HEADER RNA BINDING PROTEIN/RNA 18-JUN-20 6XH1 TITLE CO-CRYSTAL STRUCTURE OF HIV-1 TAR RNA IN COMPLEX WITH LAB-EVOLVED RRM TITLE 2 TBP6.7 MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR BINDING PROTEIN MUTANT 6.7 Q48R/T50R; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRANS-ACTIVATION RESPONSE ELEMENT; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 10 ORGANISM_COMMON: HIV-1; SOURCE 11 ORGANISM_TAXID: 11676 KEYWDS PROTEIN-RNA COMPLEX, TAR RNA, LAB-EVOLVED PROTEIN, ARGININE FORK, KEYWDS 2 BETA HAIRPIN, MAJOR-GROOVE READOUT, BASE TRIPLE, U1A, HIV-1, TRANS- KEYWDS 3 ACTIVATION, RNA RECOGNITION MOTIF, RRM, RNA BINDING PROTEIN-RNA KEYWDS 4 COMPLEX, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.S.CHAVALI,J.L.JENKINS,J.E.WEDEKIND REVDAT 4 06-MAR-24 6XH1 1 REMARK REVDAT 3 16-DEC-20 6XH1 1 JRNL REVDAT 2 04-NOV-20 6XH1 1 JRNL REVDAT 1 14-OCT-20 6XH1 0 JRNL AUTH S.S.CHAVALI,S.M.MALI,J.L.JENKINS,R.FASAN,J.E.WEDEKIND JRNL TITL CO-CRYSTAL STRUCTURES OF HIV TAR RNA BOUND TO LAB-EVOLVED JRNL TITL 2 PROTEINS SHOW KEY ROLES FOR ARGININE RELEVANT TO THE DESIGN JRNL TITL 3 OF CYCLIC PEPTIDE TAR INHIBITORS. JRNL REF J.BIOL.CHEM. V. 295 16470 2020 JRNL REFN ESSN 1083-351X JRNL PMID 33051202 JRNL DOI 10.1074/JBC.RA120.015444 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 7660 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.320 REMARK 3 FREE R VALUE TEST SET COUNT : 561 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 39.8500 - 4.1280 0.92 1903 145 0.1880 0.2064 REMARK 3 2 4.1280 - 3.2770 0.94 1800 143 0.2083 0.2695 REMARK 3 3 3.2770 - 2.8629 0.94 1728 142 0.2559 0.2910 REMARK 3 4 2.8629 - 2.6012 0.90 1668 131 0.2888 0.3465 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.91 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 : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6XH1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000249323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL, NON FIXED EXIT SLIT REMARK 200 OPTICS : RH COATED COLLIMATING MIRRORS, K REMARK 200 -B FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MAR 15, 2019 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.74 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7660 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 39.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX 1.15.2_3472 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM NITRATE, 20% (W/V) PEG REMARK 280 -3350, PH 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 146.97450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.11300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.11300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 220.46175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.11300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.11300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.48725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.11300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.11300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 220.46175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.11300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.11300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 73.48725 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 146.97450 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER A 29 NH2 ARG A 70 6557 2.10 REMARK 500 REMARK 500 REMARK: NULL DBREF 6XH1 A 6 91 PDB 6XH1 6XH1 6 91 DBREF 6XH1 D 18 44 PDB 6XH1 6XH1 18 44 SEQRES 1 A 86 THR ARG PRO ASN HIS THR ILE TYR ILE ASN ASN LEU ASN SEQRES 2 A 86 SER