1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Kerwood, D.J. Cavaluzzi, M.J. Borer, P.N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 C10 H14 N5 O7 P 347.221 y ADENOSINE-5'-MONOPHOSPHATE RNA linking C9 H14 N3 O8 P 323.197 y CYTIDINE-5'-MONOPHOSPHATE RNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking Na 1 22.990 SODIUM ION non-polymer C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking US Biochemistry BICHAW 0033 0006-2960 40 14518 14529 10.1021/bi0111909 11724565 Structure of SL4 RNA from the HIV-1 packaging signal. 2001 10.2210/pdb1jtw/pdb pdb_00001jtw 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M 1 1.0 HIV-1 packaging signal SL4 hairpin 5232.183 5'-R(*GP*GP*GP*UP*GP*CP*GP*AP*GP*AP*GP*CP*GP*UP*CP*A)-3' 1 syn polymer 22.990 SODIUM ION 15 syn non-polymer no no GGGUGCGAGAGCGUCA GGGUGCGAGAGCGUCA A polyribonucleotide n n n n n n n n n n n n n n n n -32.151 1 19 A 2 A 15 2.253 A_G2:C15_A 1 -16.133 -0.913 -0.961 -0.107 -12.564 1 28 A 3 A 14 1.659 A_G3:U14_A 2 -6.252 -1.628 0.228 -0.180 -6.356 1 28 A 4 A 13 -3.046 A_U4:G13_A 3 -8.872 1.604 0.555 -0.325 -2.112 1 19 A 5 A 12 0.114 A_G5:C12_A 4 -20.398 -0.145 -0.141 0.013 2.942 1 19 A 6 A 11 -1.132 A_C6:G11_A 5 -18.263 0.967 -0.144 -0.224 38.355 A 7 A 10 -31.848 A_G7:A10_A 6 10.668 7.488 0.924 -5.208 1.894 24.512 A A 2 3 19.028 A A 15 14 2.791 7.794 0.236 -1.682 AA_G2G3:U14C15_AA 1 -7.880 19.239 21.897 -5.792 -2.405 2.762 42.295 A A 3 4 13.293 A A 14 13 3.175 9.515 -0.102 -1.580 AA_G3U4:G13U14_AA 2 -1.135 1.586 41.244 -3.086 0.035 1.244 30.665 A A 4 5 37.027 A A 13 12 2.879 18.126 -0.259 -1.610 AA_U4G5:C12G13_AA 3 7.247 -14.804 23.765 -5.597 1.510 2.912 38.122 A A 5 6 10.951 A A 12 11 3.089 7.113 0.166 -0.718 AA_G5C6:G11C12_AA 4 0.801 -1.233 37.469 -1.933 -0.160 3.239 45.099 A A 6 7 1.747 A A 11 10 2.405 1.324 -3.647 -1.378 AA_C6G7:A10G11_AA 5 -12.449 16.426 43.414 -1.901 3.771 atom_site database_2 pdbx_nmr_software pdbx_nmr_spectrometer pdbx_struct_assembly pdbx_struct_conn_angle pdbx_struct_oper_list struct_conn struct_site repository Initial release Version format compliance Version format compliance Atomic model Data collection Database references Derived calculations 1 0 2001-12-12 1 1 2008-04-27 1 2 2011-07-13 2 0 2022-02-23 _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_atom_id _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id RCSB Y RCSB 2001-08-22 REL REL NA SODIUM ION This sequence occurs in the packaging signal of HIV-1. sample Sodium ions which were distant from the RNA were removed. structures with the lowest energy 20 14 7.0 K DYANA structures were further refined with the molecular dynamics and minimization program, AMBER. 