HEADER RNA BINDING PROTEIN 31-MAY-12 2LTS TITLE SOLUTION STRUCTURE OF RDE-4(150-235) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN RDE-4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DSRBD2 (UNIPROT RESIDUES 150-235); COMPND 5 SYNONYM: RNA INTERFERENCE PROMOTING FACTOR; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: RDE-4, T20G5.11; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS RDE-4, DSRBD2, RNAI, RDE-4DC, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.DESHMUKH,S.CHILIVERI REVDAT 5 15-MAY-24 2LTS 1 REMARK REVDAT 4 14-JUN-23 2LTS 1 REMARK SEQADV REVDAT 3 27-APR-16 2LTS 1 DBREF REMARK SEQADV SEQRES REVDAT 2 12-FEB-14 2LTS 1 JRNL REVDAT 1 04-DEC-13 2LTS 0 JRNL AUTH S.C.CHILIVERI,M.V.DESHMUKH JRNL TITL STRUCTURE OF RDE-4 DSRBDS AND MUTATIONAL STUDIES PROVIDE JRNL TITL 2 INSIGHTS INTO DSRNA RECOGNITION IN THE CAENORHABDITIS JRNL TITL 3 ELEGANS RNAI PATHWAY. JRNL REF BIOCHEM.J. V. 458 119 2014 JRNL REFN ISSN 0264-6021 JRNL PMID 24256178 JRNL DOI 10.1042/BJ20131347 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.C.CHILIVERI,S.KUMAR,U.K.MARELLI,M.V.DESHMUKH REMARK 1 TITL BACKBONE AND SIDECHAIN METHYL ILE (DELTA1), LEU AND VAL REMARK 1 TITL 2 CHEMICAL SHIFT ASSIGNMENTS OF RDE-4 (1-243), AN RNA REMARK 1 TITL 3 INTERFERENCE INITIATION PROTEIN IN C. ELEGANS. REMARK 1 REF BIOMOL.NMR ASSIGN. 2011 REMARK 1 REFN ESSN 1874-270X REMARK 1 PMID 22002349 REMARK 1 DOI 10.1007/S12104-011-9343-0 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE PROTEIN USED IN THIS STUDY (UNP REMARK 3 RESIDUES 1-243) IS A FRAGMENT OF RDE-4, AN RNAI INITIATOR REMARK 3 PROTEIN IN C. ELEGANS. IT CONSISTS OF FOUR REGIONS, WHICH ARE REMARK 3 THE N-TERMINAL REGION (1-43), DSRBD1 (44-107), LINKER (108-168), REMARK 3 AND DSRBD2 (169-235). IN THE COURSE OF ASSIGNMENTS AND STRUCTURE REMARK 3 CALCULATION, A PART OF THE LINKER (RESIDUES 126-149) IS FOUND TO REMARK 3 BE HIGHLY FLEXIBLE. NO SPATIAL INTER-DOMAIN CONTACTS WERE REMARK 3 OBSERVED BETWEEN THE TWO DSRBDS. THEREFORE, SOLUTION STRUCTURES REMARK 3 OF DSRBD1 AND DSRBD2 WERE CALCULATED SEPARATELY. FOR 2LTR, RIGID REMARK 3 PART OF N-TERMINAL REGION (32-43), DSRBD1 (44-107) AND LINKER REMARK 3 REGION (108-136) WERE USED TO CALCULATE THE FINAL STRUCTURES, REMARK 3 WHEREAS FOR 2LTS, RIGID PART OF THE LINKER (150-168) AND DSRBD2 REMARK 3 (169-235) WERE CHOSEN FOR THE CALCULATION OF THE FINAL REMARK 3 STRUCTURES. THE RELATIVE ORIENTATION BETWEEN TWO STRUCTURES REMARK 3 COULD NOT BE DETERMINED DUE TO THE FLEXIBLE NATURE OF THE LINKER. REMARK 4 REMARK 4 2LTS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000102823. