1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Sundaram, M. Durant, P.C. Davis, D.R. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 C9 H13 N2 O9 P 324.181 n PSEUDOURIDINE-5'-MONOPHOSPHATE RNA linking C15 H21 N6 O11 P 492.335 n N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5'-MONOPHOSPHATE N-(NEBULARIN-6-YLCARBAMOYL)-L-THREONINE-5'-MONOPHOSPHATE RNA linking C9 H13 N2 O9 P 324.181 y URIDINE-5'-MONOPHOSPHATE RNA linking C11 H18 N3 O8 P S 383.315 n 5-METHYLAMINOMETHYL-2-THIOURIDINE-5'-MONOPHOSPHATE RNA linking US Biochemistry BICHAW 0033 0006-2960 39 12575 12584 10.1021/bi0014655 11027137 Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure. 2000 10.2210/pdb1fl8/pdb pdb_00001fl8 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 RESIDUES 30-40 (TRNA NUMBERING) ARE IDENTICAL TO THOSE FOUND IN THE ANTICODON DOMAIN OF E. COLI TRNA(LYS) INCLUDING MODIFIED NUCLEOSIDES 5554.438 ANTICODON DOMAIN OF TRNA(LYS) 17-MER TRNA(LYS) ANTICODON DOMAIN G27U, U28C, U29A, A41U, A42G, U43A 1 syn polymer no yes UCAGACU(U8U)UU(T6A)A(PSU)CUGA UCAGACUUUUAAUCUGA A polyribonucleotide n n n n n n n n n n n n n n n n n -1.839 1 20 A 27 A 43 3.402 A_U27:A43_A 1 -11.710 0.651 -0.767 0.183 -2.299 1 19 A 28 A 42 -3.618 A_C28:G42_A 2 -21.698 -0.727 0.228 -0.170 0.130 1 20 A 29 A 41 -3.002 A_A29:U41_A 3 -18.295 0.820 0.187 -0.092 -12.282 1 19 A 30 A 40 -1.543 A_G30:C40_A 4 -25.398 0.640 -0.447 -0.168 -20.718 1 21 A 31 A 39 -18.979 A_A31:PSU39_A 5 -25.768 1.408 0.206 -0.158 2.953 25.617 A A 27 28 22.482 A A 43 42 3.758 9.682 -0.562 -1.536 AA_U27C28:G42A43_AA 1 -4.150 9.636 23.384 -6.411 0.004 2.837 38.272 A A 28 29 19.782 A A 42 41 3.401 12.740 0.113 -1.188 AA_C28A29:U41G42_AA 2 -0.219 0.339 36.164 -3.385 -0.199 3.484 31.866 A A 29 30 18.831 A A 41 40 4.189 10.119 0.128 -1.479 AA_A29G30:C40U41_AA 3 5.364 -9.983 29.787 -4.935 0.955 3.300 37.958 A A 30 31 19.612 A A 40 39 3.919 12.526 -0.863 -1.433 AA_G30A31:PSU39C40_AA 4 -2.248 3.520 35.835 -4.024 1.001 database_2 pdbx_nmr_software pdbx_struct_assembly pdbx_struct_oper_list struct_conn repository Initial release Version format compliance Version format compliance Data collection Database references Derived calculations 1 0 2000-10-16 1 1 2008-04-27 1 2 2011-07-13 1 3 2022-02-23 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_nmr_software.name _struct_conn.pdbx_leaving_atom_flag the same anticodon loop sequence but without modified nucleosides at position 34 and 37. Pseudouridine is present at postion 39 the same anticodon loop sequence but without modified nucleosides at position 34, 37 or 39 RCSB Y RCSB 2000-08-11 REL REL This structure was determined using standard 2D homonuclear techniques and standard 1H-31P 2D correlation experiments. structures with the lowest energy 35 20 2D NOESY 2D NOESY DQF-COSY 1H-31P-COSY 1H-31P-hetero-TOCSY-TOCSY 120mM 7 ambient 285 K 120mM 7 ambient 303 K 123 NOE-derived restraints, 15 hydrogen bond restraints, 102 lower/upper bound restraints, 161 dihedral restraints, 68 chiral restraints used H5-H6 distances for distance calculations then simulated annealing/molecular dynamics in vacuo then restrained minimization in vacuo 4 closest to the average,lowest energy 1.5mM natural abundance RNA; 10mM phosphate buffer; 50mM KCl; 50mM NaCl; 10mM MgCl2 90% H2O/10% D2O 1.5mM natural abundance RNA; 10mM phosphate buffer; 50mM KCl; 50mM NaCl; 10mM MgCl2 99.99% D2O Varian collection VNMR 6.1B Varian processing VNMR 6.1B Varian data analysis VNMR 6.1B MSI processing Felix MSI data analysis Felix MSI structure solution