HEADER TRANSCRIPTION FACTOR 12-JUN-98 1RXR TITLE HIGH RESOLUTION SOLUTION STRUCTURE OF THE RETINOID X RECEPTOR DNA TITLE 2 BINDING DOMAIN, NMR, 20 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR-ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN, 130-212; COMPND 5 SYNONYM: RXR-ALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: BL21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24A KEYWDS TRANSCRIPTION FACTOR, NUCLEAR HORMONE RECEPTOR, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.M.A.HOLMBECK,M.P.FOSTER,D.R.CASIMIRO,D.S.SEM,H.J.DYSON,P.E.WRIGHT REVDAT 4 01-MAY-24 1RXR 1 REMARK SEQADV LINK REVDAT 3 14-MAR-18 1RXR 1 REMARK SEQADV REVDAT 2 24-FEB-09 1RXR 1 VERSN REVDAT 1 11-NOV-98 1RXR 0 JRNL AUTH S.M.HOLMBECK,M.P.FOSTER,D.R.CASIMIRO,D.S.SEM,H.J.DYSON, JRNL AUTH 2 P.E.WRIGHT JRNL TITL HIGH-RESOLUTION SOLUTION STRUCTURE OF THE RETINOID X JRNL TITL 2 RECEPTOR DNA-BINDING DOMAIN. JRNL REF J.MOL.BIOL. V. 281 271 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9698548 JRNL DOI 10.1006/JMBI.1998.1908 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, REMARK 3 FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 1RXR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176268. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : CBCA(CO)NH; HBHA(CBCACO)NH; REMARK 210 CBCANH; C(CO)NH-TOCSY; HCCH-COSY; REMARK 210 HCCH-TOCSY; 13C-EDITED NOESY; REMARK 210 15N-EDITED NOESY; 15N-EDITED REMARK 210 TOCSY; HNHA; HNHB; HACAHB-COSY; REMARK 210 13C-13CO; 13C-15N SPIN ECHO REMARK 210 DIFFERENCE CT-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SYBYL TRIAD TRIAD, DIANA, AMBER REMARK 210 METHOD USED : DISTANCE GEOMETRY AND RESTRAINED REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 83 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST RESTRAINT VIOLATIONS AND REMARK 210 AMBER ENERGIES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED RXR-DBD REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 4 CYS A 177 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 14 ARG A 164 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 HIS A 133 70.89 -69.06 REMARK 500 1 ILE A 137 -73.56 -80.63 REMARK 500 1 ASN A 185 -8.87 -58.42 REMARK 500 1 LYS A 201 73.78 -69.90 REMARK 500 2 THR A 131 -60.75 71.97 REMARK 500 2 CYS A 177 99.18 -50.69 REMARK 500 2 CYS A 187 35.84 -150.87 REMARK 500 2 LYS A 201 85.42 -67.75 REMARK 500 2 GLN A 206 38.76 -80.28 REMARK 500 3 LEU A 167 94.28 -63.89 REMARK 500 3 ARG A 172 48.00 -75.68 REMARK 500 3 LYS A 201 85.62 -69.37 REMARK 500 4 HIS A 133 156.09 -47.38 REMARK 500 4 ARG A 172 46.76 -76.75 REMARK 500 4 ASP A 173 -109.06 -160.25 REMARK 500 4 CYS A 177 66.33 -67.91 REMARK 500 4 ARG A 182 63.20 -112.30 REMARK 500 4 LYS A 201 86.25 -70.00 REMARK 500 5 HIS A 133 -177.57 -60.14 REMARK 500 5 ASP A 173 -139.29 -156.12 REMARK 500 5 LYS A 201 79.68 -68.88 REMARK 500 6 ASP A 173 -135.11 -131.36 REMARK 500 6 ASN A 174 -158.22 -129.10 REMARK 500 6 LYS A 175 -4.96 -54.27 REMARK 500 6 GLN A 183 45.43 -71.55 REMARK 500 6 GLN A 188 -79.68 -42.34 REMARK 500 6 LYS A 201 84.27 -65.38 REMARK 500 7 THR A 131 -70.25 -60.93 REMARK 500 7 ASN A 174 -150.12 -86.28 REMARK 500 7 LYS A 175 -6.78 -54.44 REMARK 500 7 LYS A 201 84.61 -64.82 REMARK 500 8 THR A 131 -56.68 70.17 REMARK 500 8 ILE A 137 -78.90 -80.97 REMARK 500 8 ASP A 173 -127.11 -149.67 REMARK 500 8 LYS A 201 82.01 -66.23 REMARK 500 8 ARG A 211 69.09 -63.96 REMARK 500 9 CYS A 187 34.68 -154.14 REMARK 500 9 LYS A 201 82.89 -69.89 REMARK 500 9 GLN A 206 38.85 -90.14 REMARK 500 9 GLU A 207 -77.64 -84.38 REMARK 500 9 ARG A 209 43.95 -74.12 REMARK 500 10 ARG A 186 -38.47 -38.69 REMARK 500 10 CYS A 187 50.00 -79.14 REMARK 500 10 LYS A 201 86.96 -66.68 REMARK 500 10 ARG A 209 131.39 -38.96 REMARK 500 11 THR A 131 -69.50 70.54 REMARK 500 11 ASP A 173 -110.22 -99.98 REMARK 500 11 CYS A 177 72.14 -69.55 REMARK 500 11 ARG A 209 72.19 -106.07 REMARK 500 12 THR A 131 -63.99 67.88 REMARK 500 REMARK 500 THIS ENTRY HAS 94 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 TYR A 147 0.09 SIDE CHAIN REMARK 500 1 ARG A 161 0.08 SIDE CHAIN REMARK 500 1 ARG A 172 0.12 SIDE CHAIN REMARK 500 1 TYR A 192 0.14 SIDE CHAIN REMARK 500 2 TYR A 150 0.11 SIDE CHAIN REMARK 500 2 TYR A 189 0.07 SIDE CHAIN REMARK 500 2 TYR A 192 0.14 SIDE CHAIN REMARK 500 3 TYR A 169 0.09 SIDE CHAIN REMARK 500 3 ARG A 182 0.10 SIDE CHAIN REMARK 500 4 TYR A 192 0.16 SIDE CHAIN REMARK 500 5 ARG A 141 0.10 SIDE CHAIN REMARK 500 5 TYR A 189 0.08 SIDE CHAIN REMARK 500 5 TYR A 192 0.16 SIDE CHAIN REMARK 500 6 TYR A 169 0.29 SIDE CHAIN REMARK 500 6 TYR A 189 0.07 SIDE CHAIN REMARK 500 8 TYR A 189 0.07 SIDE CHAIN REMARK 500 8 TYR A 192 0.07 SIDE CHAIN REMARK 500 9 PHE A 158 0.09 SIDE CHAIN REMARK 500 9 TYR A 189 0.07 SIDE CHAIN REMARK 500 9 TYR A 192 0.17 SIDE CHAIN REMARK 500 9 ARG A 209 0.10 SIDE CHAIN REMARK 500 10 TYR A 150 0.09 SIDE CHAIN REMARK 500 10 PHE A 158 0.10 SIDE CHAIN REMARK 500 10 ARG A 161 0.09 SIDE CHAIN REMARK 500 10 TYR A 189 0.09 SIDE CHAIN REMARK 500 10 TYR A 192 0.14 SIDE CHAIN REMARK 500 11 PHE A 158 0.08 SIDE CHAIN REMARK 500 11 TYR A 169 0.09 SIDE CHAIN REMARK 500 11 ARG A 184 0.10 SIDE CHAIN REMARK 500 11 TYR A 189 0.10 SIDE CHAIN REMARK 500 11 TYR A 192 0.08 SIDE CHAIN REMARK 500 12 TYR A 169 