HEADER RNA 28-AUG-24 9DE7 TITLE STRUCTURE OF FULL-LENGTH HIV TAR RNA G16A/A17G COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (58-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_TAXID: 11676 KEYWDS VIRAL RNA, HIV RNA, TAR RNA, RNA EXPDTA X-RAY DIFFRACTION AUTHOR C.BOU-NADER,J.ZHANG REVDAT 2 19-MAR-25 9DE7 1 JRNL REVDAT 1 12-MAR-25 9DE7 0 JRNL AUTH C.BOU-NADER,K.A.LINK,K.C.SUDDALA,J.R.KNUTSON,J.ZHANG JRNL TITL STRUCTURES OF COMPLETE HIV-1 TAR RNA PORTRAY A DYNAMIC JRNL TITL 2 PLATFORM POISED FOR PROTEIN BINDING AND STRUCTURAL JRNL TITL 3 REMODELING. JRNL REF NAT COMMUN V. 16 2252 2025 JRNL REFN ESSN 2041-1723 JRNL PMID 40050622 JRNL DOI 10.1038/S41467-025-57519-W REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18255 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1831 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.1350 - 5.2845 1.00 1273 142 0.1594 0.1823 REMARK 3 2 5.2845 - 4.1971 1.00 1267 136 0.1403 0.1666 REMARK 3 3 4.1971 - 3.6674 1.00 1269 149 0.1438 0.1552 REMARK 3 4 3.6674 - 3.3324 1.00 1253 135 0.1669 0.2308 REMARK 3 5 3.3324 - 3.0937 1.00 1278 141 0.1837 0.2292 REMARK 3 6 3.0937 - 2.9114 1.00 1261 145 0.2271 0.2291 REMARK 3 7 2.9114 - 2.7657 1.00 1263 144 0.2604 0.2832 REMARK 3 8 2.7657 - 2.6454 0.99 1276 136 0.2829 0.2839 REMARK 3 9 2.6454 - 2.5436 1.00 1269 142 0.2835 0.3217 REMARK 3 10 2.5436 - 2.4558 0.99 1232 134 0.2871 0.3802 REMARK 3 11 2.4558 - 2.3791 1.00 1297 147 0.3313 0.3419 REMARK 3 12 2.3791 - 2.3111 0.98 1217 135 0.3150 0.3235 REMARK 3 13 2.3111 - 2.2502 0.99 1269 145 0.3402 0.3917 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -26.1291 10.1945 -9.3093 REMARK 3 T TENSOR REMARK 3 T11: 0.2982 T22: 0.2624 REMARK 3 T33: 0.2310 T12: -0.0107 REMARK 3 T13: -0.0097 T23: -0.0273 REMARK 3 L TENSOR REMARK 3 L11: 2.9471 L22: 4.6612 REMARK 3 L33: 2.2180 L12: -2.4266 REMARK 3 L13: 1.5324 L23: -1.8241 REMARK 3 S TENSOR REMARK 3 S11: -0.0551 S12: 0.0404 S13: -0.0361 REMARK 3 S21: 0.1120 S22: 0.0577 S23: -0.3035 REMARK 3 S31: -0.0578 S32: 0.0941 S33: 0.0047 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A SEPARATE DATASET OF LOWER QUALITY, REMARK 3 WHICH WAS NOT DEPOSITED, WAS USED FOR SAD PHASING. REMARK 4 REMARK 4 9DE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1000287916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70998 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 33.135 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.570 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM SODIUM CACODYLATE PH 6.5, 80 MM REMARK 280 NACL, 12 MM SPERMINE AND 30% V/V 2-METHYL-2,4-PENTANEDIOL (MPD), REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 66.26900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.29000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 66.26900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.29000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 134 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 U A 23 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U A 23 C6 REMARK 470 C A 24 N1 C2 O2 N3 C4 N4 C5 REMARK 470 C A 24 C6 REMARK 470 U A 25 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U A 25 C6 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 C A 5 N1 DBREF1 9DE7 A 2 59 GB MW061005.1 DBREF2 9DE7 A 1945658931 5187 5244 SEQADV 9DE7 A A 16 GB 194565893 G 5201 ENGINEERED MUTATION SEQADV 9DE7 G A 17 GB 194565893 A 5202 ENGINEERED MUTATION SEQADV 9DE7 G A 31 GB 194565893 U 5216 ENGINEERED MUTATION SEQADV 9DE7 A A 32 GB 194565893 G 5217 ENGINEERED MUTATION SEQADV 9DE7 A A 59 GB 194565893 C 5244 ENGINEERED MUTATION SEQRES 1 A 58 GTP G U C U C U C U G G U U SEQRES 2 A 58 A A G C C A G A U C U G A SEQRES 3 A 58 G C C G A A A A G C U C U SEQRES 4 A 58 C U G G C U A A C U A G G SEQRES 5 A 58 G A A C C A MODRES 9DE7 GTP A 2 G MODIFIED RESIDUE HET GTP A 2 32 