HEADER RNA 08-SEP-20 7K1Z OBSLTE 17-MAR-21 7K1Z 7LVA TITLE SOLUTION STRUCTURE OF THE HIV-1 PBS-SEGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (103-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_TAXID: 11676 KEYWDS PRIMER BINDING SITE, REVERSE TRANSCRIPTION, RNA EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 10 AUTHOR X.HENG,Z.SONG REVDAT 2 17-MAR-21 7K1Z 1 OBSLTE REVDAT 1 23-SEP-20 7K1Z 0 JRNL AUTH Z.SONG,X.HENG JRNL TITL STRUCTURE OF THE HIV-1 PBS-SEGMENT IS CONSERVED FOR VIRAL JRNL TITL 2 INFECTIVITY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, X-PLOR NIH REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), SCHWIETERS, REMARK 3 KUSZEWSKI, TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE SAXS SCATTERING DATA OF STRUCTURES REMARK 3 WERE BACK CALCULATED THE STRUCTURES WITH LOWEST CHI^2 COMPARED REMARK 3 WITH EXPERIMENTAL SAXS DATA WERE FILTERED REMARK 4 REMARK 4 7K1Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1000248263. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 3 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 250 UM RNA (103-MER), 100% D2O; REMARK 210 250 UM A-8D, C-D, G-H, U-5,6-D2 REMARK 210 RNA (103-MER), 100% D2O; 250 UM REMARK 210 A-8D, C-D, G-8D, U-H RNA (103- REMARK 210 MER), 100% D2O; 250 UM A-8D, C-5, REMARK 210 6-D2, G-D, U-5,6-D2 RNA (103-MER) REMARK 210 , 100% D2O; 250 UM A-8D, C-D, G- REMARK 210 8D, U-D RNA (103-MER), 100% D2O; REMARK 210 250 UM A-H, C-D, G-H, U-D RNA REMARK 210 (103-MER), 100% D2O; 250 UM A-H, REMARK 210 C-H, G-D, U-D RNA (103-MER), 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRDRAW, NMRVIEW, CYANA REMARK 210 METHOD USED : NA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1200 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 265 REMARK 265 EXPERIMENTAL DETAILS 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 1 C A 125 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 127 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 132 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 132 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 132 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 A A 133 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 133 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 133 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 C A 134 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 A A 136 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 136 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 136 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 138 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 138 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 138 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 A A 140 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 140 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 A A 140 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 U A 141 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 C A 142 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 1 C A 143 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 C A 144 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 C A 146 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 147 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 147 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 147 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 A A 149 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 149 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 C A 150 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 C A 151 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 C A 152 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 A A 157 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 157 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 157 N1 - C6 - N6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 C A 160 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 161 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A A 161 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 161 N1 - C6 - N6 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 A A 168 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 A A 168 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 168 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 A A 169 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 169 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 169 N1 - C6 - N6 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 A A 170 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 170 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 A A 170 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 A A 171 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A A 171 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 A A 171 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1101 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 142 0.06 SIDE CHAIN REMARK 500 1 A A 180 0.07 SIDE CHAIN REMARK 500 1 G A 183 0.06 SIDE CHAIN REMARK 500 1 G A 184 0.06 SIDE CHAIN REMARK 500 1 A A 203 0.05 SIDE CHAIN REMARK 500 2 C A 142 0.06 SIDE CHAIN REMARK 500 2 A A 180 0.07 SIDE CHAIN REMARK 500 2 G A 183 0.06 SIDE CHAIN REMARK 500 3 C A 142 0.06 SIDE CHAIN REMARK 500 3 A A 180 0.07 SIDE CHAIN REMARK 500 3 G A 183 0.06 SIDE CHAIN REMARK 500 3 A A 203 0.05 SIDE CHAIN REMARK 500 4 U A 182 0.07 SIDE CHAIN REMARK 500 4 G A 184 0.05 SIDE CHAIN REMARK 500 4 G A 212 0.07 SIDE CHAIN REMARK 500 5 C A 143 0.06 SIDE CHAIN REMARK 500 5 A A 180 0.06 SIDE CHAIN REMARK 500 5 A A 203 0.07 SIDE CHAIN REMARK 500 6 G A 184 0.06 SIDE CHAIN REMARK 500 6 G A 186 0.06 SIDE CHAIN REMARK 500 6 C A 187 0.06 SIDE CHAIN REMARK 500 6 A A 203 0.07 SIDE CHAIN REMARK 500 6 G A 212 0.06 SIDE CHAIN REMARK 500 7 C A 143 0.06 SIDE CHAIN REMARK 500 7 A A 180 0.06 SIDE CHAIN REMARK 500 7 A A 203 0.06 SIDE CHAIN REMARK 500 8 A A 180 0.06 SIDE CHAIN REMARK 500 8 G A 184 0.05 SIDE CHAIN REMARK 500 8 C A 187 0.06 SIDE CHAIN REMARK 500 9 G A 184 0.06 SIDE CHAIN REMARK 500 9 C A 187 0.06 SIDE CHAIN REMARK 500 10 U A 182 0.06 SIDE CHAIN REMARK 500 10 G A 183 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 50230 RELATED DB: BMRB REMARK 900 THE LIST OF ASSIGNED CHEMICAL SHIT REMARK 900 RELATED ID: SASDJU7 RELATED DB: SASBDB REMARK 900 SASDJU7 CONTAINS THE SAXS DATA OF THE SAME RNA MOLECULE. REMARK 900 RELATED ID: 30794 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE HIV-1 PBS-SEGMENT DBREF 7K1Z A 123 225 PDB 7K1Z 7K1Z 123 225 SEQRES 1 A 103 G G C U C U G G U A A C U SEQRES 2 A 103 A G A G A U C C C U C A G SEQRES 3 A 103 A C C C U U U U A G U C A SEQRES 4 A 103 G U G U G G A A A A U C U SEQRES 5 A 103 C U A G C A G U G G C G C SEQRES 6 A 103 C C G A A C A G G G A C U SEQRES 7 A 103 U G A A A G C G A A A G U SEQRES 8 A 103 A A A G C C A G A G C 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