HEADER RNA BINDING PROTEIN/RNA 18-JUN-20 6XH3 TITLE CO-CRYSTAL STRUCTURE OF HIV-1 TAR RNA IN COMPLEX WITH LAB-EVOLVED RRM TITLE 2 TBP6.3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAR BINDING PROTEIN TBP 6.3; 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 6XH3 1 REMARK REVDAT 3 16-DEC-20 6XH3 1 JRNL REVDAT 2 04-NOV-20 6XH3 1 JRNL REVDAT 1 14-OCT-20 6XH3 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. 2.35 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 11000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.530 REMARK 3 FREE R VALUE TEST SET COUNT : 1433 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 39.1100 - 5.0661 0.99 1773 137 0.1943 0.2308 REMARK 3 2 5.0661 - 4.0224 0.99 1782 151 0.1836 0.2039 REMARK 3 3 4.0224 - 3.5143 1.00 1800 146 0.1887 0.2296 REMARK 3 4 3.5143 - 3.1932 0.99 1779 133 0.2081 0.2974 REMARK 3 5 3.1932 - 2.9644 1.00 1800 144 0.2342 0.2549 REMARK 3 6 2.9644 - 2.7897 1.00 1791 149 0.2452 0.2699 REMARK 3 7 2.7897 - 2.6500 1.00 1791 147 0.2388 0.2897 REMARK 3 8 2.6500 - 2.5346 0.99 1700 145 0.2606 0.3104 REMARK 3 9 2.5346 - 2.4371 0.97 1781 147 0.2785 0.3070 REMARK 3 10 2.4371 - 2.3530 0.89 1588 134 0.3040 0.3471 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.06 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 6XH3 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_1000249317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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) : 0.9840 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11000 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 39.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 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: 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): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE, 0.2 M REMARK 280 AMMONIUM FORMATE, 17.5% (W/V) PEG-3350, PH 6.0, VAPOR DIFFUSION, REMARK 280 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 145.99000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 20.30100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 20.30100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 218.98500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 20.30100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 20.30100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 72.99500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 20.30100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.30100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 218.98500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 20.30100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.30100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 72.99500 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 145.99000 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 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 ILE A 93 CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG1 THR A 48 O HOH A 101 2.16 REMARK 500 REMARK 500 REMARK: NULL DBREF 6XH3 A 6 93 PDB 6XH3 6XH3 6 93 DBREF 6XH3 D 18 44 PDB 6XH3 6XH3 18 44 SEQRES 1 A 88 THR ARG PRO ASN HIS THR ILE TYR ILE ASN ASN LEU ASN SEQRES 2 A 88 SER LYS ILE LYS LYS ASP GLU LEU LYS LYS SER LEU HIS SEQRES 3 A 88 ALA ILE PHE SER ARG PHE GLY GLN ILE LEU ASP ILE LEU SEQRES 4 A 88 VAL PRO ARG THR ARG ARG PRO ARG GLY GLN ALA PHE VAL SEQRES 5 A 88 ILE PHE LYS GLU VAL SER SER ALA THR ASN ALA LEU ARG SEQRES 6 A 88 SER MET GLN GLY PHE PRO PHE TYR ASP LYS PRO MET ALA SEQRES 7 A 88 ILE GLN TYR ALA LYS THR ASP ARG THR ILE 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 *65(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 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 40.602 40.602 291.980 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 0.024629 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003425 0.00000