1 closest to the average ~0.7mM SL4 concentration in buffer: 25mM NaCl, 5mM NaHPO4 (pH 7.0), 0.1mM EDTA, 0.01% NaN3 99.96% D2O or 90% H2O, 10% D2O Wuthrich refinement DYANA 1.5 Kollman structure solution Amber 5 500 Bruker AVANCE 600 Bruker AVANCE NA 17 2 NA NA 17 A NA 18 2 NA NA 18 A NA 19 2 NA NA 19 A NA 20 2 NA NA 20 A NA 21 2 NA NA 21 A NA 22 2 NA NA 22 A NA 23 2 NA NA 23 A NA 24 2 NA NA 24 A NA 25 2 NA NA 25 A NA 26 2 NA NA 26 A NA 27 2 NA NA 27 A NA 28 2 NA NA 28 A NA 29 2 NA NA 29 A NA 30 2 NA NA 30 A NA 31 2 NA NA 31 A G 1 n 1 G 1 A G 2 n 2 G 2 A G 3 n 3 G 3 A U 4 n 4 U 4 A G 5 n 5 G 5 A C 6 n 6 C 6 A G 7 n 7 G 7 A A 8 n 8 A 8 A G 9 n 9 G 9 A A 10 n 10 A 10 A G 11 n 11 G 11 A C 12 n 12 C 12 A G 13 n 13 G 13 A U 14 n 14 U 14 A C 15 n 15 C 15 A A 16 n 16 A 16 A author_defined_assembly 1 monomeric A G 2 A OP2 G 2 1_555 A NA 27 L NA NA 1_555 A G 3 A OP2 G 3 1_555 146.7 A G 3 A O6 G 3 1_555 A NA 18 C NA NA 1_555 A U 4 A O4 U 4 1_555 76.5 A G 3 A O6 G 3 1_555 A NA 18 C NA NA 1_555 A G 13 A O6 G 13 1_555 87.6 A U 4 A O4 U 4 1_555 A NA 18 C NA NA 1_555 A G 13 A O6 G 13 1_555 79.2 A G 3 A O6 G 3 1_555 A NA 18 C NA NA 1_555 A U 14 A O4 U 14 1_555 79.7 A U 4 A O4 U 4 1_555 A NA 18 C NA NA 1_555 A U 14 A O4 U 14 1_555 143.4 A G 13 A O6 G 13 1_555 A NA 18 C NA NA 1_555 A U 14 A O4 U 14 1_555 72.3 A G 3 A OP1 G 3 1_555 A NA 19 D NA NA 1_555 A U 4 A OP2 U 4 1_555 148.2 A U 4 A OP1 U 4 1_555 A NA 20 E NA NA 1_555 A U 4 A O5' U 4 1_555 52.6 A U 4 A OP1 U 4 1_555 A NA 20 E NA NA 1_555 A G 5 A OP2 G 5 1_555 149.5 A U 4 A O5' U 4 1_555 A NA 20 E NA NA 1_555 A G 5 A OP2 G 5 1_555 97.1 A G 7 A OP1 G 7 1_555 A NA 22 G NA NA 1_555 A G 7 A OP2 G 7 1_555 52.1 A G 7 A OP1 G 7 1_555 A NA 22 G NA NA 1_555 A A 8 A OP1 A 8 1_555 134.5 A G 7 A OP2 G 7 1_555 A NA 22 G NA NA 1_555 A A 8 A OP1 A 8 1_555 149.8 A A 8 A OP2 A 8 1_555 A NA 24 I NA NA 1_555 A G 9 A OP2 G 9 1_555 116.2 A G 9 A OP1 G 9 1_555 A NA 25 J NA NA 1_555 A G 9 A O5' G 9 1_555 50.8 A G 9 A OP1 G 9 1_555 A NA 25 J NA NA 1_555 A A 10 A OP2 A 10 1_555 152.9 A G 9 A O5' G 9 