0.021337 0.012319 0.000000 0.000000 0.024638 0.000000 0.000000 0.000000 0.004672 0.00000 0.00000 0.00000 Kiliszek, A. Blaszczyk, L. Rypniewski, W. Micura, R. Nakatani, K. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 24 90.00 90.00 120.00 46.866 46.866 214.028 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 H16 N3 O7 P Se 400.184 n (D)-2'-METHYLSELENYL-2'-DEOXYCYTIDINE-5'-PHOSPHATE (D)-2'-DEOXY-2'-SE-METHYLCYTIDINE-5'-PHOSPHATE DNA linking C10 H14 N5 O8 P 363.221 y GUANOSINE-5'-MONOPHOSPHATE RNA linking H2 O 18.015 WATER non-polymer C26 H26 N7 O4 1 500.529 CMBL3a non-polymer UK Nucleic Acids Res. NARHAD 0389 1362-4962 47 10906 10913 10.1093/nar/gkz832 31566242 Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats. 2019 100 1 N PIXEL 2018-01-13 DECTRIS PILATUS3 S 6M SINGLE WAVELENGTH M x-ray 1 0.9756 1.0 P13 (MX1) PETRA III, EMBL c/o DESY 0.9756 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 2641.604 RNA (5'-R(*GP*CP*AP*G)-D(P*(CSL))-R(P*AP*GP*C)-3') 2 syn polymer 500.529 CMBL3a 2 syn non-polymer 18.015 water 6 nat water no yes GCAG(CSL)AGC GCAGCAGC A,B polyribonucleotide n n n n n n n n 1 VAPOR DIFFUSION, SITTING DROP 7.5 5mM MgCl2 and 30% PEG 400 292 -0.906 1 19 A 1 B 8 -2.925 A_G1:C8_B 1 -7.267 0.050 0.110 -0.280 -1.363 1 19 A 2 B 7 4.739 A_C2:G7_B 2 -12.381 -0.387 0.429 0.060 -0.618 1 19 A 7 B 2 -1.231 A_G7:C2_B 3 -5.032 -0.075 0.112 -0.207 3.839 1 19 A 8 B 1 2.553 A_C8:G1_B 4 -6.340 0.207 -0.090 -0.150 -2.950 1 19 A 1 A 8 -19.397 A_G1:C8_A 5 2.827 26.600 -28.147 17.745 2.950 1 19 A 8 A 1 19.397 A_C8:G1_A 6 -2.827 -26.600 28.147 -17.745 -12.444 1 19 A 4 A 5 -4.748 A_G4:CSL5_A 7 14.885 0.528 -0.506 0.051 12.444 1 19 A 5 A 4 -4.748 A_CSL5:G4_A 8 14.885 -0.528 -0.506 0.051 -43.368 1 19 B 1 B 8 -5.136 B_G1:C8_B 9 -40.141 27.261 -24.321 14.911 43.368 1 19 B 8 B 1 5.136 B_C8:G1_B 10 40.141 -27.261 24.321 -14.911 -14.846 1 19 B 4 B 5 4.574 B_G4:CSL5_B 11 8.109 -0.062 -0.048 0.132 14.846 1 19 B 5 B 4 4.574 B_CSL5:G4_B 12 8.109 0.062 -0.048 0.132 2.887 27.846 A A 1 2 8.562 B B 8 7 3.208 4.084 -0.303 -2.010 AA_G1C2:G7C8_BB 1 -5.019 10.522 27.098 -5.101 -0.506 3.280 32.504 A A 7 8 -2.217 B B 2 1 3.202 -1.239 0.118 -2.171 AA_G7C8:G1C2_BB 2 2.644 -4.731 32.376 -3.664 0.248 0.000 -180.000 A A 1 8 11.737 A A 8 1 0.000 -23.457 -2.355 5.050 AA_G1C8:G1C8_AA 3 -12.984 -6.476 -180.000 -2.525 -1.182 0.067 21.116 A A 4 5 84.508 A A 5 4 2.918 21.018 0.000 -0.218 AA_G4CSL5:G4CSL5_AA 4 0.000 0.000 2.044 -7.983 0.000 0.000 180.000 B B 1 8 11.021 B B 8 1 0.000 22.043 5.514 3.081 BB_G1C8:G1C8_BB 5 1.146 -0.573 180.000 1.541 -2.757 1.939 32.648 B B 4 5 25.256 B B 5 4 2.579 13.775 0.000 -0.996 BB_G4CSL5:G4CSL5_BB 6 0.000 0.000 29.671 -3.507 0.000 citation citation repository Initial release Data collection Database references Database references 1 0 2019-09-25 1 1 2019-10-09 1 2 2019-11-20 _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.journal_volume _citation.page_first _citation.page_last Poland NCN 2017/26/E/NZ1/00950 N PDBE Y PDBE 2019-01-21 REL REL J48 CMBL3a HOH water 9606 Human Homo sapiens sample 1 8 MBL 2 2 J48 J48 101 A MBL 1 2 J48 J48 101 B HOH 1 3 HOH HOH 201 A HOH 4 3 HOH HOH 202 A HOH 6 3 HOH HOH 201 B HOH 3 3 HOH HOH 202 B HOH 2 3 HOH HOH 203 B HOH 5 3 HOH HOH 204 B G 1 n 1 G 1 A C 2 n 2 C 2 A A 3 n 3 A 3 A G 4 n 4 G 4 A CSL 5 n 5 CSL 5 A A 6 n 6 A 6 A G 7 n 7 G 7 A C 8 n 