HEADER RNA/PEPTIDE 30-JUL-09 2KMJ TITLE HIGH RESOLUTION NMR SOLUTION STRUCTURE OF A COMPLEX OF HIV-2 TAR RNA TITLE 2 AND A SYNTHETIC TRIPEPTIDE IN A 1:2 STOICHIOMETRY COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (28-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: UUCG-TAR RNA; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PYRIMIDINYLPEPTIDE; COMPND 8 CHAIN: B, C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 2; SOURCE 3 ORGANISM_TAXID: 11709; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PUC19; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS RNA-LIGAND COMPLEX, BINDING STOICHIOMETRY, HIV-2 TAR, RNA-PEPTIDE KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.FERNER,M.SUHARTONO,S.BREITUNG,H.R.A.JONKER,M.HENNIG,J.WOEHNERT, AUTHOR 2 M.GOEBEL,H.SCHWALBE REVDAT 4 15-NOV-23 2KMJ 1 ATOM REVDAT 3 16-MAR-22 2KMJ 1 REMARK DBREF LINK REVDAT 2 06-OCT-09 2KMJ 1 AUTHOR JRNL REVDAT 1 18-AUG-09 2KMJ 0 JRNL AUTH J.FERNER,M.SUHARTONO,S.BREITUNG,H.R.A.JONKER,M.HENNIG, JRNL AUTH 2 J.WOHNERT,M.GOBEL,H.SCHWALBE JRNL TITL STRUCTURES OF HIV TAR RNA-LIGAND COMPLEXES REVEAL HIGHER JRNL TITL 2 BINDING STOICHIOMETRIES. JRNL REF CHEMBIOCHEM V. 10 1490 2009 JRNL REFN ISSN 1439-4227 JRNL PMID 19444830 JRNL DOI 10.1002/CBIC.200900220 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, ARIA 1.2, HADDOCK 2.1 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), LINGE, O'DONOGHUE AND REMARK 3 NILGES (ARIA), DOMINGUEZ, BOELENS AND BONVIN REMARK 3 (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KMJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000101305. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 283 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 75; 75 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.65 MM [U-100% 13C; U-100% 15N] REMARK 210 UUCG-TAR-1, 5.2 MM REMARK 210 PYRIMIDINYLPEPTIDE-2, 50 MM REMARK 210 POTASSIUM CHLORIDE-3, 25 MM REMARK 210 POTASSIUM PHOSPHATE-4, 90% H2O/ REMARK 210 10% D2O; 0.65 MM [U-100% 13C; U- REMARK 210 100% 15N] UUCG-TAR-5, 5.2 MM REMARK 210 PYRIMIDINYLPEPTIDE-6, 50 MM REMARK 210 POTASSIUM CHLORIDE-7, 25 MM REMARK 210 POTASSIUM PHOSPHATE-8, 100% D2O; REMARK 210 0.65 MM UUCG-TAR-9, 5.2 MM REMARK 210 PYRIMIDINYLPEPTIDE-10, 50 MM REMARK 210 POTASSIUM CHLORIDE-11, 25 MM REMARK 210 POTASSIUM PHOSPHATE-12, 90% H2O / REMARK 210 10% D2O; 0.65 MM UUCG-TAR-13, REMARK 210 5.2 MM PYRIMIDINYLPEPTIDE-14, 50 REMARK 210 MM POTASSIUM CHLORIDE-15, 25 MM REMARK 210 POTASSIUM PHOSPHATE-16, 100% D2O; REMARK 210 0.2 MM [U-100% 13C; U-100% 15N] REMARK 210 UUCG-TAR-17, 0.8 MM REMARK 210 PYRIMIDINYLPEPTIDE-18, 50 MM REMARK 210 POTASSIUM CHLORIDE-19, 25 MM REMARK 210 POTASSIUM PHOSPHATE-20, 16 MG/ML REMARK 210 PF1 PHAGE-21, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 2D H(C)N; 2D 1H-15N HSQC (2J); REMARK 210 2D HNN-COSY; 2D H5NN-COSY; 3D REMARK 210 FORWARD-DIRECTED HCC-TOCSY-CCH REMARK 210 E.COSY; 2D 1H-15N CPMG-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 700 MHZ; 600 REMARK 210 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, SPARKY 3.114, CNS REMARK 210 1.1 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 : TOP-RANKED ENSEMBLE 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: 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 ZUK B 2 121.78 106.27 REMARK 500 3 ZUK C 2 -78.73 105.99 REMARK 500 4 ZUK B 2 91.21 89.49 REMARK 500 5 ZUK B 2 101.38 89.00 REMARK 500 8 ZUK B 2 93.26 105.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 2KMJ A 16 46 PDB 2KMJ 2KMJ 16 46 DBREF 2KMJ B 1 4 PDB 2KMJ 2KMJ 1 4 DBREF 2KMJ C 1 4 PDB 2KMJ 2KMJ 1 4 SEQRES 1 A 28 G G C C A G A U U G A G C SEQRES 2 A 28 U U C G G C U C U C U G G SEQRES 3 A 28 U C SEQRES 1 B 4 DAR ZUK DAR NH2 SEQRES 1 C 4 DAR ZUK DAR NH2 HET DAR B 1 26 HET ZUK B 2 24 HET DAR B 3 24 HET NH2 B 4 3 HET DAR C 1 26 HET ZUK C 2 24 HET DAR C 3 24 HET NH2 C 4 3 HETNAM DAR D-ARGININE HETNAM ZUK 5-PYRIMIDIN-2-YL-D-NORVALINE HETNAM NH2 AMINO GROUP FORMUL 2 DAR 4(C6 H15 N4 O2 1+) FORMUL 2 ZUK 2(C9 H13 N3 O2) FORMUL 2 NH2 2(H2 N) LINK C DAR B 1 N ZUK B 2 1555 1555 1.33 LINK C ZUK B 2 N DAR B 3 1555 1555 1.33 LINK C DAR B 3 N NH2 B 4 1555 1555 1.33 LINK C DAR C 1 N ZUK C 2 1555 1555 1.33 LINK C ZUK C 2 N DAR C 3 1555 1555 1.33 LINK C DAR C 3 N NH2 C 4 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