HEADER TRANSCRIPTION 02-MAY-22 7UW4 TITLE CRYSTAL STRUCTURE OF HUMAN RETINOID X RECEPTOR ALPHA LIGAND BINDING TITLE 2 DOMAIN COMPLEX WITH UAB113 AND COACTIVATOR PEPTIDE GRIP-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X COMPND 5 RECEPTOR ALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 2; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: NCOA-2,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 75,BHLHE75, COMPND 11 TRANSCRIPTIONAL INTERMEDIARY FACTOR 2,HTIF2; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RXRA, NR2B1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS RETINOID X RECEPTOR, RETINOID X RECEPTOR ALPHA, LIGAND BINDING KEYWDS 2 DOMAIN, COACTIVATOR COMPLEX, INHIBITOR COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR D.CHATTOPADHYAY,Z.YANG,V.ATIGADDA REVDAT 2 25-OCT-23 7UW4 1 REMARK REVDAT 1 15-MAR-23 7UW4 0 JRNL AUTH V.R.ATIGADDA,M.P.KASHYAP,Z.YANG,D.CHATTOPADHYAY,N.MELO, JRNL AUTH 2 R.SINHA,O.V.BELYAEVA,C.F.CHOU,P.L.CHANG,N.Y.KEDISHVILI, JRNL AUTH 3 C.J.GRUBBS,M.B.RENFROW,D.D.MUCCIO,C.A.ELMETS,M.ATHAR JRNL TITL CONFORMATIONALLY DEFINED REXINOIDS FOR THE PREVENTION OF JRNL TITL 2 INFLAMMATION AND NONMELANOMA SKIN CANCERS. JRNL REF J.MED.CHEM. V. 65 14409 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 36318154 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00735 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 709 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 35.8400 - 3.5900 1.00 3025 155 0.1955 0.2041 REMARK 3 2 3.5900 - 2.8500 1.00 2862 143 0.2604 0.2810 REMARK 3 3 2.8500 - 2.4900 1.00 2856 123 0.2498 0.3012 REMARK 3 4 2.4900 - 2.2600 1.00 2787 152 0.2426 0.3295 REMARK 3 5 2.2600 - 2.1000 1.00 2787 136 0.2912 0.3344 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) : 0.268 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.58 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 : 0.003 1806 REMARK 3 ANGLE : 0.608 2436 REMARK 3 CHIRALITY : 0.040 279 REMARK 3 PLANARITY : 0.004 311 REMARK 3 DIHEDRAL : 14.331 688 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 7UW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000264592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.0 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 : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15104 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 65.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.20 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.10 REMARK 200 R MERGE FOR SHELL (I) : 1.01400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: 4K4J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS, PH 7.0, 7% PEG4000, REMARK 280 5% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K 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 56.21950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.90100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.90100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 84.32925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.90100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.90100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.10975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.90100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.90100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 84.32925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.90100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.90100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.10975 