HEADER RNA BINDING PROTEIN/RNA 26-APR-10 2KX5 TITLE RECOGNITION OF HIV TAR RNA BY PEPTIDE MIMETIC OF TAT PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV TAR RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HIV-1 TAR RNA HAIRPIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CYCLIC PEPTIDE MIMETIC OF TAT PROTEIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: KP-Z-41; COMPND 10 ENGINEERED: YES; COMPND 11 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS HIV-1 TAR, TAT, RNA RECOGNITION, IMMUNODEFICIENCY VIRUS; TAR RNA, RNA KEYWDS 2 BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.DAVIDSON,K.PATORA-KOMISARSKA,J.ROBINSON,G.VARANI REVDAT 3 26-JAN-11 2KX5 1 JRNL REVDAT 2 29-SEP-10 2KX5 1 JRNL REMARK REVDAT 1 07-JUL-10 2KX5 0 JRNL AUTH A.DAVIDSON,K.PATORA-KOMISARSKA,J.A.ROBINSON,G.VARANI JRNL TITL ESSENTIAL STRUCTURAL REQUIREMENTS FOR SPECIFIC RECOGNITION JRNL TITL 2 OF HIV TAR RNA BY PEPTIDE MIMETICS OF TAT PROTEIN. JRNL REF NUCLEIC ACIDS RES. V. 39 248 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 20724442 JRNL DOI 10.1093/NAR/GKQ713 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 2KX5 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB101683. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277; 298 REMARK 210 PH : 6.6; 6.6 REMARK 210 IONIC STRENGTH : 0.01; 0.01 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM HIV-1 TAR/KP-Z-41-1, 100% REMARK 210 D2O; 1 MM HIV-1 TAR/KP-Z-41-2, REMARK 210 90% H2O/10% D2O; 1 MM [U-98% 13C; REMARK 210 U-98% 15N] HIV-1 TAR/KP-Z-41-3, REMARK 210 100% D2O; 1 MM [U-2H] HIV-1 TAR/ REMARK 210 KP-Z-41-4, 100% D2O; 1 MM [U-98% REMARK 210 13C; U-98% 15N] HIV-1 TAR/KP-Z- REMARK 210 41-5, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H NOESY; 3D HCCH-TOCSY; 3D REMARK 210 1H-13C NOESY; 2D F1FF2F NOESY; 2D REMARK 210 F1FF2F TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR_NIH, NMRPIPE, 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 : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS AND 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 H22 G A 32 HO2' G A 33 1.40 REMARK 500 H21 G A 32 HH11 ARG B 10 1.46 REMARK 500 OP1 C A 24 H2' U A 25 1.56 REMARK 500 H4' U A 23 OP1 G A 26 1.58 REMARK 500 H ARG B 7 O ARG B 10 1.70 REMARK 500 H ARG B 5 O ILE B 12 1.72 REMARK 500 O ARG B 3 H ILE B 14 1.73 REMARK 500 O ARG B 5 H ILE B 12 1.73 REMARK 500 O2' U A 31 H5' G A 32 1.73 REMARK 500 O ARG B 1 H ILE B 16 1.73 REMARK 500 H ARG B 3 O ILE B 14 1.75 REMARK 500 H1 ARG B 1 O ILE B 16 1.75 REMARK 500 N1 A A 27 H3 U A 38 1.76 REMARK 500 OP2 G A 21 HE ARG B 3 1.76 REMARK 500 O2' G A 34 H5' A A 35 1.76 REMARK 500 N1 A A 20 H3 U A 42 1.77 REMARK 500 H3 U A 23 N7 A A 27 1.77 REMARK 500 O LYS B 8 H ARG B 10 1.77 REMARK 500 N2 G A 32 HH11 ARG B 10 1.78 REMARK 500 N1 A A 22 H3 U A 40 1.81 REMARK 500 H5'' C A 24 OP2 A A 27 1.83 REMARK 500 H21 G A 28 O2 C A 37 1.86 REMARK 500 H21 G A 18 O2 C A 44 1.87 REMARK 500 H21 G A 17 O2 C