1_555 A NA 25 J NA NA 1_555 A A 10 A OP2 A 10 1_555 102.3 A G 11 A OP1 G 11 1_555 A NA 26 K NA NA 1_555 A G 11 A OP2 G 11 1_555 56.7 A G 11 A O3' G 11 1_555 A NA 29 N NA NA 1_555 A C 12 A OP1 C 12 1_555 56.3 A C 12 A OP2 C 12 1_555 A NA 28 M NA NA 1_555 A G 13 A OP2 G 13 1_555 148.5 A U 14 A OP2 U 14 1_555 A NA 30 O NA NA 1_555 A U 14 A O5' U 14 1_555 51.8 A U 14 A OP2 U 14 1_555 A NA 30 O NA NA 1_555 A C 15 A OP2 C 15 1_555 147.7 A U 14 A O5' U 14 1_555 A NA 30 O NA NA 1_555 A C 15 A OP2 C 15 1_555 96.6 A C 15 A O5' C 15 1_555 A NA 31 P NA NA 1_555 A A 16 A OP2 A 16 1_555 102.8 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 13 A C3' G 1 WRONG HAND 13 A C2' G 1 WRONG HAND 13 A C4' G 2 WRONG HAND 13 A C3' G 3 WRONG HAND 1 A G 7 0.073 SIDE CHAIN 1 A G 11 0.056 SIDE CHAIN 2 A G 7 0.095 SIDE CHAIN 2 A C 15 0.063 SIDE CHAIN 3 A G 7 0.071 SIDE CHAIN 3 A G 9 0.050 SIDE CHAIN 4 A G 1 0.057 SIDE CHAIN 4 A G 7 0.115 SIDE CHAIN 4 A C 15 0.065 SIDE CHAIN 5 A G 7 0.079 SIDE CHAIN 5 A G 9 0.067 SIDE CHAIN 6 A G 5 0.069 SIDE CHAIN 6 A G 7 0.049 SIDE CHAIN 7 A G 2 0.051 SIDE CHAIN 7 A G 7 0.086 SIDE CHAIN 7 A G 11 0.064 SIDE CHAIN 8 A G 5 0.054 SIDE CHAIN 8 A G 7 0.082 SIDE CHAIN 9 A G 5 0.060 SIDE CHAIN 9 A G 7 0.081 SIDE CHAIN 9 A G 11 0.064 SIDE CHAIN 9 A C 15 0.080 SIDE CHAIN 10 A G 2 0.064 SIDE CHAIN 10 A G 7 0.115 SIDE CHAIN 11 A G 2 0.057 SIDE CHAIN 11 A U 4 0.064 SIDE CHAIN 11 A G 7 0.056 SIDE CHAIN 11 A C 15 0.094 SIDE CHAIN 12 A G 7 0.077 SIDE CHAIN 12 A A 16 0.069 SIDE CHAIN 13 A G 2 0.058 SIDE CHAIN 13 A G 7 0.083 SIDE CHAIN 13 A G 11 0.070 SIDE CHAIN 13 A C 15 0.085 SIDE CHAIN 14 A G 5 0.076 SIDE CHAIN 14 A G 9 0.059 SIDE CHAIN 14 A A 16 0.086 SIDE CHAIN 3 4.99 0.70 108.50 113.49 A A A O4' C1' N1 U U U 4 4 4 N 5 4.37 0.70 108.50 112.87 A A A O4' C1' N1 U U U 4 4 4 N 6 5.03 0.70 108.50 113.53 A A A O4' C1' N1 U U U 4 4 4 N 8 4.70 0.70 108.50 113.20 A A A O4' C1' N1 C C C 12 12 12 N 10 4.91 0.70 108.50 113.41 A A A O4' C1' N1 U U U 4 4 4 N 10 4.77 0.70 108.50 113.27 A A A O4' C1' N1 U U U 14 14 14 N 11 4.67 0.70 108.50 113.17 A A A O4' C1' N1 C C C 6 6 6 N 12 4.62 0.70 108.50 113.12 A A A O4' C1' N1 U U U 4 4 4 N 12 4.23 0.70 108.50 112.73 A A A O4' C1' N1 U U U 14 14 14 N 12 4.23 0.70 108.50 112.73 A A A O4' C1' N1 C C C 15 15 15 N 12 4.95 0.70 108.50 113.45 A A A O4' C1' N9 A A A 16 16 16 N 13 6.08 0.70 108.50 114.58 A A