HEADER RNA 05-APR-06 2GM0 TITLE LINEAR DIMER OF STEMLOOP SL1 FROM HIV-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (35-MER); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: STEM-LOOP SL1 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 SOURCE 4 RNA POLYMERASE KEYWDS LINEAR DIMER, A-RICH INTERNAL LOOP, G-RICH INTERNAL LOOP, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR N.B.ULYANOV,A.MUJEEB,Z.DU,M.TONELLI,T.G.PARSLOW,T.L.JAMES REVDAT 4 09-MAR-22 2GM0 1 REMARK REVDAT 3 24-FEB-09 2GM0 1 VERSN REVDAT 2 20-JUN-06 2GM0 1 JRNL REVDAT 1 25-APR-06 2GM0 0 JRNL AUTH N.B.ULYANOV,A.MUJEEB,Z.DU,M.TONELLI,T.G.PARSLOW,T.L.JAMES JRNL TITL NMR STRUCTURE OF THE FULL-LENGTH LINEAR DIMER OF STEM-LOOP-1 JRNL TITL 2 RNA IN THE HIV-1 DIMER INITIATION SITE. JRNL REF J.BIOL.CHEM. V. 281 16168 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16603544 JRNL DOI 10.1074/JBC.M601711200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1, DYANA 1.5, MINICARLO REMARK 3 AUTHORS : GUNTERT (DYANA), ZHURKIN & ULYANOV (MINICARLO) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE DETERMINED BASED ON REMARK 3 A TOTAL OF 842 RESTRAINTS; 608 ARE NOE-DERIVED DISTANCE REMARK 3 RESTRAINTS, 104 HYDROGEN BOND RESTRAINTS, AND 130 RESIDUAL REMARK 3 DIPOLAR COUPLING (RDC) RESTRAINTS REMARK 4 REMARK 4 2GM0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037280. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 288 REMARK 210 PH : 6.4; 6.4 REMARK 210 IONIC STRENGTH : 10 MM POTASSIUM PHOSPHATE REMARK 210 BUFFER, 250 MM NACL, 0.1 MM MG REMARK 210 CL2; 10 MM POTASSIUM PHOSPHATE REMARK 210 BUFFER, 250 MM NACL, 0.1 MM MG REMARK 210 CL2 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75 MM UNLABELED SL1 RNA, 10 MM REMARK 210 POTASSIUM PHOSPHATE BUFFER, 250 REMARK 210 MM NACL, 0.1 MM MGCL2, PH 6.4, REMARK 210 D2O; 0.75 MM UNLABELED SL1 RNA, REMARK 210 10 MM POTASSIUM PHOSPHATE BUFFER, REMARK 210 250 MM NACL, 0.1 MM MGCL2,PH REMARK 210 6.4, 90% H2O, 10% D2O; 0.75 MM REMARK 210 OF UNIFORMLY 13C, 15N-LABELED REMARK 210 SL1 RNA, 10 MM POTASSIUM REMARK 210 PHOSPHATE BUFFER, 250 MM NACL, REMARK 210 0.1 MM MGCL2, PH 6.4, D2O; 0.75 REMARK 210 MM OF UNIFORMLY 13C, 15N-LABELED REMARK 210 SL1 RNA, 10 MM POTASSIUM REMARK 210 PHOSPHATE BUFFER, 250 MM NACL, REMARK 210 0.1 MM MGCL2, PH 6.4, 90% H2O, REMARK 210 10% D2O; 0.75 MM OF UNIFORMLY REMARK 210 13C, 15N-LABELED SL1 RNA, 10 MM REMARK 210 POTASSIUM PHOSPHATE BUFFER, 250 REMARK 210 MM NACL, 0.1 MM MGCL2, PH 6.4, REMARK 210 FILAMENTOUS PHAGE PF1, D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_13C REMARK 210 -SEPARATED_NOESY; NON-DECOUPLED REMARK 210 CONSTANT-TIME 1H-13C TROSY-HSQC; REMARK 210 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITY INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, MARDIGRAS 3.21, REMARK 210 SPARKY 3.110 REMARK 210 METHOD USED : RESTRAINED METROPOLIS MONTE REMARK 210 CARLO AND RESTRAINED REMARK 210 MINIMIZATION IN HELICAL REMARK 210 PARAMETER'S SPACE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 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: 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 10 A A 21 C3' - C2' - C1' ANGL. DEV. = 5.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2GM0 A 1 35 PDB 2GM0 2GM0 1 35 DBREF 2GM0 B 36 70 PDB 2GM0 2GM0 36 70 SEQRES 1 A 35 G A C G G C U U G C U G A SEQRES 2 A 35 A G C G C G C A C G G C A SEQRES 3 A 35 A G A G G C G U C SEQRES 1 B 35 G A C G G C U U G C U G A SEQRES 2 B 35 A G C G C G C A C G G C A SEQRES 3 B 35 A G A G G C G U C 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