HEADER RNA BINDING PROTEIN/RNA 08-APR-05 1ZBN TITLE SOLUTION STRUCTURE OF BIV TAR HAIRPIN COMPLEXED TO JDV TAT ARGININE- TITLE 2 RICH MOTIF COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIV MRNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: A4G, U31C; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: JDV TAT PROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: ARGININE-RICH DOMAIN; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN BOVINE SOURCE 4 IMMUNODEFICIENCY VIRUS (BIV).; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN JEMBRANA DISEASE SOURCE 8 VIRUS (JDV). KEYWDS RNA-PEPTIDE COMPLEX, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR V.CALABRO,M.D.DAUGHERTY,A.D.FRANKEL REVDAT 4 02-MAR-22 1ZBN 1 REMARK REVDAT 3 24-FEB-09 1ZBN 1 VERSN REVDAT 2 10-MAY-05 1ZBN 1 JRNL REVDAT 1 19-APR-05 1ZBN 0 JRNL AUTH V.CALABRO,M.D.DAUGHERTY,A.D.FRANKEL JRNL TITL A SINGLE INTERMOLECULAR CONTACT MEDIATES INTRAMOLECULAR JRNL TITL 2 STABILIZATION OF BOTH RNA AND PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 6849 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15857951 JRNL DOI 10.1073/PNAS.0409282102 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.SMITH,V.CALABRO,A.D.FRANKEL REMARK 1 TITL AN RNA-BINDING CHAMELEON REMARK 1 REF MOL.CELL V. 6 1067 2000 REMARK 1 REFN ISSN 1097-2765 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.D.PUGLISI,L.CHEN,S.BLANCHARD,A.D.FRANKEL REMARK 1 TITL SOLUTION STRUCTURE OF A BOVINE IMMUNODEFICIENCY VIRUS REMARK 1 TITL 2 TAT-TAR PEPTIDE-RNA COMPLEX REMARK 1 REF SCIENCE V. 270 1200 1995 REMARK 1 REFN ISSN 0036-8075 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 1.X, CNS 1.1 REMARK 3 AUTHORS : GUENTERT (CYANA), BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 STRUCTURES WERE CALCULATED BEGINNING WITH 1,000 RANDOM STRUCTURES REMARK 3 AND INCREMENTALLY ADDING DISTANCE CONSTRAINTS IN FOUR ITERATIONS. REMARK 3 THE FINAL 30 STRUCTURES WITH THE LOWEST NUMBER OF VIOLATIONS WERE REMARK 3 SUBJECTED TO RMD. REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 700 DISTANCE CONSTRAINTS, REMARK 3 61 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1ZBN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032536. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 290; 285; 300 REMARK 210 PH : 6.5; 6.5; 6.5 REMARK 210 IONIC STRENGTH : 50MM NACL, 10MM SODIUM REMARK 210 PHOSPHATE; 50MM NACL, 10MM REMARK 210 SODIUM PHOSPHATE; 50MM NACL, REMARK 210 10MM SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM RNA, 1.5MM PEPTIDE, 90% REMARK 210 H2O, 10% D2O; 1.5MM RNA, 1.5MM REMARK 210 PEPTIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D TOCSY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE NA, SPARKY 3 REMARK 210 METHOD USED : DISTANCE GEOMETRY AND RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 O4 U A 13 H61 A A 18 1.44 REMARK 500 H61 A A 10 O4 U A 21 1.45 REMARK 500 H1' U A 7 O5' G A 8 1.50 REMARK 500 O2' C A 23 H8 G A 24 1.57 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 ARG B 2 84.19 -58.29 REMARK 500 1 ARG B 3 -178.47 -177.04 REMARK 500 1 LYS B 5 100.77 28.66 REMARK 500 1 ARG B 6 -58.01 -163.60 REMARK 500 1 LYS B 11 43.30 -163.60 REMARK 500 1 LYS B 14 171.91 64.11 REMARK 500 1 HIS B 16 90.56 35.02 REMARK 500 2 ARG B 3 139.63 62.56 REMARK 500 2 LYS B 4 38.24 34.62 REMARK 500 2 ARG B 6 -51.55 -151.20 REMARK 500 2 LYS B 11 36.32 113.68 REMARK 500 2 LYS B 14 158.50 -36.27 REMARK 500 2 HIS B 16 80.61 -152.31 REMARK 500 3 ARG B 3 -174.33 179.96 REMARK 500 3 LYS B 5 -156.11 44.84 REMARK 500 3 ARG B 6 -62.54 76.17 REMARK 500 3 LYS B 11 38.24 105.95 REMARK 500 3 LYS B 14 168.63 47.31 REMARK 500 4 ARG B 2 153.49 72.56 REMARK 500 4 ARG B 3 179.01 94.65 REMARK 500 4 LYS B 5 114.75 24.50 REMARK 500 4 ARG B 6 -50.12 -178.43 REMARK 500 4 LYS B 11 45.68 -163.39 REMARK 500 4 LYS B 14 170.36 44.64 REMARK 500 4 HIS B 16 86.52 9.86 REMARK 500 5 ARG B 2 113.74 33.07 REMARK 500 5 ARG B 3 147.27 72.19 REMARK 500 5 ARG B 6 -49.79 -132.05 REMARK 500 5 LYS B 11 45.76 -166.25 REMARK 500 5 LYS B 14 169.63 45.42 REMARK 500 5 HIS B 16 86.11 11.64 REMARK 500 6 ARG B 2 126.54 50.95 REMARK 500 6 ARG B 3 132.35 70.59 REMARK 500 6 ARG B 6 -51.18 -176.64 REMARK 500 6 ARG B 9 30.13 -96.72 REMARK 500 6 LYS B 11 38.66 104.09 REMARK 500 6 LYS B 14 158.72 64.28 REMARK 500 6 HIS B 16 89.36 21.07 REMARK 500 7 ARG B 2 78.55 -9.16 REMARK 500 7 ARG B 3 106.74 173.19 REMARK 500 7 LYS B 4 40.47 38.22 REMARK 500 7 ARG B 6 -48.05 179.09 REMARK 500 7 LYS B 11 38.14 104.11 REMARK 500 7 LYS B 14 163.97 53.91 REMARK 500 7 HIS B 16 83.75 -158.46 REMARK 500 8 ARG B 3 -145.11 81.09 REMARK 500 8 LYS B 4 -44.45 -23.55 REMARK 500 8 LYS B 5 76.38 10.66 REMARK 500 8 ARG B 6 -54.64 -135.66 REMARK 500 8 LYS B 11 38.47 102.89 REMARK 500 REMARK 500 THIS ENTRY HAS 69 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BIV RELATED DB: PDB REMARK 900 THE SAME RNA COMPLEXED WITH BIV TAT (65-81) ARGININE-RICH DOMAIN REMARK 900 RELATED ID: 1MNB RELATED DB: PDB REMARK 900 THE SAME RNA COMPLEXED WITH BIV TAT (68-81) ARGININE-RICH DOMAIN DBREF 1ZBN A 1 28 PDB 1ZBN 1ZBN 1 28 DBREF 1ZBN B 1 17 PDB 1ZBN 1ZBN 1 17 SEQRES 1 A 28 G G C U C G U G U A G C U SEQRES 2 A 28 C A U U A G C U C C G A G SEQRES 3 A 28 C C SEQRES 1 B 17 GLY ARG ARG LYS LYS ARG GLY THR ARG GLY LYS GLY ARG SEQRES 2 B 17 LYS ILE HIS TYR 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