HEADER RNA,DNA 27-SEP-16 5TGG TITLE SOLUTION STRUCTURE OF PARALLEL STRANDED ADENOSINE DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA/DNA (5'-D(P*T)-R(*(A2M)P*(A2M)P*(A2M)P*(A2M))-D(P*A)- COMPND 3 R(P*(A2M)P*(A2M)P*(A2M))-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS PARALLEL STRANDED DUPLEX, RNA, DNA EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR A.DENISOV,A.NORONHA,K.GEHRING,C.WILDS REVDAT 8 15-MAY-24 5TGG 1 REMARK REVDAT 7 14-JUN-23 5TGG 1 REMARK REVDAT 6 08-JAN-20 5TGG 1 REMARK REVDAT 5 11-OCT-17 5TGG 1 JRNL REVDAT 4 20-SEP-17 5TGG 1 REMARK REVDAT 3 30-AUG-17 5TGG 1 SOURCE REVDAT 2 23-AUG-17 5TGG 1 JRNL REVDAT 1 09-AUG-17 5TGG 0 JRNL AUTH W.COPP,A.Y.DENISOV,J.XIE,A.M.NORONHA,C.LICZNER,N.SAFAEE, JRNL AUTH 2 C.J.WILDS,K.GEHRING JRNL TITL INFLUENCE OF NUCLEOTIDE MODIFICATIONS AT THE C2' POSITION ON JRNL TITL 2 THE HOOGSTEEN BASE-PAIRED PARALLEL-STRANDED DUPLEX OF JRNL TITL 3 POLY(A) RNA. JRNL REF NUCLEIC ACIDS RES. V. 45 10321 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28973475 JRNL DOI 10.1093/NAR/GKX713 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5TGG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000224197. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298 REMARK 210 PH : 4.0; 4.0 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.0 MM TA8 DUPLEX, 90% H2O/10% REMARK 210 D2O; 1.0 MM TA8 DUPLEX, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY; 2D 31P-1H HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; VNMRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR, NMRPIPE, NMRVIEW REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS AND THE REMARK 210 LOWEST 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-11 REMARK 465 RES C SSSEQI REMARK 465 DT A 1 REMARK 465 DT B 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-11 REMARK 470 RES CSSEQI ATOMS REMARK 470 A2M A 2 P OP1 OP2 REMARK 470 A2M B 2 P OP1 OP2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JRD RELATED DB: PDB REMARK 900 RELATED ID: 30184 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF PARALLEL STRANDED ADENOSINE DUPLEX R(AAAA)-DA- REMARK 900 R(AAA) DBREF 5TGG A 1 9 PDB 5TGG 5TGG 1 9 DBREF 5TGG B 1 9 PDB 5TGG 5TGG 1 9 SEQRES 1 A 9 DT A2M A2M A2M A2M DA A2M A2M A2M SEQRES 1 B 9 DT A2M A2M A2M A2M DA A2M A2M A2M HET A2M A 2 33 HET A2M A 3 36 HET A2M A 4 36 HET A2M A 5 36 HET A2M A 7 36 HET A2M A 8 36 HET A2M A 9 37 HET A2M B 2 33 HET A2M B 3 36 HET A2M B 4 36 HET A2M B 5 36 HET A2M B 7 36 HET A2M B 8 36 HET A2M B 9 37 HETNAM A2M 2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 1 A2M 14(C11 H16 N5 O7 P) LINK O3' A2M A 2 P A2M A 3 1555 1555 1.61 LINK O3' A2M A 3 P A2M A 4 1555 1555 1.61 LINK O3' A2M A 4 P A2M A 