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 0.15; 0.3 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 200 UM [U-100% 15N] RDE-4DC, 90% REMARK 210 H2O/10% D2O; 500 UM [U-100% 13C; REMARK 210 U-100% 15N; U-80% 2H] RDE-4DC, REMARK 210 90% H2O/10% D2O; 500 UM [U-100% REMARK 210 15N; U-100% 13C; U-100% 2H] RDE- REMARK 210 4DC WITH [U-100% 1H] VAL, LEU, REMARK 210 AND ILE RDE-4DC, 90% H2O/10% D2O; REMARK 210 500 UM [U-100% 15N; U-100% 2H] REMARK 210 RDE-4DC WITH [U-100% 13C-METHYL] REMARK 210 VAL, LEU, AND ILE (D1) AND [U- REMARK 210 100% 1H] ILE, LEU, VAL AND PHE REMARK 210 RDE-4DC, 500 UM [U-100% 15N; U- REMARK 210 100% 2H] RDE-4DC WITH [U-100% REMARK 210 13C-METHYL] VAL, LEU, AND ILE REMARK 210 (D1) AND [U-100% 1H] ILE, LEU, REMARK 210 VAL AND TYR RDE-4DC, 90% H2O/10% REMARK 210 D2O; 200 UM [U-10% 13C] RDE-4DC, REMARK 210 90% H2O/10% D2O; 300 UM RDE-4DC, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HN(COCA)CB; 3D HN(CO)CA; REMARK 210 3D HN(CA)CO; 3D HNCACB; 3D REMARK 210 H(CCCO)NH TOCSY; 3D (H)C(CCO)NH REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C(ME-ONLY) NOESY; 3D 1H-13C REMARK 210 NOESY AROMATIC; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PROCHECKNMR, TOPSPIN, NMRVIEW, REMARK 210 CARA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 LEU A 3 REMARK 465 THR A 4 REMARK 465 LYS A 5 REMARK 465 LEU A 6 REMARK 465 THR A 7 REMARK 465 PHE A 8 REMARK 465 GLU A 9 REMARK 465 SER A 10 REMARK 465 VAL A 11 REMARK 465 PHE A 12 REMARK 465 GLY A 13 REMARK 465 GLY A 14 REMARK 465 SER A 15 REMARK 465 ASP A 16 REMARK 465 VAL A 17 REMARK 465 PRO A 18 REMARK 465 MET A 19 REMARK 465 LYS A 20 REMARK 465 PRO A 21 REMARK 465 SER A 22 REMARK 465 ARG A 23 REMARK 465 SER A 24 REMARK 465 GLU A 25 REMARK 465 ASP A 26 REMARK 465 ASN A 27 REMARK 465 LYS A 28 REMARK 465 THR A 29 REMARK 465 PRO A 30 REMARK 465 ARG A 31 REMARK 465 ASN A 32 REMARK 465 ARG A 33 REMARK 465 THR A 34 REMARK 465 ASP A 35 REMARK 465 LEU A 36 REMARK 465 GLU A 37 REMARK 465 MET A 38 REMARK 465 PHE A 39 REMARK 465 LEU A 40 REMARK 465 LYS A 41 REMARK 465 LYS A 42 REMARK 465 THR A 43 REMARK 465 PRO A 44 REMARK 465 LEU A 45 REMARK 465 MET A 46 REMARK 465 VAL A 47 REMARK 465 LEU A 48 REMARK 465 GLU A 49 REMARK 465 GLU A 50 REMARK 465 ALA A 51 REMARK 465 ALA A 52 REMARK 465 LYS A 53 REMARK 465 ALA A 54 REMARK 465 VAL A 55 REMARK 465 TYR A 56 REMARK 465 GLN A 57 REMARK 465 LYS A 58 REMARK 465 THR A 59 REMARK 465 PRO A 60 REMARK 465 THR A 61 REMARK 465 TRP A 62 REMARK 465 GLY A 63 REMARK 465 THR A 64 REMARK 465 VAL A 65 REMARK 465 GLU A 66 REMARK 465 LEU A 67 REMARK 465 PRO A 68 REMARK 465 GLU A 69 REMARK 465 GLY A 70 REMARK 465 PHE A 71 REMARK 465 GLU A 72 REMARK 465 MET A 73 REMARK 465 THR A 74 REMARK 465 LEU A 75 REMARK 465 ILE A 76 REMARK 465 LEU A 77 REMARK 465 ASN A 78 REMARK 465 GLU A 79 REMARK 465 ILE A 80 REMARK 465 THR A 81 REMARK 465 VAL A 82 REMARK 465 LYS A 83 REMARK 465 GLY A 84 REMARK 465 GLN