PDB Short entry for 1JU1 HEADER RNA 23-AUG-01 1JU1 TITLE DIMER INITIATION SEQUENCE OF HIV-1LAI GENOMIC RNA: NMR SOLUTION TITLE 2 STRUCTURE OF THE EXTENDED DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1LAI SL1; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS HIV, DIMER INITIATION SEQUENCE, SL1, RNA, EXTENDED DUPLEX, STABLE KEYWDS 2 DIMER EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR F.GIRARD,F.BARBAULT,G.LANCELOT REVDAT 3 23-FEB-22 1JU1 1 REMARK REVDAT 2 24-FEB-09 1JU1 1 VERSN REVDAT 1 23-AUG-02 1JU1 0 JRNL AUTH F.GIRARD,F.BARBAULT,C.GOUYETTE,T.HUYNH-DINH,J.PAOLETTI, JRNL AUTH 2 G.LANCELOT JRNL TITL DIMER INITIATION SEQUENCE OF HIV-1LAI GENOMIC RNA: NMR JRNL TITL 2 SOLUTION STRUCTURE OF THE EXTENDED DUPLEX. JRNL REF J.BIOMOL.STRUCT.DYN. V. 16 1145 1999 JRNL REFN ISSN 0739-1102 JRNL PMID 10447199 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JU1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-AUG-01. REMARK 100 THE DEPOSITION ID IS D_1000014184. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 288 REMARK 210 PH : 5.8; 5.8 REMARK 210 IONIC STRENGTH : 100MM NACL; 100MM NACL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM OLIGONUCLEOTIDE, 10MM REMARK 210 PHOSPHATE BUFFER 100 MM NACL; REMARK 210 2MM OLIGONUCLEOTIDE, 10MM REMARK 210 PHOSPHATE BUFFER, 100 MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR, X-PLOR 3.851, CURVES 5.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 15 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM, REMARK 210 STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS, STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 11 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 HO2' G A 10 O5' C A 11 1.53 REMARK 500 HO2' C A 11 O4' G A 12 1.53 REMARK 500 HO2' C B 40 O4' G B 41 1.60 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 1 C B 38 C2' C B 38 C1' -0.050 REMARK 500 2 G A 10 C2' G A 10 C1' -0.050 REMARK 500 2 C A 15 C2' C A 15 C1' -0.053 REMARK 500 2 G B 33 C2' G B 33 C1' -0.053 REMARK 500 2 C B 38 C2' C B 38 C1' -0.049 REMARK 500 2 A B 39 C2' A B 39 C1' -0.050 REMARK 500 3 C A 1 N1 C A 1 C6 -0.039 REMARK 500 3 C B 38 C2' C B 38 C1' -0.049 REMARK 500 4 C A 15 C2' C A 15 C1' -0.049 REMARK 500 4 C B 24 N1 C B 24 C6 -0.037 REMARK 500 4 C B 38 C2' C B 38 C1' -0.053 REMARK 500 5 C A 15 C2' C A 15 C1' -0.052 REMARK 500 5 C B 24 N1 C B 24 C6 -0.036 REMARK 500 5 G B 33 C2' G B 33 C1' -0.048 REMARK 500 5 G B 37 C8 G B 37 N9 -0.042 REMARK 500 5 C B 38 C2' C B 38 C1' -0.054 REMARK 500 5 A B 39 C2' A B 39 C1' -0.053 REMARK 500 6 C A 15 C2' C A 15 C1' -0.051 REMARK 500 6 C B 24 N1 C B 24 C6 -0.040 REMARK 500 7 G B 37 C8 G B 37 N9 -0.043 REMARK 500 7 C B 38 C2' C B 38 C1' -0.051 REMARK 500 8 G A 10 C2' G A 10 C1' -0.049 REMARK 500 8 G A 14 C8 G A 14 N9 -0.043 REMARK 500 8 G B 37 C8 G B 37 N9 -0.043 REMARK 500 8 C B 38 C2' C B 38 C1' -0.054 REMARK 500 9 C A 1 N1 C A 1 C6 -0.037 REMARK 500 9 C B 24 N1 C B 24 C6 -0.037 REMARK 500 9 C B 38 C2' C B 38 C1' -0.049 REMARK 500 10 G A 4 C2' G A 4 C1' -0.053 REMARK 500 10 G A 14 C2' G A 14 C1' -0.051 REMARK 500 10 G B 27 C2' G B 27 C1' -0.049 REMARK 500 10 A B 39 C2' A B 39 C1' -0.075 REMARK 500 11 G B 27 C2' G B 27 C1' -0.049 REMARK 500 12 C A 15 C2' C A 15 C1' -0.051 REMARK 500 12 A B 39 C2' A B 39 C1' -0.069 REMARK 500 15 C A 15 C2' C A 15 C1' -0.048 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 A 1 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 C A 1 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 U A 2 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U A 2 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES REMARK 500 1 U A 3 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES REMARK 500 1 U A 3 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 G A 4 C3' - C2' - C1' ANGL. DEV. = 6.1 DEGREES REMARK 500 1 G A 4 O4' - C1' - N9 ANGL. DEV. = 9.5 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 C A 5 O4' - C1' - N1 ANGL. DEV. = 8.8 DEGREES REMARK 500 1 U A 6 C5' - C4' - O4' ANGL. DEV. = 5.8 DEGREES REMARK 500 1 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 7 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 A A 9 O4' - C1' - N9 ANGL. DEV. = 7.6 DEGREES REMARK 500 1 A A 9 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 1 G A 10 C1' - O4' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 G A 10 O4' - C1' - N9 ANGL. DEV. = 16.9 DEGREES REMARK 500 1 G A 10 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 G A 10 