5 1555 1555 1.61 LINK O3' A2M A 5 P DA A 6 1555 1555 1.61 LINK O3' DA A 6 P A2M A 7 1555 1555 1.61 LINK O3' A2M A 7 P A2M A 8 1555 1555 1.61 LINK O3' A2M A 8 P A2M A 9 1555 1555 1.61 LINK O3' A2M B 2 P A2M B 3 1555 1555 1.61 LINK O3' A2M B 3 P A2M B 4 1555 1555 1.61 LINK O3' A2M B 4 P A2M B 5 1555 1555 1.61 LINK O3' A2M B 5 P DA B 6 1555 1555 1.61 LINK O3' DA B 6 P A2M B 7 1555 1555 1.61 LINK O3' A2M B 7 P A2M B 8 1555 1555 1.61 LINK O3' A2M B 8 P A2M B 9 1555 1555 1.61 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 HETATM 1 O5' A2M A 2 6.711 -0.158 -12.688 1.00 0.44 O HETATM 2 C5' A2M A 2 7.885 0.616 -12.953 1.00 0.51 C HETATM 3 C4' A2M A 2 7.583 2.095 -12.870 1.00 0.56 C HETATM 4 O4' A2M A 2 6.897 2.501 -14.087 1.00 0.62 O HETATM 5 C3' A2M A 2 6.646 2.505 -11.742 1.00 0.50 C HETATM 6 O3' A2M A 2 7.339 2.737 -10.520 1.00 0.50 O HETATM 7 C2' A2M A 2 5.986 3.760 -12.295 1.00 0.57 C HETATM 8 O2' A2M A 2 6.850 4.880 -12.212 1.00 0.66 O HETATM 9 C1' A2M A 2 5.827 3.372 -13.763 1.00 0.61 C HETATM 10 CM' A2M A 2 6.089 6.075 -12.386 1.00 0.65 C HETATM 11 N9 A2M A 2 4.571 2.672 -14.020 1.00 0.55 N HETATM 12 C8 A2M A 2 4.376 1.317 -14.141 1.00 0.52 C HETATM 13 N7 A2M A 2 3.126 0.978 -14.339 1.00 0.49 N HETATM 14 C5 A2M A 2 2.452 2.191 -14.357 1.00 0.50 C HETATM 15 C6 A2M A 2 1.095 2.517 -14.526 1.00 0.48 C HETATM 16 N6 A2M A 2 0.134 1.611 -14.707 1.00 0.47 N HETATM 17 N1 A2M A 2 0.755 3.823 -14.495 1.00 0.50 N HETATM 18 C2 A2M A 2 1.719 4.733 -14.302 1.00 0.54 C HETATM 19 N3 A2M A 2 3.025 4.551 -14.129 1.00 0.57 N HETATM 20 C4 A2M A 2 3.330 3.243 -14.168 1.00 0.54 C HETATM 21 H5' A2M A 2 8.258 0.383 -13.950 1.00 0.57 H HETATM 22 H5'' A2M A 2 8.655 0.374 -12.223 1.00 0.49 H HETATM 23 H4' A2M A 2 8.526 2.616 -12.705 1.00 0.61 H HETATM 24 H3' A2M A 2 5.922 1.722 -11.530 1.00 0.43 H HETATM 25 H2' A2M A 2 5.020 3.932 -11.816 1.00 0.53 H HETATM 26 H1' A2M A 2 5.888 4.229 -14.435 1.00 0.68 H HETATM 27 HM'1 A2M A 2 5.271 6.091 -11.666 1.00 1.23 H HETATM 28 HM'2 A2M A 2 5.686 6.102 -13.398 1.00 0.64 H HETATM 29 HM'3 A2M A 2 6.734 6.940 -12.227 1.00 0.96 H HETATM 30 H8 A2M A 2 5.180 0.598 -14.076 1.00 0.52 H HETATM 31 H61 A2M A 2 0.372 0.628 -14.726 1.00 0.47 H HETATM 32 H62 A2M A 2 -0.824 1.908 -14.818 1.00 0.46 H HETATM 33 H2 A2M A 2 1.385 5.771 -14.279 1.00 0.56 H HETATM 34 P A2M A 3 6.635 2.359 -9.123 1.00 0.43 P HETATM 35 OP1 A2M A 3 7.607 2.662 -8.042 1.00 0.48 O HETATM 36 O5' A2M A 3 5.424 3.390 -9.012 1.00 0.47 O HETATM 37 C5' A2M A 3 5.664 4.795 -9.005 1.00 0.40 C HETATM 38 C4' A2M A 3 4.373 5.555 -9.211 1.00 0.43 C HETATM 39 O4' A2M A 3 3.729 5.120 -10.441 1.00 0.42 O HETATM 40 C3' A2M A 3 3.299 5.350 -8.152 1.00 0.40 C HETATM 41 O3' A2M A 3 3.524 6.111 -6.972 1.00 