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 56.21950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 223 REMARK 465 SER A 224 REMARK 465 SER A 225 REMARK 465 ALA A 226 REMARK 465 ASN A 227 REMARK 465 GLU A 228 REMARK 465 PRO A 244 REMARK 465 LYS A 245 REMARK 465 THR A 246 REMARK 465 GLU A 247 REMARK 465 THR A 248 REMARK 465 TYR A 249 REMARK 465 VAL A 250 REMARK 465 GLU A 251 REMARK 465 ALA A 252 REMARK 465 ASN A 253 REMARK 465 MET A 254 REMARK 465 GLY A 255 REMARK 465 LEU A 256 REMARK 465 ASN A 257 REMARK 465 PRO A 258 REMARK 465 SER A 259 REMARK 465 SER A 260 REMARK 465 PRO A 261 REMARK 465 ASN A 262 REMARK 465 PRO A 458 REMARK 465 HIS A 459 REMARK 465 GLN A 460 REMARK 465 MET A 461 REMARK 465 THR A 462 REMARK 465 LYS B 686 REMARK 465 SER B 697 REMARK 465 SER B 698 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 242 34.15 -97.02 REMARK 500 ASN A 385 86.60 -153.58 REMARK 500 REMARK 500 REMARK: NULL DBREF 7UW4 A 223 462 UNP P19793 RXRA_HUMAN 223 462 DBREF 7UW4 B 686 698 UNP Q15596 NCOA2_HUMAN 686 698 SEQRES 1 A 240 THR SER SER ALA ASN GLU ASP MET PRO VAL GLU ARG ILE SEQRES 2 A 240 LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS THR GLU THR SEQRES 3 A 240 TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SER SER PRO SEQRES 4 A 240 ASN ASP PRO VAL THR ASN ILE CYS GLN ALA ALA ASP LYS SEQRES 5 A 240 GLN LEU PHE THR LEU VAL GLU TRP ALA LYS ARG ILE PRO SEQRES 6 A 240 HIS PHE SER GLU LEU PRO LEU ASP ASP GLN VAL ILE LEU SEQRES 7 A 240 LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE ALA SER PHE SEQRES 8 A 240 SER HIS ARG SER ILE ALA VAL LYS ASP GLY ILE LEU LEU SEQRES 9 A 240 ALA THR GLY LEU HIS VAL HIS ARG ASN SER ALA HIS SER SEQRES 10 A 240 ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL LEU THR GLU SEQRES 11 A 240 LEU VAL SER LYS MET ARG ASP MET GLN MET ASP LYS THR SEQRES 12 A 240 GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU PHE ASN PRO SEQRES 13 A 240 ASP SER LYS GLY LEU SER ASN PRO ALA GLU VAL GLU ALA SEQRES 14 A 240 LEU ARG GLU LYS VAL TYR ALA SER LEU GLU ALA TYR CYS SEQRES 15 A 240 LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG PHE ALA LYS SEQRES 16 A 240 LEU LEU LEU ARG LEU PRO ALA LEU ARG SER ILE GLY LEU SEQRES 17 A 240 LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS LEU ILE GLY SEQRES 18 A 240 ASP THR PRO ILE ASP THR PHE LEU MET GLU MET LEU GLU SEQRES 19 A 240 ALA PRO HIS GLN MET THR SEQRES 1 B 13 LYS HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP SER SER HET OI5 A 501 26 HETNAM OI5 (2E,4E,6Z,8E)-3,7-DIMETHYL-8-[2-(3-METHYLBUTYL)-3- HETNAM 2 OI5 PROPYLCYCLOHEX-2-EN-1-YLIDENE]OCTA-2,4,6-TRIENOIC ACID FORMUL 3 OI5 C24 H36 O2 FORMUL 4 HOH *34(H2 O) HELIX 1 AA1 PRO A 231 VAL A 242 1 12 HELIX 2 AA2 PRO A 264 ARG A 285 1 22 HELIX 3 AA3 PRO A 293 SER A 317 1 25 HELIX 4 AA4 ILE A 318 VAL A 320 5 3 HELIX 5 AA5 ARG A 334 ALA A 340 1 7 HELIX 6 AA6 VAL A 342 LEU A 353 1 12 HELIX 7 AA7 LEU A 353 GLN A 361 1 9 HELIX 8 AA8 ASP A 363 PHE A 376 1 14 HELIX 9 AA9 ASN A 385 TYR A 408 1 24 HELIX 10 AB1 GLY A 413 LEU A 420 1 8 HELIX 11 AB2 ARG A 421 GLY A 443 1 23 HELIX 12 AB3 ASP A 448 LEU A 455 1 8 HELIX 13 AB4 LYS B 688 ASP B 696 1 9 SHEET 1 AA1 2 GLY A 323 LEU A 325 0 SHEET 2 AA1 2 HIS A 331 HIS A 333 -1 O VAL A 332 N ILE A 324 CRYST1 65.802 65.802 112.439 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 0.015197 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008894 0.00000