8 C 8 A G 1 n 1 G 1 B C 2 n 2 C 2 B A 3 n 3 A 3 B G 4 n 4 G 4 B CSL 5 n 5 CSL 5 B A 6 n 6 A 6 B G 7 n 7 G 7 B C 8 n 8 C 8 B 1.9649 0.4141 -0.0931 1.5609 0.7684 0.9644 -0.3134 -0.9380 -0.1052 0.1990 0.4531 -0.0802 0.0728 0.7278 -0.0867 0.8666 0.0667 0.0699 1.1315 0.1185 1.1133 refined -3.8444 12.4394 -1.3703 X-RAY DIFFRACTION 4.2559 -3.4050 0.4939 3.4158 -0.7447 5.2793 -0.5137 -0.5882 1.1596 0.6188 0.1795 -0.3494 -0.7577 0.3344 -0.9626 0.4811 0.0132 0.0519 0.6911 -0.0232 0.4280 refined -8.9398 18.9758 -6.9403 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain 'A' and (resid 1 through 8 ) X-RAY DIFFRACTION 2 chain 'B' and (resid 1 through 8 ) author_and_software_defined_assembly PISA 2 dimeric none 2160 -2 3530 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 -2.50 0.40 120.30 117.80 A A A C6 N1 C2 C C C 2 2 2 N 0.2271 0.2045 0.2057 2.519 40.587 449 8867 5.06 99.51 0.54 1 FREE R-VALUE 1.92 SAD 33.36 0.70 0.90 ML FLAT BULK SOLVENT MODEL 2.519 40.587 6 422 74 342 0 0.012 460 1.988 702 13.280 280 0.096 76 0.006 106 0.4591 0.3809 2.8832 152 2819 100.00 0.2380 0.2339 3.6322 151 2783 99.00 0.2013 0.1765 40.5924 146 2816 100.00 2.519 40.587 6QIQ 8907 0.99 0.113 1 18.3 27.9 99.9 2.873 2.519 2.67 1.0 1420 0.65 1 28.5 99.9 refinement PHENIX (1.13_2998: ???) data reduction XDS data scaling XDS phasing Auto-Rickshaw N RNA (5'-R(*GP*CP*AP*G)-D(P*(CSL))-R(P*AP*GP*C)-3') Crystal structure of seleno-derivative CAG repeats with synthetic CMBL3a compound 1 N N 1 N N 2 N N 2 N N 3 N N 3 N N covale 1.591 both A G 4 A O3' G 4 1_555 A CSL 5 A P CSL 5 1_555 covale 1.570 both A CSL 5 A O3' CSL 5 1_555 A A 6 A P A 6 1_555 covale 1.547 both B G 4 B O3' G 4 1_555 B CSL 5 B P CSL 5 1_555 covale 1.592 both B CSL 5 B O3' CSL 5 1_555 B A 6 B P A 6 1_555 hydrog WATSON-CRICK A G 1 A N1 G 1 1_555 B C 8 B N3 C 8 1_555 hydrog WATSON-CRICK A G 1 A N2 G 1 1_555 B C 8 B O2 C 8 1_555 hydrog WATSON-CRICK A G 1 A O6 G 1 1_555 B C 8 B N4 C 8 1_555 hydrog WATSON-CRICK A C 2 A N3 C 2 1_555 B G 7 B N1 G 7 1_555 hydrog WATSON-CRICK A C 2 A N4 C 2 1_555 B G 7 B O6 G 7 1_555 hydrog WATSON-CRICK A C 2 A O2 C 2 1_555 B G 7 B N2 G 7 1_555 hydrog WATSON-CRICK A G 7 A N1 G 7 1_555 B C 2 B N3 C 2 1_555 hydrog WATSON-CRICK A G 7 A N2 G 7 1_555 B C 2 B O2 C 2 1_555 hydrog WATSON-CRICK A G 7 A O6 G 7 1_555 B C 2 B N4 C 2 1_555 hydrog WATSON-CRICK A C 8 A N3 C 8 1_555 B G 1 B N1 G 1 1_555 hydrog WATSON-CRICK A C 8 A N4 C 8 1_555 B G 1 B O6 G 1 1_555 hydrog WATSON-CRICK A C 8 A O2 C 8 1_555 B G 1 B N2 G 1 1_555 RNA CAG repeats, CMBL, RNA complex with ligand, RNA 6QIQ PDB 1 1 6QIQ 1 8 6QIQ 1 8 6QIQ A 1 1 8 1 8 6QIQ 1 8 6QIQ B 1 1 8 binding site for residue J48 A 101 A J48 101 Software 7 binding site for residue J48 B 101 B J48 101 Software 7 binding site for Di-nucleotide G B 4 and CSL B 5 B G 4 Software 3 binding site for Di-nucleotide CSL B 5 and A B 6 B CSL 5 Software 5 A A 3 A A 3 7 1_555 A CSL 5 A CSL 5 7 1_555 A A 6 A A 6 7 1_555 A G 7 A G 7 7 1_555 B C 2 B C 2 7 1_555 B A 3 B A 3 7 1_555 B J48 101 D J48 7 1_555 A C 2 A C 2 7 1_555 A A 3 A A 3 7 1_555 A J48 101 C J48 7 1_555 B A 3 B A 3 7 1_555 B CSL 5 B CSL 5 7 1_555 B A 6 B A 6 7 1_555 B G 7 B G 7 7 1_555 B A 3 B A 3 3 1_555 B A 6 B A 6 3 1_555 B J48 101 D J48 3 1_555 B A 3 B A 3 5 1_555 B G 4 B G 4 5 1_555 B G 4 B G 4 5 12_564 B G 7 B G 7 5 1_555 B J48 101 D J48 5 1_555 179 P 65 2 2