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 1 C A 11 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 1 C A 11 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 C A 11 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 12 C3' - C2' - C1' ANGL. DEV. = 5.8 DEGREES REMARK 500 1 G A 12 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 C A 13 C3' - C2' - C1' ANGL. DEV. = 5.8 DEGREES REMARK 500 1 C A 13 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 C A 13 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 14 C3' - C2' - C1' ANGL. DEV. = 7.2 DEGREES REMARK 500 1 G A 14 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 C A 15 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES REMARK 500 1 C A 15 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 16 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 A A 16 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 A A 16 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 1 C A 17 O4' - C1' - N1 ANGL. DEV. = 11.2 DEGREES REMARK 500 1 G A 18 C3' - C2' - C1' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 G A 18 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 18 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 G A 19 C3' - C2' - C1' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 19 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 G A 19 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 C A 20 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 A A 21 C3' - C2' - C1' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 A A 21 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 1 A A 22 C3' - C2' - C1' ANGL. DEV. = 5.6 DEGREES REMARK 500 1 A A 22 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 1 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 G A 23 O4' - C1' - N9 ANGL. DEV. = 8.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1450 ANGLE DEVIATIONS. 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 1 0.10 SIDE CHAIN REMARK 500 1 G A 4 0.10 SIDE CHAIN REMARK 500 1 C A 5 0.10 SIDE CHAIN REMARK 500 1 U A 6 0.13 SIDE CHAIN REMARK 500 1 A A 8 0.08 SIDE CHAIN REMARK 500 1 G A 10 0.11 SIDE CHAIN REMARK 500 1 C A 11 0.12 SIDE CHAIN REMARK 500 1 G A 12 0.10 SIDE CHAIN REMARK 500 1 C A 13 0.10 SIDE CHAIN REMARK 500 1 G A 14 0.12 SIDE CHAIN REMARK 500 1 C A 15 0.08 SIDE CHAIN REMARK 500 1 C A 17 0.11 SIDE CHAIN REMARK 500 1 G A 18 0.10 SIDE CHAIN REMARK 500 1 G A 19 0.06 SIDE CHAIN REMARK 500 1 C A 20 0.14 SIDE CHAIN REMARK 500 1 G A 23 0.09 SIDE CHAIN REMARK 500 1 C B 24 0.26 SIDE CHAIN REMARK 500 1 U B 25 0.15 SIDE CHAIN REMARK 500 1 U B 26 0.12 SIDE CHAIN REMARK 500 1 G B 27 0.10 SIDE CHAIN REMARK 500 1 C B 28 0.14 SIDE CHAIN REMARK 500 1 U B 29 0.12 SIDE CHAIN REMARK 500 1 G B 30 0.06 SIDE CHAIN REMARK 500 1 A B 31 0.17 SIDE CHAIN REMARK 500 1 A B 32 0.17 SIDE CHAIN REMARK 500 1 G B 33 0.13 SIDE CHAIN REMARK 500 1 C B 34 0.15 SIDE CHAIN REMARK 500 1 G B 35 0.15 SIDE CHAIN REMARK 500 1 C B 36 0.07 SIDE CHAIN REMARK 500 1 C B 38 0.10 SIDE CHAIN REMARK 500 1 A B 39 0.08 SIDE CHAIN REMARK 500 1 C B 40 0.23 SIDE CHAIN REMARK 500 1 C B 43 0.10 SIDE CHAIN REMARK 500 1 G B 46 0.10 SIDE CHAIN REMARK 500 2 C A 1 0.19 SIDE CHAIN REMARK 500 2 U A 2 0.08 SIDE CHAIN REMARK 500 2 G A 4 0.09 SIDE CHAIN REMARK 500 2 C A 5 0.11 SIDE CHAIN REMARK 500 2 U A 6 0.08 SIDE CHAIN REMARK 500 2 G A 7 0.10 SIDE CHAIN REMARK 500 2 A A 8 0.07 SIDE CHAIN REMARK 500 2 A A 9 0.14 SIDE CHAIN REMARK 500 2 G A 10 0.07 SIDE CHAIN REMARK 500 2 C A 11 0.12 SIDE CHAIN REMARK 500 2 G A 12 0.20 SIDE CHAIN REMARK 500 2 G A 14 0.10 SIDE CHAIN REMARK 500 2 C A 15 0.07 SIDE CHAIN REMARK 500 2 A A 16 0.10 SIDE CHAIN REMARK 500 2 C A 17 0.10 SIDE CHAIN REMARK 500 2 G A 18 0.12 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 535 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JTJ RELATED DB: PDB REMARK 900 1JTJ IS THE SOLUTION STRUCTURE OF HIV-1LAI MUTATED SL1 HAIRPIN REMARK 900 RELATED ID: 1JU0 RELATED DB: PDB REMARK 900 1JU0 IS THE NMR SOLUTION STRUCTURE OF A DNA KISSING COMPLEX REMARK 900 RELATED ID: 1JUA RELATED DB: PDB REMARK 900 1JUA IS THE SOLUTION STRUCTURE OF THE DEOXYRIBOSE HIV-1LAI REMARK 900 INITIATION SEQUENCE STABLE DIMER DBREF 1JU1 A 1 23 PDB 1JU1 1JU1 1 23 DBREF 1JU1 B 24 46 PDB 1JU1 1JU1 24 46 SEQRES 1 A 23 C U U G C U G A A G C G C SEQRES 2 A 23 G C A C G G C A A G SEQRES 1 B 23 C U U G C U G A A G C G C SEQRES 2 B 23 G C A C G G C A A G CRYST1 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