A O4' C1' N9 G G G 2 2 2 N 13 5.43 0.70 108.50 113.93 A A A O4' C1' N1 U U U 4 4 4 N 14 5.17 0.70 108.50 113.67 A A A O4' C1' N1 U U U 4 4 4 N 14 4.28 0.70 108.50 112.78 A A A O4' C1' N1 C C C 12 12 12 N 14 4.50 0.70 108.50 113.00 A A A O4' C1' N9 A A A 16 16 16 N Structure of SL4 RNA from the HIV-1 Packaging Signal 1 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N 2 N N metalc 2.486 A G 2 A OP1 G 2 1_555 A NA 17 B NA NA 1_555 metalc 2.729 A G 2 A OP2 G 2 1_555 A NA 27 L NA NA 1_555 metalc 2.617 A G 3 A O6 G 3 1_555 A NA 18 C NA NA 1_555 metalc 2.627 A G 3 A OP1 G 3 1_555 A NA 19 D NA NA 1_555 metalc 2.621 A G 3 A OP2 G 3 1_555 A NA 27 L NA NA 1_555 metalc 2.744 A U 4 A O4 U 4 1_555 A NA 18 C NA NA 1_555 metalc 2.536 A U 4 A OP2 U 4 1_555 A NA 19 D NA NA 1_555 metalc 2.626 A U 4 A OP1 U 4 1_555 A NA 20 E NA NA 1_555 metalc 2.969 A U 4 A O5' U 4 1_555 A NA 20 E NA NA 1_555 metalc 2.679 A G 5 A OP2 G 5 1_555 A NA 20 E NA NA 1_555 metalc 2.497 A C 6 A OP1 C 6 1_555 A NA 23 H NA NA 1_555 metalc 2.953 A G 7 A OP1 G 7 1_555 A NA 22 G NA NA 1_555 metalc 2.845 A G 7 A OP2 G 7 1_555 A NA 22 G NA NA 1_555 metalc 2.696 A A 8 A OP1 A 8 1_555 A NA 22 G NA NA 1_555 metalc 2.595 A A 8 A OP2 A 8 1_555 A NA 24 I NA NA 1_555 metalc 2.559 A G 9 A OP2 G 9 1_555 A NA 24 I NA NA 1_555 metalc 2.853 A G 9 A OP1 G 9 1_555 A NA 25 J NA NA 1_555 metalc 2.943 A G 9 A O5' G 9 1_555 A NA 25 J NA NA 1_555 metalc 2.620 A A 10 A OP2 A 10 1_555 A NA 25 J NA NA 1_555 metalc 2.722 A G 11 A OP1 G 11 1_555 A NA 26 K NA NA 1_555 metalc 2.613 A G 11 A OP2 G 11 1_555 A NA 26 K NA NA 1_555 metalc 2.619 A G 11 A O3' G 11 1_555 A NA 29 N NA NA 1_555 metalc 2.689 A C 12 A OP2 C 12 1_555 A NA 28 M NA NA 1_555 metalc 2.660 A C 12 A OP1 C 12 1_555 A NA 29 N NA NA 1_555 metalc 2.592 A G 13 A O6 G 13 1_555 A NA 18 C NA NA 1_555 metalc 2.556 A G 13 A OP2 G 13 1_555 A NA 28 M NA NA 1_555 metalc 2.901 A U 14 A O4 U 14 1_555 A NA 18 C NA NA 1_555 metalc 2.575 A U 14 A OP1 U 14 1_555 A NA 21 F NA NA 1_555 metalc 2.664 A U 14 A OP2 U 14 1_555 A NA 30 O NA NA 1_555 metalc 2.990 A U 14 A O5' U 14 1_555 A NA 30 O NA NA 1_555 metalc 2.535 A C 15 A OP2 C 15 1_555 A NA 30 O NA NA 1_555 metalc 2.893 A C 15 A O5' C 15 1_555 A NA 31 P NA NA 1_555 metalc 2.594 A A 16 A OP2 A 16 1_555 A NA 31 P NA NA 1_555 hydrog WATSON-CRICK A G 2 A N1 G 2 1_555 A C 15 A N3 C 15 1_555 hydrog