0.46 O HETATM 42 C2' A2M A 3 2.035 5.756 -8.898 1.00 0.41 C HETATM 43 O2' A2M A 3 1.933 7.166 -9.011 1.00 0.50 O HETATM 44 C1' A2M A 3 2.321 5.173 -10.281 1.00 0.40 C HETATM 45 CM' A2M A 3 0.590 7.514 -9.343 1.00 0.36 C HETATM 46 N9 A2M A 3 1.774 3.823 -10.406 1.00 0.32 N HETATM 47 C8 A2M A 3 2.445 2.626 -10.421 1.00 0.28 C HETATM 48 N7 A2M A 3 1.656 1.580 -10.494 1.00 0.24 N HETATM 49 C5 A2M A 3 0.380 2.128 -10.539 1.00 0.24 C HETATM 50 C6 A2M A 3 -0.899 1.547 -10.612 1.00 0.23 C HETATM 51 N6 A2M A 3 -1.119 0.233 -10.639 1.00 0.24 N HETATM 52 N1 A2M A 3 -1.963 2.378 -10.650 1.00 0.23 N HETATM 53 C2 A2M A 3 -1.749 3.697 -10.604 1.00 0.26 C HETATM 54 N3 A2M A 3 -0.598 4.361 -10.526 1.00 0.30 N HETATM 55 C4 A2M A 3 0.440 3.508 -10.498 1.00 0.28 C HETATM 56 H5' A2M A 3 6.361 5.054 -9.803 1.00 0.37 H HETATM 57 H5'' A2M A 3 6.096 5.089 -8.050 1.00 0.38 H HETATM 58 H4' A2M A 3 4.616 6.617 -9.204 1.00 0.50 H HETATM 59 H3' A2M A 3 3.263 4.312 -7.831 1.00 0.33 H HETATM 60 H2' A2M A 3 1.153 5.302 -8.440 1.00 0.37 H HETATM 61 H1' A2M A 3 1.919 5.785 -11.090 1.00 0.45 H HETATM 62 HM'1 A2M A 3 0.500 8.600 -9.389 1.00 0.73 H HETATM 63 HM'2 A2M A 3 -0.084 7.123 -8.581 1.00 1.15 H HETATM 64 HM'3 A2M A 3 0.335 7.086 -10.312 1.00 0.27 H HETATM 65 H8 A2M A 3 3.521 2.550 -10.373 1.00 0.29 H HETATM 66 OP2 A2M A 3 6.069 0.989 -9.242 1.00 0.33 O HETATM 67 H61 A2M A 3 -0.343 -0.411 -10.606 1.00 0.24 H HETATM 68 H62 A2M A 3 -2.070 -0.109 -10.658 1.00 0.25 H HETATM 69 H2 A2M A 3 -2.645 4.318 -10.632 1.00 0.26 H HETATM 70 P A2M A 4 3.145 5.483 -5.539 1.00 0.44 P HETATM 71 OP1 A2M A 4 3.598 6.442 -4.500 1.00 0.53 O HETATM 72 O5' A2M A 4 1.551 5.461 -5.538 1.00 0.43 O HETATM 73 C5' A2M A 4 0.807 6.642 -5.826 1.00 0.23 C HETATM 74 C4' A2M A 4 -0.665 6.322 -5.963 1.00 0.25 C HETATM 75 O4' A2M A 4 -0.885 5.446 -7.104 1.00 0.29 O HETATM 76 C3' A2M A 4 -1.303 5.568 -4.807 1.00 0.22 C HETATM 77 O3' A2M A 4 -1.612 6.392 -3.690 1.00 0.22 O HETATM 78 C2' A2M A 4 -2.538 4.964 -5.462 1.00 0.27 C HETATM 79 O2' A2M A 4 -3.553 5.936 -5.649 1.00 0.32 O HETATM 80 C1' A2M A 4 -1.973 4.578 -6.827 1.00 0.29 C HETATM 81 CM' A2M A 4 -4.779 5.281 -5.971 1.00 0.40 C HETATM 82 N9 A2M A 4 -1.497 3.196 -6.813 1.00 0.27 N HETATM 83 C8 A2M A 4 -0.207 2.731 -6.757 1.00 0.26 C HETATM 84 N7 A2M A 4 -0.120 1.423 -6.694 1.00 0.24 N HETATM 85 C5 A2M A 4 -1.443 0.999 -6.721 1.00 0.24 C HETATM 86 C6 A2M A 4 -2.033 -0.278 -6.674 1.00 0.24 C HETATM 87 N6 A2M A 4 -1.342 -1.414 -6.570 1.00 0.24 N HETATM 88 N1 A2M A 4 -3.381 -0.350 -6.730 1.00 0.25 N HETATM 89 C2 A2M A 4 -4.079 0.789 -6.816 1.00 0.25 C HETATM 90 N3 A2M A 4 -3.641 2.045 -6.859 1.00 0.26 N HETATM 91 C4 A2M A 4 -2.299 2.080 -6.808 1.00 0.25 C HETATM 92 H5' A2M A 4 1.166 