A 45 1.87 REMARK 500 H1 G A 26 N3 C A 39 1.88 REMARK 500 H21 G A 21 O2 C A 41 1.88 REMARK 500 O2 C A 19 H21 G A 43 1.89 REMARK 500 H41 C A 29 O6 G A 36 1.89 REMARK 500 H1 G A 21 N3 C A 41 1.89 REMARK 500 O6 G A 17 H41 C A 45 1.90 REMARK 500 O6 G A 28 H41 C A 37 1.90 REMARK 500 N3 C A 19 H1 G A 43 1.91 REMARK 500 H61 A A 27 O4 U A 38 1.91 REMARK 500 O6 G A 18 H41 C A 44 1.92 REMARK 500 H1 G A 18 N3 C A 44 1.92 REMARK 500 C LYS B 8 H ARG B 10 1.93 REMARK 500 H21 G A 26 O2 C A 39 1.93 REMARK 500 H1 G A 28 N3 C A 37 1.93 REMARK 500 O6 G A 21 H41 C A 41 1.93 REMARK 500 H1 G A 17 N3 C A 45 1.94 REMARK 500 H41 C A 19 O6 G A 43 1.94 REMARK 500 O2' G A 21 H5' A A 22 1.94 REMARK 500 O2' A A 27 H5' G A 28 1.95 REMARK 500 H61 A A 20 O4 U A 42 1.95 REMARK 500 O2 C A 29 H21 G A 36 1.96 REMARK 500 OP2 A A 22 HH22 ARG B 3 1.96 REMARK 500 O2' G A 28 H5' C A 29 1.97 REMARK 500 O2' A A 22 H5' U A 23 1.97 REMARK 500 N3 C A 29 H1 G A 36 1.98 REMARK 500 H61 A A 22 O4 U A 40 1.98 REMARK 500 REMARK 500 THIS ENTRY HAS 771 CLOSE CONTACTS 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 2 G A 43 C4' G A 43 C3' 0.101 REMARK 500 5 G A 43 C4' G A 43 C3' 0.074 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 2 G A 43 O4' - C4' - C3' ANGL. DEV. = -6.0 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 DPR B 17 -94.09 30.65 REMARK 500 2 LYS B 8 45.32 32.96 REMARK 500 2 DPR B 17 -90.74 28.76 REMARK 500 4 DPR B 17 -92.18 28.47 REMARK 500 5 DPR B 17 -92.30 28.86 REMARK 500 6 DPR B 17 -94.47 30.10 REMARK 500 7 LYS B 8 45.12 36.65 REMARK 500 7 DPR B 17 -130.20 38.44 REMARK 500 8 DPR B 17 -94.61 30.29 REMARK 500 9 LYS B 8 64.13 60.31 REMARK 500 9 DPR B 17 -128.63 38.53 REMARK 500 10 DPR B 17 -94.89 30.00 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 C A 39 0.08 SIDE CHAIN REMARK 500 2 C A 39 0.08 SIDE CHAIN REMARK 500 3 C A 39 0.07 SIDE CHAIN REMARK 500 4 C A 39 0.07 SIDE CHAIN REMARK 500 5 C A 39 0.08 SIDE CHAIN REMARK 500 6 C A 39 0.09 SIDE CHAIN REMARK 500 7 C A 39 0.07 SIDE CHAIN REMARK 500 8 C A 39 0.07 SIDE CHAIN REMARK 500 9 C A 39 0.07 SIDE CHAIN REMARK 500 10 C A 39 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KDQ RELATED DB: PDB REMARK 900 HIV-1 AND PEPTIDE MIMIC OF TAT PROTEIN REMARK 900 RELATED ID: 2A9X RELATED DB: PDB REMARK 900 BIV TAR AND BIV TAT MIMIC DBREF 2KX5 A 17 45 PDB 2KX5 2KX5 17 45 DBREF 2KX5 B 1 18 PDB 2KX5 2KX5 1 18 SEQRES 1 A 29 G G C A G A U C U G A G C SEQRES 2 A 29 C U G G G A G C U C U C U SEQRES 3 A 29 G C C SEQRES 1 B 18 ARG VAL ARG CYS ARG GLN ARG LYS GLY ARG ARG ILE CYS SEQRES 2 B 18 ILE ARG ILE DPR PRO HET DPR B 17 14 HETNAM DPR D-PROLINE FORMUL 2 DPR C5 H9 N O2 SHEET 1 A 2 VAL B 2 ARG B 7 0 SHEET 2 A 2 ARG B 10 ARG B 15 -1 O ARG B 10 N ARG B 7 SSBOND 1 CYS B 4 CYS B 13 1555 1555 2.02 LINK C DPR B 17 N PRO B 18 1555 1555 1.30 LINK N ARG B 1 C PRO B 18 1555 1555 1.33 LINK C ILE B 16 N DPR B 17 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 235 0 1 0 2 0 0 6 0 0 0 5 END