WATSON-CRICK A G 2 A N2 G 2 1_555 A C 15 A O2 C 15 1_555 hydrog WATSON-CRICK A G 2 A O6 G 2 1_555 A C 15 A N4 C 15 1_555 hydrog TYPE_28_PAIR A G 3 A N1 G 3 1_555 A U 14 A O2 U 14 1_555 hydrog TYPE_28_PAIR A G 3 A O6 G 3 1_555 A U 14 A N3 U 14 1_555 hydrog TYPE_28_PAIR A U 4 A N3 U 4 1_555 A G 13 A O6 G 13 1_555 hydrog TYPE_28_PAIR A U 4 A O2 U 4 1_555 A G 13 A N1 G 13 1_555 hydrog WATSON-CRICK A G 5 A N1 G 5 1_555 A C 12 A N3 C 12 1_555 hydrog WATSON-CRICK A G 5 A N2 G 5 1_555 A C 12 A O2 C 12 1_555 hydrog WATSON-CRICK A G 5 A O6 G 5 1_555 A C 12 A N4 C 12 1_555 hydrog WATSON-CRICK A C 6 A N3 C 6 1_555 A G 11 A N1 G 11 1_555 hydrog WATSON-CRICK A C 6 A N4 C 6 1_555 A G 11 A O6 G 11 1_555 hydrog WATSON-CRICK A C 6 A O2 C 6 1_555 A G 11 A N2 G 11 1_555 hydrog G-A MISPAIR A G 7 A N2 G 7 1_555 A A 10 A N7 A 10 1_555 RNA hairpin, tandem G-U pairs, GAGA tetraloops, RNA 1JTW PDB 1 1JTW 1 16 1JTW 1 16 1JTW A 1 1 16 BINDING SITE FOR RESIDUE NA A 17 A NA 17 Software 1 BINDING SITE FOR RESIDUE NA A 18 A NA 18 Software 4 BINDING SITE FOR RESIDUE NA A 19 A NA 19 Software 2 BINDING SITE FOR RESIDUE NA A 20 A NA 20 Software 2 BINDING SITE FOR RESIDUE NA A 21 A NA 21 Software 2 BINDING SITE FOR RESIDUE NA A 22 A NA 22 Software 2 BINDING SITE FOR RESIDUE NA A 23 A NA 23 Software 1 BINDING SITE FOR RESIDUE NA A 24 A NA 24 Software 3 BINDING SITE FOR RESIDUE NA A 25 A NA 25 Software 3 BINDING SITE FOR RESIDUE NA A 26 A NA 26 Software 2 BINDING SITE FOR RESIDUE NA A 27 A NA 27 Software 2 BINDING SITE FOR RESIDUE NA A 28 A NA 28 Software 2 BINDING SITE FOR RESIDUE NA A 29 A NA 29 Software 2 BINDING SITE FOR RESIDUE NA A 30 A NA 30 Software 2 BINDING SITE FOR RESIDUE NA A 31 A NA 31 Software 2 A G 2 A G 2 1 1_555 A G 3 A G 3 4 1_555 A U 4 A U 4 4 1_555 A G 13 A G 13 4 1_555 A U 14 A U 14 4 1_555 A G 3 A G 3 2 1_555 A U 4 A U 4 2 1_555 A U 4 A U 4 2 1_555 A G 5 A G 5 2 1_555 A G 13 A G 13 2 1_555 A U 14 A U 14 2 1_555 A G 7 A G 7 2 1_555 A A 8 A A 8 2 1_555 A C 6 A C 6 1 1_555 A G 7 A G 7 3 1_555 A A 8 A A 8 3 1_555 A G 9 A G 9 3 1_555 A G 7 A G 7 3 1_555 A G 9 A G 9 3 1_555 A A 10 A A 10 3 1_555 A A 10 A A 10 2 1_555 A G 11 A G 11 2 1_555 A G 2 A G 2 2 1_555 A G 3 A G 3 2 1_555 A C 12 A C 12 2 1_555 A G 13 A G 13 2 1_555 A G 11 A G 11 2 1_555 A C 12 A C 12 2 1_555 A U 14 A U 14 2 1_555 A C 15 A C 15 2 1_555 A C 15 A C 15 2 1_555 A A 16 A A 16 2 1_555