Discover MSI refinement Discover 600 Varian UNITYPLUS 500 Varian UNITY U 27 n 1 U 27 A C 28 n 2 C 28 A A 29 n 3 A 29 A G 30 n 4 G 30 A A 31 n 5 A 31 A C 32 n 6 C 32 A U 33 n 7 U 33 A U8U 34 n 8 U8U 34 A U 35 n 9 U 35 A U 36 n 10 U 36 A T6A 37 n 11 T6A 37 A A 38 n 12 A 38 A PSU 39 n 13 PSU 39 A C 40 n 14 C 40 A U 41 n 15 U 41 A G 42 n 16 G 42 A A 43 n 17 A 43 A author_defined_assembly 1 monomeric A U8U 34 A U8U 8 U A T6A 37 A T6A 11 A A PSU 39 PSEUDOURIDINE-5'-MONOPHOSPHATE A PSU 13 U 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 1 4.21 0.70 108.50 112.71 A A A O4' C1' N1 C C C 32 32 32 N 1 -7.55 1.20 119.70 112.15 A A A C3' O3' P U8U U8U U 34 34 35 Y 2 -7.64 1.20 119.70 112.06 A A A C3' O3' P U8U U8U U 34 34 35 Y 3 -7.49 1.20 119.70 112.21 A A A C3' O3' P U8U U8U U 34 34 35 Y 4 -7.51 1.20 119.70 112.19 A A A C3' O3' P U8U U8U U 34 34 35 Y 5 -7.32 1.20 119.70 112.38 A A A C3' O3' P U8U U8U U 34 34 35 Y 6 -7.53 1.20 119.70 112.17 A A A C3' O3' P U8U U8U U 34 34 35 Y 7 4.25 0.70 108.50 112.75 A A A O4' C1' N1 C C C 32 32 32 N 7 -7.33 1.20 119.70 112.37 A A A C3' O3' P U8U U8U U 34 34 35 Y 8 -7.41 1.20 119.70 112.29 A A A C3' O3' P U8U U8U U 34 34 35 Y 9 -7.51 1.20 119.70 112.19 A A A C3' O3' P U8U U8U U 34 34 35 Y 10 4.23 0.70 108.50 112.73 A A A O4' C1' N1 C C C 32 32 32 N 10 -7.40 1.20 119.70 112.30 A A A C3' O3' P U8U U8U U 34 34 35 Y 10 -7.21 1.20 119.70 112.49 A A A C3' O3' P PSU PSU C 39 39 40 Y 11 4.25 0.70 108.50 112.75 A A A O4' C1' N1 C C C 32 32 32 N 11 -7.66 1.20 119.70 112.04 A A A C3' O3' P U8U U8U U 34 34 35 Y 12 -7.41 1.20 119.70 112.29 A A A C3' O3' P U8U U8U U 34 34 35 Y 13 -7.61 1.20 119.70 112.09 A A A C3' O3' P U8U U8U U 34 34 35 Y 14 -7.56 1.20 119.70 112.14 A A A C3' O3' P U8U U8U U 34 34 35 Y 15 4.20 0.70 108.50 112.70 A A A O4' C1' N1 U U U 33 33 33 N 16 -7.52 1.20 119.70 112.18 A A A C3' O3' P U8U U8U U 34 34 35 Y 17 -7.50 1.20 119.70 112.20 A A A C3' O3' P U8U U8U U 34 34 35 Y 18 -7.42 1.20 119.70 112.28 A A A C3' O3' P U8U U8U U 34 34 35 Y 19 -7.51 1.20 119.70 112.19 A A A C3' O3' P U8U U8U U 34 34 35 Y 20 -7.54 1.20 119.70 112.16 A A A C3' O3' P U8U U8U U 34 34 35 Y HYPERMODIFIED NUCLEOSIDES IN THE ANTICODON OF TRNALYS STABILIZE A CANONICAL U-TURN STRUCTURE 1 N N covale 1.612 both A U 33 A O3' U 7 1_555 A U8U 34 A P U8U 8 1_555 covale 1.621 both A U8U 34 A O3' U8U 8 1_555 A U 35 A P U 9 1_555 covale 1.615 both A U 36 A O3' U 10 1_555 A T6A 37 A P T6A 11 1_555 covale 1.624 both A T6A 37 A O3' T6A 11 1_555 A A 38 A P A 12 1_555 covale 1.615 both A A 38 A O3' A 12 1_555 A PSU 39 A P PSU 13 1_555 covale 1.622 both A PSU 39 A O3' PSU 13 1_555 A C 40 A P C 14 1_555 hydrog WATSON-CRICK A U 27 A N3 U 1 1_555 A A 43 A N1 A 17 1_555 hydrog WATSON-CRICK A U 27 A O4 U 1 1_555 A A 43 A N6 A 17 1_555 hydrog WATSON-CRICK A C 28 A N3 C 2 1_555 A G 42 A N1 G 16 1_555 hydrog WATSON-CRICK A C 28 A N4 C 2 1_555 A G 42 A O6 G 16 1_555 hydrog WATSON-CRICK A C 28 A O2 C 2 1_555 A G 42 A N2 G 16 1_555 hydrog WATSON-CRICK A A 29 A N1 A 3 1_555 A U 41 A N3 U 15 1_555 hydrog WATSON-CRICK A A 29 A N6 A 3 1_555 A U 41 A O4 U 15 1_555 hydrog WATSON-CRICK A G 30 A N1 G 4 1_555 A C 40 A N3 C 14 1_555 hydrog WATSON-CRICK A G 30 A N2 G 4 1_555 A C 40 A O2 C 14 1_555 hydrog WATSON-CRICK A G 30 A O6 G 4 1_555 A C 40 A N4 C 14 1_555 hydrog REVERSED WATSON-CRICK A A 31 A N1 A 5 1_555 A PSU 39 A N3 PSU 13 1_555 hydrog REVERSED WATSON-CRICK A A 31 A N6 A 5 1_555 A PSU 39 A O2 PSU 13 1_555 RNA tRNA, anticodon, pseudouridine, mnm5s2U, t6a, RNA 1FL8 PDB 1 1FL8 27 43 1FL8 27 43 1FL8 A 1 1 17 1 P 1