LYS ILE LYS LYS ASP GLU LEU LYS LYS SER LEU HIS SEQRES 3 A 86 ALA ILE PHE SER ARG PHE GLY GLN ILE LEU ASP ILE LEU SEQRES 4 A 86 VAL PRO ARG ARG ARG ARG PRO ARG GLY GLN ALA PHE VAL SEQRES 5 A 86 ILE PHE LYS GLU VAL SER SER ALA THR ASN ALA LEU ARG SEQRES 6 A 86 SER MET GLN GLY PHE PRO PHE TYR ASP LYS PRO MET ALA SEQRES 7 A 86 ILE GLN TYR ALA LYS THR ASP LYS SEQRES 1 D 27 G G A G A U C U G A G C C SEQRES 2 D 27 U G G G A G C U C U C U C SEQRES 3 D 27 C FORMUL 3 HOH *43(H2 O) HELIX 1 AA1 LYS A 22 SER A 35 1 14 HELIX 2 AA2 ARG A 36 GLY A 38 5 3 HELIX 3 AA3 GLU A 61 MET A 72 1 12 SHEET 1 AA1 4 ILE A 40 LEU A 44 0 SHEET 2 AA1 4 GLN A 54 PHE A 59 -1 O ILE A 58 N LEU A 41 SHEET 3 AA1 4 THR A 11 ASN A 15 -1 N ILE A 14 O ALA A 55 SHEET 4 AA1 4 ALA A 83 TYR A 86 -1 O GLN A 85 N TYR A 13 CRYST1 40.226 40.226 293.949 90.00 90.00 90.00 P 43 21 2 8 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 0.024860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003402 0.00000 TER 1444 LYS A 91 TER 2310 C D 44 HETATM 2311 O HOH A 101 54.498 5.850 318.588 1.00 32.76 O HETATM 2312 O HOH A 102 74.678 17.394 325.572 1.00 39.59 O HETATM 2313 O HOH A 103 43.714 10.698 316.949 1.00 46.48 O HETATM 2314 O HOH A 104 64.865 18.984 329.180 1.00 30.39 O HETATM 2315 O HOH A 105 44.820 13.326 334.355 1.00 31.40 O HETATM 2316 O HOH A 106 45.855 7.422 329.294 1.00 33.72 O HETATM 2317 O HOH A 107 46.794 7.884 322.546 1.00 36.39 O HETATM 2318 O HOH A 108 38.923 20.663 324.095 1.00 33.70 O HETATM 2319 O HOH A 109 45.440 17.542 332.189 1.00 30.49 O HETATM 2320 O HOH A 110 62.720 19.980 330.414 1.00 31.41 O HETATM 2321 O HOH A 111 68.799 24.647 328.490 1.00 34.44 O HETATM 2322 O HOH A 112 47.563 23.842 328.481 1.00 36.29 O HETATM 2323 O HOH A 113 52.103 3.973 323.627 1.00 29.09 O HETATM 2324 O HOH A 114 65.061 26.902 309.834 1.00 38.50 O HETATM 2325 O HOH A 115 60.785 16.941 314.401 1.00 50.55 O HETATM 2326 O HOH A 116 46.217 4.690 324.822 1.00 23.83 O HETATM 2327 O HOH A 117 52.512 5.769 337.889 1.00 29.45 O HETATM 2328 O HOH A 118 53.467 5.214 321.861 1.00 35.76 O HETATM 2329 O HOH A 119 40.197 10.957 321.667 1.00 41.40 O HETATM 2330 O HOH A 120 39.722 20.117 318.535 1.00 37.06 O HETATM 2331 O HOH A 121 55.801 19.556 339.977 1.00 33.06 O HETATM 2332 O HOH D 101 75.046 29.060 315.143 1.00 27.98 O HETATM 2333 O HOH D 102 53.927 22.293 297.572 1.00 57.15 O HETATM 2334 O HOH D 103 61.603 20.848 307.192 1.00 57.42 O HETATM 2335 O HOH D 104 75.888 30.615 298.472 1.00 45.37 O HETATM 2336 O HOH D 105 58.342 43.074 332.772 1.00 47.51 O HETATM 2337 O HOH D 106 58.453 41.761 328.980 1.00 29.83 O HETATM 2338 O HOH D 107 65.981 38.052 305.148 1.00 49.17 O HETATM 2339 O HOH D 108 60.269 29.065 324.297 1.00 35.45 O HETATM 2340 O HOH D 109 73.356 24.377 306.895 1.00 35.78 O HETATM 2341 O HOH D 110 72.931 32.420 314.646 1.00 44.52 O HETATM 2342 O HOH D 111 60.826 39.537 307.989 1.00 39.58 O HETATM 2343 O HOH D 112 65.259 28.596 311.732 1.00 37.31 O HETATM 2344 O HOH D 113 63.387 30.226 311.936 1.00 46.44 O HETATM 2345 O HOH D 114 69.002 38.996 317.497 1.00 27.97 O HETATM 2346 O HOH D 115 62.189 24.098 299.698 1.00 43.67 O HETATM 2347 O HOH D 116 69.915 22.592 319.184 1.00 38.49 O HETATM 2348 O HOH D 117 68.958 40.009 325.886 1.00 30.53 O HETATM 2349 O HOH D 118 69.127 23.051 296.671 1.00 41.40 O HETATM 2350 O HOH D 119 66.388 37.505 323.149 1.00 39.41 O HETATM 2351 O HOH D 120 61.841 41.006 310.259 1.00 46.20 O HETATM 2352 O HOH D 121 64.842 37.228 325.592 1.00 38.10 O HETATM 2353 O HOH D 122 68.103 37.868 305.836 1.00 40.89 O MASTER 227 0 0 3 4 0 0 6 1322 2 0 10 END