HEADER RNA BINDING PROTEIN/RNA 18-JUN-20 6XH0 TITLE CO-CRYSTAL STRUCTURE OF HIV-1 TAR RNA IN COMPLEX WITH LAB-EVOLVED RRM TITLE 2 TBP6.9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR BINDING PROTEIN 6.9; 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 6XH0 1 REMARK REVDAT 3 16-DEC-20 6XH0 1 JRNL REVDAT 2 04-NOV-20 6XH0 1 JRNL REVDAT 1 14-OCT-20 6XH0 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. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15_3448 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 4920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.288 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 493 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 38.9600 - 4.9186 0.99 1200 134 0.1956 0.2571 REMARK 3 2 4.9186 - 3.9052 1.00 1105 123 0.2207 0.2899 REMARK 3 3 3.9052 - 3.4119 1.00 1062 118 0.2573 0.3002 REMARK 3 4 3.4119 - 3.1001 1.00 1060 118 0.3346 0.3869 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) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.34 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 : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 5 THROUGH 91) REMARK 3 ORIGIN FOR THE GROUP (A): 58.0959 17.5605 316.2741 REMARK 3 T TENSOR REMARK 3 T11: 0.6845 T22: 0.6743 REMARK 3 T33: 0.7619 T12: 0.0102 REMARK 3 T13: 0.0065 T23: 0.0696 REMARK 3 L TENSOR REMARK 3 L11: 2.9228 L22: 4.3126 REMARK 3 L33: 5.0029 L12: 1.7198 REMARK 3 L13: -2.4469 L23: 1.5894 REMARK 3 S TENSOR REMARK 3 S11: -0.2422 S12: 0.1818 S13: 0.1264 REMARK 3 S21: 0.0801 S22: 0.1045 S23: 0.1302 REMARK 3 S31: 0.4108 S32: 0.1082 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'D' AND RESID 18 THROUGH 44) REMARK 3 ORIGIN FOR THE GROUP (A): 67.7858 29.5363 302.2904 REMARK 3 T TENSOR REMARK 3 T11: 0.8970 T22: 1.0265 REMARK 3 T33: 0.8711 T12: 0.0258 REMARK 3 T13: 0.0813 T23: 0.0511 REMARK 3 L TENSOR REMARK 3 L11: 1.6061 L22: 3.4090 REMARK 3 L33: 1.8233 L12: -1.9020 REMARK 3 L13: -1.0819 L23: 0.1914 REMARK 3 S TENSOR REMARK 3 S11: 0.3453 S12: 0.3902 S13: 0.3850 REMARK 3 S21: -0.5138 S22: -0.2205 S23: -0.4947 REMARK 3 S31: -0.1708 S32: -0.1085 S33: 0.0001 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 6XH0 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_1000248109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.9795 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL SI(111) 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 JAN 26, 2018 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 : 27/03/18 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4920 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17.5% PEG 4000, 0.05 M MES MONOHYDRATE REMARK 280 PH 6.0, 0.005 M MGCL2(H20)6, PH 5.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 143.20050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.24700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.24700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 214.80075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.24700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.24700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 71.60025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.24700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.24700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 214.80075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.24700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.24700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 71.60025 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 143.20050 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 101 DBREF 6XH0 A 5 91 PDB 6XH0 6XH0 5 91 DBREF 6XH0 D 18 44 PDB 6XH0 6XH0 18 44 SEQRES 1 A 87 GLY THR ARG PRO ASN HIS THR ILE TYR ILE ASN ASN LEU SEQRES 2 A 87 ASN SER LYS ILE LYS LYS ASP GLU LEU LYS LYS SER LEU SEQRES 3 A 87 HIS ALA ILE PHE SER ARG PHE GLY GLN ILE LEU ASP ILE SEQRES 4 A 87 LEU VAL PRO ARG ARG ARG THR PRO ARG GLY GLN ALA PHE SEQRES 5 A 87 VAL ILE PHE LYS GLU VAL SER SER ALA THR ASN ALA LEU SEQRES 6 A 87 ARG SER MET GLN GLY PHE PRO PHE TYR ASP LYS PRO MET SEQRES 7 A 87 ALA ILE GLN TYR ALA LYS THR ASP ARG SEQRES 1 D 27 G C 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 G SEQRES 3 D 27 C HET MG D 101 1 HET MG D 102 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 5 HOH *3(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 GLN A 73 1 13 SHEET 1 AA1 4 ILE A 40 LEU A 44 0 SHEET 2 AA1 4 ALA A 55 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 SHEET 1 AA2 2 PRO A 76 PHE A 77 0 SHEET 2 AA2 2 LYS A 80 PRO A 81 -1 O LYS A 80 N PHE A 77 SITE 1 AC1 1 U D 31 CRYST1 40.494 40.494 286.401 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 0.024695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003492 0.00000