HEADER RNA BINDING PROTEIN/RNA 14-JAN-09 2KDQ TITLE SIMULTANEOUS RECOGNITION OF HIV-1 TAR RNA BULGE AND LOOP SEQUENCES BY TITLE 2 CYCLIC PEPTIDE MIMIC OF TAT PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-22 CYCLIC PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HIV-1 TAR RNA; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE L-22 PEPTIDE WAS SYNTHESIZED BY SOLID PHASE SOURCE 4 SYNTHESIS AND PURIFIED BY REVERSE PHASE HPLC; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: RNA WAS TRANSCRIBED IN VITRO FROM DNA OLIGONUCLEOTIDE SOURCE 8 TEMPLATES WITH T7 RNA POLYMERASE PURIFIED IN HOUSE WITH UNLABELED OR SOURCE 9 13C/15N ENRICHED NTPS (ISOTEC) AND PURIFIED BY DENATURING PAGE. KEYWDS PEPTIDOMIMETICS, PEPTIDE STRUCTURE, RNA RECOGNITION, IMMUNODEFICIENCY KEYWDS 2 VIRUS, TAR RNA, MIMIC OF RNA BINDING PROTEIN, RNA BINDING PROTEIN- KEYWDS 3 RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.DAVIDSON,T.C.LEEPER,G.VARANI REVDAT 5 30-OCT-24 2KDQ 1 REMARK REVDAT 4 16-MAR-22 2KDQ 1 REMARK DBREF LINK REVDAT 3 28-JUL-09 2KDQ 1 JRNL REVDAT 2 21-JUL-09 2KDQ 1 JRNL REVDAT 1 23-JUN-09 2KDQ 0 JRNL AUTH A.DAVIDSON,T.C.LEEPER,Z.ATHANASSIOU,K.PATORA-KOMISARSKA, JRNL AUTH 2 J.KARN,J.A.ROBINSON,G.VARANI JRNL TITL SIMULTANEOUS RECOGNITION OF HIV-1 TAR RNA BULGE AND LOOP JRNL TITL 2 SEQUENCES BY CYCLIC PEPTIDE MIMICS OF TAT PROTEIN JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 11931 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19584251 JRNL DOI 10.1073/PNAS.0900629106 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.16.0, X-PLOR NIH 2.16.0 REMARK 3 AUTHORS : C.D. SCHWIETERS, J.J. KUSZEWSKI, N. TJANDRA AND REMARK 3 G.M. CLORE (X-PLOR NIH), C.D. SCHWIETERS, J.J. REMARK 3 KUSZEWSKI, N. TJANDRA AND G.M. CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES OF THE HIV-1 TAR RNA/L-22 REMARK 3 COMPLEX WERE CALCULATED WITH XPLOR-NIH. BACKBONE DIHEDRAL ANGLE REMARK 3 RESTRAINTS FOR THE PEPTIDE WERE ESTIMATED USING CHEMICAL SHIFT REMARK 3 DATA AND TALOS. STRUCTURES WERE ORIGINALLY CALCULATED WITHOUT REMARK 3 RDCS TO TEST FOR CONVERGENCE AND ADHERENCE TO THE NOE DATA. RDC REMARK 3 RESTRAINTS WERE THEN APPLIED AS SUSCEPTIBILITY ANISOTROPY REMARK 3 RESTRAINTS WITH A HARMONIC POTENTIAL WELL. REMARK 4 REMARK 4 2KDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100993. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 277 REMARK 210 PH : 6.6; 6.6 REMARK 210 IONIC STRENGTH : 10 MM POTASSIUM PHOSPHATE; 10 MM REMARK 210 POTASSIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0MM HIV-1 TAR RNA-1, 1.0MM L REMARK 210 -22 CYCLIC PEPTIDE-2, 100% D2O; REMARK 210 1.0MM HIV-1 TAR RNA-3, 1.0MM L- REMARK 210 22 CYCLIC PEPTIDE-4, 90 % H2O, REMARK 210 10% D2O; 1.0MM [U-98% 13C; U-98% REMARK 210 15N] HIV-1 TAR RNA-5, 1.0MM L-22 REMARK 210 CYCLIC PEPTIDE-6, 100% D2O; REMARK 210 1.0MM [U-98% 13C; U-98% 15N] HIV- REMARK 210 1 TAR RNA-7, 1.0MM L-22 CYCLIC REMARK 210 PEPTIDE-8, 90 % H2O, 10% D2O; REMARK 210 1.0MM [U-2H] HIV-1 TAR RNA-9, REMARK 210 1.0MM L-22 