A 85 REMARK 465 ALA A 86 REMARK 465 THR A 87 REMARK 465 SER A 88 REMARK 465 LYS A 89 REMARK 465 LYS A 90 REMARK 465 ALA A 91 REMARK 465 ALA A 92 REMARK 465 ARG A 93 REMARK 465 GLN A 94 REMARK 465 LYS A 95 REMARK 465 ALA A 96 REMARK 465 ALA A 97 REMARK 465 VAL A 98 REMARK 465 GLU A 99 REMARK 465 TYR A 100 REMARK 465 LEU A 101 REMARK 465 ARG A 102 REMARK 465 LYS A 103 REMARK 465 VAL A 104 REMARK 465 VAL A 105 REMARK 465 GLU A 106 REMARK 465 LYS A 107 REMARK 465 GLY A 108 REMARK 465 LYS A 109 REMARK 465 HIS A 110 REMARK 465 GLU A 111 REMARK 465 ILE A 112 REMARK 465 PHE A 113 REMARK 465 PHE A 114 REMARK 465 ILE A 115 REMARK 465 PRO A 116 REMARK 465 GLY A 117 REMARK 465 THR A 118 REMARK 465 THR A 119 REMARK 465 LYS A 120 REMARK 465 GLU A 121 REMARK 465 GLU A 122 REMARK 465 ALA A 123 REMARK 465 LEU A 124 REMARK 465 SER A 125 REMARK 465 ASN A 126 REMARK 465 ILE A 127 REMARK 465 ASP A 128 REMARK 465 GLN A 129 REMARK 465 ILE A 130 REMARK 465 SER A 131 REMARK 465 ASP A 132 REMARK 465 LYS A 133 REMARK 465 ALA A 134 REMARK 465 GLU A 135 REMARK 465 GLU A 136 REMARK 465 LEU A 137 REMARK 465 LYS A 138 REMARK 465 ARG A 139 REMARK 465 SER A 140 REMARK 465 THR A 141 REMARK 465 SER A 142 REMARK 465 ASP A 143 REMARK 465 ALA A 144 REMARK 465 VAL A 145 REMARK 465 GLN A 146 REMARK 465 ASP A 147 REMARK 465 ASN A 148 REMARK 465 ASP A 149 REMARK 465 ILE A 236 REMARK 465 GLU A 237 REMARK 465 SER A 238 REMARK 465 LEU A 239 REMARK 465 GLU A 240 REMARK 465 SER A 241 REMARK 465 TYR A 242 REMARK 465 ASP A 243 REMARK 465 LEU A 244 REMARK 465 GLU A 245 REMARK 465 HIS A 246 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 SER A 153 92.93 160.48 REMARK 500 1 GLU A 159 138.24 -173.56 REMARK 500 1 GLU A 168 108.93 -56.39 REMARK 500 1 LYS A 182 60.07 67.95 REMARK 500 1 GLU A 197 73.82 50.00 REMARK 500 1 ASN A 207 32.14 -145.51 REMARK 500 1 SER A 215 -142.20 -59.05 REMARK 500 1 LYS A 216 168.55 -36.41 REMARK 500 1 LEU A 227 -70.28 -67.77 REMARK 500 2 SER A 153 93.06 157.37 REMARK 500 2 PRO A 161 105.05 -42.38 REMARK 500 2 PRO A 162 -142.38 -54.97 REMARK 500 2 SER A 165 99.57 -34.99 REMARK 500 2 ASN A 207 29.52 -145.48 REMARK 500 2 SER A 215 -142.00 -61.46 REMARK 500 2 LYS A 216 169.12 -36.57 REMARK 500 3 SER A 153 92.63 159.88 REMARK 500 3 ARG A 198 -159.73 -146.09 REMARK 500 3 ASN A 207 27.32 -150.62 REMARK 500 3 SER A 215 -143.27 -55.80 REMARK 500 3 LYS A 216 168.85 -36.93 REMARK 500 4 ASP A 151 -77.50 -54.09 REMARK 500 4 ASP A 152 -57.04 -142.13 REMARK 500 4 SER A 153 93.95 153.19 REMARK 500 4 PRO A 161 98.41 -34.35 REMARK 500 4 GLU A 197 72.15 52.53 REMARK 500 4 ASN A 207 31.68 -146.80 REMARK 500 4 SER A 215 -141.99 -56.96 REMARK 500 4 LYS A 216 169.75 -36.66 REMARK 500 5 ASP A 152 -56.69 -142.18 REMARK 500 5 SER A 153 93.48 157.17 REMARK 500 5 GLU A 