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 HOH *38(H2 O) LINK O3' GTP A 2 P G A 3 1555 1555 1.60 CRYST1 132.538 32.580 46.211 90.00 90.00 90.00 P 21 21 2 4 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 0.007545 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021640 0.00000 HETATM 1 PG GTP A 2 -10.932 -16.675 5.500 1.00122.32 P ANISOU 1 PG GTP A 2 15776 13530 17169 1745 -2287 756 P HETATM 2 O1G GTP A 2 -10.131 -16.964 6.749 1.00123.90 O ANISOU 2 O1G GTP A 2 16016 13725 17335 1872 -2464 878 O HETATM 3 O2G GTP A 2 -12.424 -16.657 5.741 1.00121.54 O ANISOU 3 O2G GTP A 2 15797 13412 16971 1621 -2178 917 O HETATM 4 O3G GTP A 2 -10.539 -17.564 4.343 1.00122.82 O ANISOU 4 O3G GTP A 2 15768 13444 17453 1811 -2283 612 O HETATM 5 O3B GTP A 2 -10.527 -15.171 5.063 1.00121.07 O ANISOU 5 O3B GTP A 2 15507 13586 16910 1688 -2224 594 O HETATM 6 PB GTP A 2 -11.309 -13.966 4.350 1.00117.67 P ANISOU 6 PB GTP A 2 15060 13293 16355 1542 -2058 502 P HETATM 7 O1B GTP A 2 -10.333 -12.908 3.939 1.00117.88 O ANISOU 7 O1B GTP A 2 14924 13458 16407 1546 -2068 364 O HETATM 8 O2B GTP A 2 -12.262 -14.532 3.342 1.00117.52 O ANISOU 8 O2B GTP A 2 15074 13169 16410 1473 -1938 465 O HETATM 9 O3A GTP A 2 -12.154 -13.385 5.583 1.00115.02 O ANISOU 9 O3A GTP A 2 14889 13038 15777 1503 -2066 668 O HETATM 10 PA GTP A 2 -11.930 -13.188 7.162 1.00114.16 P ANISOU 10 PA GTP A 2 14924 12976 15474 1610 -2213 815 P HETATM 11 O1A GTP A 2 -13.037 -12.326 7.674 1.00113.92 O ANISOU 11 O1A GTP A 2 15038 13061 15183 1569 -2105 903 O HETATM 12 O2A GTP A 2 -11.765 -14.535 7.784 1.00116.69 O ANISOU 12 O2A GTP A 2 15305 13151 15882 1713 -2299 977 O HETATM 13 O5' GTP A 2 -10.535 -12.388 7.251 1.00111.02 O ANISOU 13 O5' GTP A 2 14410 12650 15124 1659 -2398 663 O HETATM 14 C5' GTP A 2 -9.287 -13.104 7.038 1.00107.26 C ANISOU 14 C5' GTP A 2 13778 12090 14885 1747 -2525 616 C HETATM 15 C4' GTP A 2 -8.107 -12.279 7.497 1.00103.50 C ANISOU 15 C4' GTP A 2 13201 11672 14450 1790 -2749 550 C HETATM 16 O4' GTP A 2 -6.888 -13.045 7.300 1.00104.48 O ANISOU 16 O4' GTP A 2 13141 11719 14838 1891 -2860 537 O HETATM 17 C3' GTP A 2 -7.867 -10.936 6.787 1.00 98.78 C ANISOU 17 C3' GTP A 2 12451 11183 13899 1674 -2712 419 C HETATM 18 O3' GTP A 2 -8.436 -9.833 7.481 1.00 94.05 O ANISOU 18 O3' GTP A 2 12023 10654 13056 1632 -2784 413 O HETATM 19 C2' GTP A 2 -6.341 -10.831 6.795 1.00101.72 C ANISOU 19 C2' GTP A 2 12580 11533 14535 1733 -2917 389 C HETATM 20 O2' GTP A 2 -5.887 -10.387 8.055 1.00103.22 O ANISOU 20 O2' GTP A 2 12880 11701 14638 1791 -3235 420 O HETATM 21 C1' GTP A 2 -5.965 -12.288 6.553 1.00103.81 C ANISOU 21 C1' GTP A 2 12789 11699 14954 1852 -2871 436 C HETATM 22 N9 GTP A 2 -6.010 -12.710 5.156 1.00102.91 N ANISOU 22 N9 GTP A 2 12529 11588 14984 1848 -2617 366 N HETATM 23 C8 GTP A 2 -6.975 -13.479 4.556 1.00101.84 C ANISOU 23 C8 GTP A 2 12523 11391 14782 1839 -2429 351 C HETATM 24 N7 GTP A 2 -6.751 -13.697 3.283 1.00101.67 N ANISOU 24 N7 GTP A 2 12367 11377 14886 1878 -2256 256 N HETATM 25 C5 GTP A 2 -5.562 -13.025 3.027 1.00102.68 C ANISOU 25 C5 GTP A 2 12233 11598 15184 1914 -2287 241 C HETATM 26 C6 GTP A 2 -4.827 -12.903 1.822 1.00103.38 C ANISOU 26 C6 GTP A 2 12082 11756 15440 1999 -2113 190 C HETATM 27 O6 GTP A 2 -5.086 -13.380 0.708 1.00102.88 O ANISOU 27 O6 GTP A 2 12039 11685 15364 2085 -1908 109 O HETATM 28 N1 GTP A 2 -3.679 -12.132 2.006 1.00104.99 N ANISOU 28 N1 GTP A 2 12007 12040 15845 1998 -2211 255 N HETATM 29 C2 GTP A 2 -3.287 -11.555 3.189 1.00105.39 C ANISOU 29 C2 GTP A 2 12039 12075 15928 1922 -2497 322 C HETATM 30 N2 GTP A 2 -2.148 -10.851 3.163 1.00107.09 N ANISOU 30 N2 GTP A 2 11942 12339 16408 1915 -2603 389 N HETATM 31 N3 GTP A 2 -3.975 -11.667 4.324 1.00104.52 N ANISOU 31 N3 GTP A 2 12205 11901 15607 1874 -2676 334 N HETATM 32 C4 GTP A 2 -5.097 -12.413 4.171 1.00103.28 C ANISOU 32 C4 GTP A 2 12294 11693 15256 1876 -2531 309 C