CYCLIC PEPTIDE-10, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D-13C HMQC NOESY, 3D HCCH REMARK 210 TOCSY, IPAP-HSQC; 15N HSQC; 2D REMARK 210 NOESY; 2D WATERGATE NOESY; REMARK 210 F1FF2F-TYPE NOESY, F1FF2F-TYPE REMARK 210 TOCSY, 2D HCCH-COSY; 2D 1H-1H REMARK 210 NOESY; F1FF2F-TYPE WATERGATE REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX; INOVA; AVIII REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, TOPSPIN, TALOS, SPARKY 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 : LOWEST ENERGY, LEAST RESTRAINT REMARK 210 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: 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 H3' C B 24 H5' U B 25 1.25 REMARK 500 H4' G B 32 H5' G B 33 1.29 REMARK 500 H2' A B 27 H8 G B 28 1.30 REMARK 500 HH21 ARG A 1 HH12 ARG A 3 1.34 REMARK 500 HO2' G B 34 OP1 A B 35 1.42 REMARK 500 OP1 C B 24 HO2' U B 25 1.47 REMARK 500 O ARG A 5 H ARG A 8 1.50 REMARK 500 HO2' G B 18 O4' C B 19 1.52 REMARK 500 N1 A B 20 H3 U B 42 1.53 REMARK 500 O4 U B 23 H62 A B 27 1.55 REMARK 500 OP2 U B 31 HO2' G B 32 1.56 REMARK 500 H4' G B 33 O5' G B 34 1.56 REMARK 500 O ARG A 9 H2' G B 34 1.58 REMARK 500 H3 U B 23 N7 A B 27 1.59 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 3 G B 34 C4' G B 34 C3' 0.090 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 C B 24 C5' - C4' - C3' ANGL. DEV. = -8.4 DEGREES REMARK 500 3 A B 35 C5' - C4' - C3' ANGL. DEV. = -10.9 DEGREES REMARK 500 5 U B 23 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 6 U B 23 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 6 G B 34 C5' - C4' - C3' ANGL. DEV. = -8.4 DEGREES REMARK 500 10 C B 24 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 10 G B 33 C5' - C4' - C3' ANGL. DEV. = -8.6 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 2 DPR A 13 -108.43 58.61 REMARK 500 3 LYS A 6 27.64 40.88 REMARK 500 4 LYS A 6 28.45 40.54 REMARK 500 4 DPR A 13 -108.72 59.49 REMARK 500 5 ARG A 9 93.62 -65.91 REMARK 500 6 LYS A 6 29.30 40.04 REMARK 500 7 LYS A 6 29.13 38.71 REMARK 500 8 LYS A 6 43.71 38.61 REMARK 500 9 LYS A 6 28.17 42.89 REMARK 500 9 DPR A 13 -103.56 56.21 REMARK 500 10 LYS A 6 25.71 45.42 REMARK 500 10 DPR A 13 -105.53 48.71 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 8 G B 34 0.06 SIDE CHAIN REMARK 500 9 G B 34 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2A9X RELATED DB: PDB REMARK 900 BIV TAR AND CYCLIC PEPTIDE MIMICKING BIV TAT REMARK 900 RELATED ID: 2NS4 RELATED DB: PDB REMARK 900 UNBOUND L-22 SOLUTION STRUCTURE DBREF 2KDQ A 1 14 PDB 2KDQ 2KDQ 1 14 DBREF 2KDQ B 17 45 PDB 2KDQ 2KDQ 17 45 SEQRES 1 A 14 ARG VAL ARG THR ARG LYS GLY ARG ARG ILE ARG 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 DPR A 13 14 HETNAM DPR D-PROLINE FORMUL 1 DPR C5 H9 N O2 SHEET 1 A 2 VAL A 2 ARG A 5 0 SHEET 2 A 2 ARG A 8 ARG A 11 -1 O ARG A 8 N ARG A 5 LINK N ARG A 1 C PRO A 14 1555 1555 1.31 LINK C ILE A 12 N DPR A 13 1555 1555 1.31 LINK C DPR A 13 N PRO A 14 1555 1555 1.31 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