197 72.92 52.92 REMARK 500 5 CYS A 206 -54.26 -28.21 REMARK 500 5 ASN A 207 31.17 -149.42 REMARK 500 5 SER A 215 -142.33 -60.72 REMARK 500 5 LYS A 216 169.40 -36.73 REMARK 500 6 ASP A 151 -77.02 -123.52 REMARK 500 6 ASP A 152 -41.20 -139.65 REMARK 500 6 SER A 153 93.58 157.82 REMARK 500 6 SER A 165 111.61 -33.43 REMARK 500 6 PRO A 166 -4.21 -46.69 REMARK 500 6 LYS A 182 60.00 75.29 REMARK 500 6 ASN A 207 36.27 -140.03 REMARK 500 6 SER A 215 -141.45 -61.93 REMARK 500 6 LYS A 216 169.72 -36.53 REMARK 500 7 ASP A 151 31.25 -85.88 REMARK 500 7 ASP A 152 -53.55 -121.54 REMARK 500 7 SER A 153 92.98 158.30 REMARK 500 7 GLU A 197 72.53 53.09 REMARK 500 7 ASN A 207 34.69 -141.55 REMARK 500 REMARK 500 THIS ENTRY HAS 72 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17703 RELATED DB: BMRB REMARK 900 BACKBONE AND STEREO-SPECIFIC ILE(D1), LEU, VAL METHYL SIDECHAIN REMARK 900 CHEMICAL SHIFT ASSIGNMENTS OF RDE-4 (1-243) REMARK 900 RELATED ID: 2LTR RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF RDE-4(32-136) DBREF 2LTS A 1 243 UNP G5EBF5 G5EBF5_CAEEL 1 243 SEQADV 2LTS LEU A 244 UNP G5EBF5 EXPRESSION TAG SEQADV 2LTS GLU A 245 UNP G5EBF5 EXPRESSION TAG SEQADV 2LTS HIS A 246 UNP G5EBF5 EXPRESSION TAG SEQRES 1 A 246 MET ASP LEU THR LYS LEU THR PHE GLU SER VAL PHE GLY SEQRES 2 A 246 GLY SER ASP VAL PRO MET LYS PRO SER ARG SER GLU ASP SEQRES 3 A 246 ASN LYS THR PRO ARG ASN ARG THR ASP LEU GLU MET PHE SEQRES 4 A 246 LEU LYS LYS THR PRO LEU MET VAL LEU GLU GLU ALA ALA SEQRES 5 A 246 LYS ALA VAL TYR GLN LYS THR PRO THR TRP GLY THR VAL SEQRES 6 A 246 GLU LEU PRO GLU GLY PHE GLU MET THR LEU ILE LEU ASN SEQRES 7 A 246 GLU ILE THR VAL LYS GLY GLN ALA THR SER LYS LYS ALA SEQRES 8 A 246 ALA ARG GLN LYS ALA ALA VAL GLU TYR LEU ARG LYS VAL SEQRES 9 A 246 VAL GLU LYS GLY LYS HIS GLU ILE PHE PHE ILE PRO GLY SEQRES 10 A 246 THR THR LYS GLU GLU ALA LEU SER ASN ILE ASP GLN ILE SEQRES 11 A 246 SER ASP LYS ALA GLU GLU LEU LYS ARG SER THR SER ASP SEQRES 12 A 246 ALA VAL GLN ASP ASN ASP ASN ASP ASP SER ILE PRO THR SEQRES 13 A 246 SER ALA GLU PHE PRO PRO GLY ILE SER PRO THR GLU ASN SEQRES 14 A 246 TRP VAL GLY LYS LEU GLN GLU LYS SER GLN LYS SER LYS SEQRES 15 A 246 LEU GLN ALA PRO ILE TYR GLU ASP SER LYS ASN GLU ARG SEQRES 16 A 246 THR GLU ARG PHE LEU VAL ILE CYS THR MET CYS ASN GLN SEQRES 17 A 246 LYS THR ARG GLY ILE ARG SER LYS LYS LYS ASP ALA LYS SEQRES 18 A 246 ASN LEU ALA ALA TRP LEU MET TRP LYS ALA LEU GLU ASP SEQRES 19 A 246 GLY ILE GLU SER LEU GLU SER TYR ASP LEU GLU HIS HELIX 1 1 TRP A 170 LYS A 182 1 13 HELIX 2 2 LYS A 216 ASP A 234 1 19 SHEET 1 A 3 ILE A 187 SER A 191 0 SHEET 2 A 3 PHE A 199 MET A 205 -1 O LEU A 200 N SER A 191 SHEET 3 A 3 GLN A 208 ARG A 214 -1 O GLN A 208 N MET A 205 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