0.08 SIDE CHAIN REMARK 500 13 TYR A 169 0.11 SIDE CHAIN REMARK 500 13 ARG A 186 0.10 SIDE CHAIN REMARK 500 13 TYR A 192 0.07 SIDE CHAIN REMARK 500 14 TYR A 169 0.11 SIDE CHAIN REMARK 500 14 ARG A 184 0.10 SIDE CHAIN REMARK 500 14 TYR A 189 0.07 SIDE CHAIN REMARK 500 14 TYR A 192 0.07 SIDE CHAIN REMARK 500 15 TYR A 150 0.09 SIDE CHAIN REMARK 500 15 TYR A 169 0.08 SIDE CHAIN REMARK 500 16 ARG A 141 0.08 SIDE CHAIN REMARK 500 16 TYR A 150 0.08 SIDE CHAIN REMARK 500 16 TYR A 169 0.08 SIDE CHAIN REMARK 500 16 TYR A 189 0.07 SIDE CHAIN REMARK 500 17 ARG A 191 0.08 SIDE CHAIN REMARK 500 17 TYR A 192 0.07 SIDE CHAIN REMARK 500 18 TYR A 147 0.09 SIDE CHAIN REMARK 500 18 TYR A 192 0.07 SIDE CHAIN REMARK 500 19 TYR A 169 0.11 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 53 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 213 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 135 SG REMARK 620 2 CYS A 138 SG 108.2 REMARK 620 3 CYS A 152 SG 110.0 108.5 REMARK 620 4 CYS A 155 SG 108.2 112.5 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 214 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 171 SG REMARK 620 2 CYS A 177 SG 112.9 REMARK 620 3 CYS A 187 SG 107.7 110.8 REMARK 620 4 CYS A 190 SG 108.3 109.0 108.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 214 DBREF 1RXR A 130 212 UNP P19793 RXRA_HUMAN 130 212 SEQADV 1RXR ALA A 195 UNP P19793 CYS 195 ENGINEERED MUTATION SEQRES 1 A 83 PHE THR LYS HIS ILE CYS ALA ILE CYS GLY ASP ARG SER SEQRES 2 A 83 SER GLY LYS HIS TYR GLY VAL TYR SER CYS GLU GLY CYS SEQRES 3 A 83 LYS GLY PHE PHE LYS ARG THR VAL ARG LYS ASP LEU THR SEQRES 4 A 83 TYR THR CYS ARG ASP ASN LYS ASP CYS LEU ILE ASP LYS SEQRES 5 A 83 ARG GLN ARG ASN ARG CYS GLN TYR CYS ARG TYR GLN LYS SEQRES 6 A 83 ALA LEU ALA MET GLY MET LYS ARG GLU ALA VAL GLN GLU SEQRES 7 A 83 GLU ARG GLN ARG GLY HET ZN A 213 1 HET ZN A 214 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 GLU A 153 LYS A 165 1 13 HELIX 2 2 GLN A 188 MET A 198 1 11 HELIX 3 3 ARG A 202 GLU A 207 5 6 SHEET 1 A 2 GLY A 144 HIS A 146 0 SHEET 2 A 2 VAL A 149 SER A 151 -1 N SER A 151 O GLY A 144 LINK SG CYS A 135 ZN ZN A 213 1555 1555 2.29 LINK SG CYS A 138 ZN ZN A 213 1555 1555 2.30 LINK SG CYS A 152 ZN ZN A 213 1555 1555 2.30 LINK SG CYS A 155 ZN ZN A 213 1555 1555 2.30 LINK SG CYS A 171 ZN ZN A 214 1555 1555 2.30 LINK SG CYS A 177 ZN ZN A 214 1555 1555 2.30 LINK SG CYS A 187 ZN ZN A 214 1555 1555 2.30 LINK SG CYS A 190 ZN ZN A 214 1555 1555 2.30 SITE 1 AC1 4 CYS A 135 CYS A 138 CYS A 152 CYS A 155 SITE 1 AC2 4 CYS A 171 CYS A 177 CYS A 187 CYS A 190 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1