARG A 8 4J5 A 11 -1 O ARG A 8 N ARG A 5 LINK C DAB A 1 N VAL A 2 1555 1555 1.34 LINK N DAB A 1 C PRO A 14 1555 1555 1.33 LINK C ILE A 10 N 4J5 A 11 1555 1555 1.33 LINK C 4J5 A 11 N ILE A 12 1555 1555 1.32 LINK C ILE A 12 N DPR A 13 1555 1555 1.32 LINK C DPR A 13 N PRO A 14 1555 1555 1.33 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 HETATM 1 N DAB A 1 -3.350 -9.223 -2.869 1.00 0.00 N HETATM 2 CA DAB A 1 -3.350 -8.028 -3.720 1.00 0.00 C HETATM 3 C DAB A 1 -1.935 -7.494 -3.924 1.00 0.00 C HETATM 4 O DAB A 1 -1.063 -7.674 -3.067 1.00 0.00 O HETATM 5 CB DAB A 1 -4.210 -6.941 -3.076 1.00 0.00 C HETATM 6 CG DAB A 1 -5.652 -7.436 -2.958 1.00 0.00 C HETATM 7 ND DAB A 1 -6.064 -8.068 -4.243 1.00 0.00 N HETATM 8 H1 DAB A 1 -3.082 -9.140 -1.919 1.00 0.00 H HETATM 9 HA DAB A 1 -3.771 -8.279 -4.683 1.00 0.00 H HETATM 10 HB2 DAB A 1 -3.826 -6.714 -2.092 1.00 0.00 H HETATM 11 HB3 DAB A 1 -4.185 -6.051 -3.686 1.00 0.00 H HETATM 12 HG2 DAB A 1 -5.720 -8.162 -2.162 1.00 0.00 H HETATM 13 HG3 DAB A 1 -6.305 -6.602 -2.742 1.00 0.00 H HETATM 14 HD1 DAB A 1 -5.977 -9.101 -4.164 1.00 0.00 H HETATM 15 HD2 DAB A 1 -5.451 -7.726 -5.010 1.00 0.00 H HETATM 16 HD3 DAB A 1 -7.051 -7.819 -4.453 1.00 0.00 H