7.084 -6.756 1.00 0.41 H HETATM 93 H5'' A2M A 4 0.937 7.364 -5.020 1.00 0.28 H HETATM 94 H4' A2M A 4 -1.194 7.273 -6.042 1.00 0.28 H HETATM 95 H3' A2M A 4 -0.631 4.799 -4.428 1.00 0.19 H HETATM 96 H2' A2M A 4 -2.883 4.090 -4.906 1.00 0.26 H HETATM 97 H1' A2M A 4 -2.697 4.687 -7.634 1.00 0.34 H HETATM 98 HM'1 A2M A 4 -4.975 4.498 -5.238 1.00 1.28 H HETATM 99 HM'2 A2M A 4 -4.703 4.841 -6.965 1.00 0.54 H HETATM 100 HM'3 A2M A 4 -5.591 6.008 -5.956 1.00 0.41 H HETATM 101 H8 A2M A 4 0.655 3.381 -6.759 1.00 0.27 H HETATM 102 OP2 A2M A 4 3.625 4.075 -5.500 1.00 0.39 O HETATM 103 H61 A2M A 4 -0.334 -1.385 -6.521 1.00 0.23 H HETATM 104 H62 A2M A 4 -1.836 -2.295 -6.502 1.00 0.26 H HETATM 105 H2 A2M A 4 -5.162 0.670 -6.858 1.00 0.26 H HETATM 106 P A2M A 5 -1.492 5.785 -2.205 1.00 0.21 P HETATM 107 OP1 A2M A 5 -1.735 6.893 -1.247 1.00 0.27 O HETATM 108 O5' A2M A 5 -2.710 4.762 -2.106 1.00 0.27 O HETATM 109 C5' A2M A 5 -4.022 5.151 -2.502 1.00 0.31 C HETATM 110 C4' A2M A 5 -4.952 3.958 -2.506 1.00 0.26 C HETATM 111 O4' A2M A 5 -4.584 3.042 -3.576 1.00 0.20 O HETATM 112 C3' A2M A 5 -4.928 3.082 -1.263 1.00 0.29 C HETATM 113 O3' A2M A 5 -5.674 3.624 -0.180 1.00 0.38 O HETATM 114 C2' A2M A 5 -5.496 1.770 -1.784 1.00 0.26 C HETATM 115 O2' A2M A 5 -6.903 1.837 -1.949 1.00 0.28 O HETATM 116 C1' A2M A 5 -4.847 1.710 -3.165 1.00 0.20 C HETATM 117 CM' A2M A 5 -7.420 0.520 -2.139 1.00 0.30 C HETATM 118 N9 A2M A 5 -3.591 0.966 -3.112 1.00 0.20 N HETATM 119 C8 A2M A 5 -2.310 1.455 -3.086 1.00 0.18 C HETATM 120 N7 A2M A 5 -1.392 0.525 -2.966 1.00 0.19 N HETATM 121 C5 A2M A 5 -2.120 -0.657 -2.924 1.00 0.21 C HETATM 122 C6 A2M A 5 -1.735 -2.005 -2.797 1.00 0.24 C HETATM 123 N6 A2M A 5 -0.471 -2.406 -2.661 1.00 0.24 N HETATM 124 N1 A2M A 5 -2.711 -2.940 -2.802 1.00 0.28 N HETATM 125 C2 A2M A 5 -3.983 -2.537 -2.914 1.00 0.28 C HETATM 126 N3 A2M A 5 -4.469 -1.304 -3.028 1.00 0.25 N HETATM 127 C4 A2M A 5 -3.473 -0.400 -3.029 1.00 0.22 C HETATM 128 H5' A2M A 5 -3.990 5.583 -3.504 1.00 0.31 H HETATM 129 H5'' A2M A 5 -4.410 5.896 -1.809 1.00 0.41 H HETATM 130 H4' A2M A 5 -5.969 4.340 -2.598 1.00 0.28 H HETATM 131 H3' A2M A 5 -3.911 2.965 -0.890 1.00 0.30 H HETATM 132 H2' A2M A 5 -5.182 0.936 -1.154 1.00 0.29 H HETATM 133 H1' A2M A 5 -5.489 1.251 -3.918 1.00 0.21 H HETATM 134 HM'1 A2M A 5 -7.189 0.184 -3.150 1.00 0.38 H HETATM 135 HM'2 A2M A 5 -8.500 0.532 -1.995 1.00 0.32 H HETATM 136 HM'3 A2M A 5 -6.963 -0.156 -1.415 1.00 0.25 H HETATM 137 H8 A2M A 5 -2.080 2.509 -3.155 1.00 0.18 H HETATM 138 OP2 A2M A 5 -0.228 5.004 -2.121 1.00 0.19 O HETATM 139 H61 A2M A 5 0.263 -1.714 -2.649 1.00 0.21 H HETATM 140 H62 A2M A 5 -0.259 -3.389 -2.540 1.00 0.28 H HETATM 141 H2 A2M A 5 -4.727 -3.334 -2.911 1.00 0.31 H