PDB Short entry for 5N8M HEADER RNA BINDING PROTEIN 23-FEB-17 5N8M TITLE STRUCTURE OF TRBP DSRBD 1 AND 2 IN COMPLEX WITH A 19 BP SIRNA (COMPLEX TITLE 2 A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RISC-LOADING COMPLEX SUBUNIT TARBP2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TAR RNA-BINDING PROTEIN 2,TRANS-ACTIVATION-RESPONSIVE RNA- COMPND 5 BINDING PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: HUTRBP N-TERMINAL DSRBD1 AND 2 (RESIDUES 16 TO 227); COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'- COMPND 10 R(*UP*UP*AP*AP*UP*UP*AP*UP*CP*UP*AP*UP*UP*CP*CP*GP*UP*AP*CP*UP*U)- COMPND 11 3'); COMPND 12 CHAIN: B; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: RNA (5'- COMPND 16 R(*GP*UP*AP*CP*GP*GP*AP*AP*UP*AP*GP*AP*UP*AP*AP*UP*UP*AP*AP*UP*U)- COMPND 17 3'); COMPND 18 CHAIN: C; COMPND 19 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: TARBP2, TRBP; 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: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 15 ORGANISM_TAXID: 32630 KEYWDS TRBP, SIRNA, PROTEIN-RNA COMPLEX, RNAI, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.MASLIAH,C.MARIS,H.-T.F.ALLAIN REVDAT 4 08-MAY-19 5N8M 1 REMARK REVDAT 3 28-MAR-18 5N8M 1 JRNL REVDAT 2 28-FEB-18 5N8M 1 JRNL REVDAT 1 21-FEB-18 5N8M 0 JRNL AUTH G.MASLIAH,C.MARIS,S.L.KONIG,M.YULIKOV,F.AESCHIMANN, JRNL AUTH 2 A.L.MALINOWSKA,J.MABILLE,J.WEILER,A.HOLLA,J.HUNZIKER, JRNL AUTH 3 N.MEISNER-KOBER,B.SCHULER,G.JESCHKE,F.H.ALLAIN JRNL TITL STRUCTURAL BASIS OF SIRNA RECOGNITION BY TRBP JRNL TITL 2 DOUBLE-STRANDED RNA BINDING DOMAINS. JRNL REF EMBO J. V. 37 2018 JRNL REFN ESSN 1460-2075 JRNL PMID 29449323 JRNL DOI 10.15252/EMBJ.201797089 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5N8M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003642. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N; U REMARK 210 -80% 2H] DSRBD1, 1 MM EL86, 90% REMARK 210 H2O/10% D2O; 1 MM [U-100% 13C; U- REMARK 210 100% 15N] DSRBD2, 1 MM EL86, 90% REMARK 210 H2O/10% D2O; 1 MM [U-100% 13C; U- REMARK 210 100% 15N; U-80% 2H] DSRBD12, 1 REMARK 210 MM EL86, 100% D2O; 1 MM [U-100% REMARK 210 13C; U-100% 15N; U-80% 2H] REMARK 210 DSRBD12, 1 MM EL86, 90% H2O/10% REMARK 210 D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N; U-80% 2H] DSRBD12, 1 MM REMARK 210 EL86, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; REMARK 210 HCCCONH; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-15N NOESY; 3D REMARK 210 HCCH-TOCSY; 3D F1-13C-FILTERED, REMARK 210 F2-13C-EDITED NOESY ALIPHATIC- REMARK 210 HMQC; TROSY IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 900 MHZ; 600 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCEIII REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, SPARKY, TOPSPIN 3.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 98 REMARK 465 SER A 99 REMARK 465 MET A 100 REMARK 465 LEU A 101 REMARK 465 GLU A 102 REMARK 465 PRO A 103 REMARK 465 ALA A 104 REMARK 465 LEU A 105 REMARK 465 GLU A 106 REMARK 465 ASP A 107 REMARK 465 SER A 108 REMARK 465 SER A 109 REMARK 465 SER A 110 REMARK 465 PHE A 111 REMARK 465 SER A 112 REMARK 465 PRO A 113 REMARK 465 LEU A 114 REMARK 465 ASP A 115 REMARK 465 SER A 116 REMARK 465 SER A 117 REMARK 465 LEU A 118 REMARK 465 PRO A 119 REMARK 465 GLU A 120 REMARK 465 ASP A 121 REMARK 465 ILE A 122 REMARK 465 PRO A 123 REMARK 465 VAL A 124 REMARK 465 PHE A 125 REMARK 465 THR A 126 REMARK 465 ALA A 127 REMARK 465 ALA A 128 REMARK 465 ALA A 129 REMARK 465 ALA A 130 REMARK 465 ALA A 131 REMARK 465 THR A 132 REMARK 465 PRO A 133 REMARK 465 VAL A 134 REMARK 465 PRO A 135 REMARK 465 SER A 136 REMARK 465 VAL A 137 REMARK 465 VAL A 138 REMARK 465 LEU A 139 REMARK 465 THR A 140 REMARK 465 ARG A 141 REMARK 465 SER A 142 REMARK 465 PRO A 143 REMARK 465 PRO A 144 REMARK 465 MET A 145 REMARK 465 GLU A 146 REMARK 465 LEU A 147 REMARK 465 GLN A 148 REMARK 465 PRO A 149 REMARK 465 PRO A 150 REMARK 465 VAL A 151 REMARK 465 SER A 152 REMARK 465 PRO A 153 REMARK 465 GLN A 154 REMARK 465 GLN A 155 REMARK 465 SER A 156 REMARK 465 GLU A 157 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 7 C C 25 O4' - C1' - N1 ANGL. DEV. = 4.2 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 ASN A 26 55.65 -156.26 REMARK 500 1 ALA A 53 87.31 -151.10 REMARK 500 1 ALA A 57 42.41 -74.27 REMARK 500 1 HIS A 58 -22.82 -151.29 REMARK 500 1 GLN A 59 57.95 -161.34 REMARK 500 2 SER A 15 -169.97 57.36 REMARK 500 2 GLN A 59 53.59 -159.07 REMARK 500 2 ASP A 70 -8.60 67.91 REMARK 500 2 ARG A 200 -21.41 -146.90 REMARK 500 3 ASN A 26 57.15 -148.34 REMARK 500 3 ALA A 57 40.75 -73.88 REMARK 500 3 HIS A 58 -26.98 -144.70 REMARK 500 3 GLN A 59 62.27 -162.13 REMARK 500 3 ARG A 189 27.52 -140.65 REMARK 500 3 ARG A 200 -6.35 -144.65 REMARK 500 4 ASN A 26 52.32 -143.17 REMARK 500 4 ARG A 200 -23.32 -148.78 REMARK 500 5 ASN A 26 56.13 -151.02 REMARK 500 5 PRO A 46 97.59 -68.36 REMARK 500 5 GLN A 59 65.24 -163.23 REMARK 500 5 ASN A 159 71.97 46.19 REMARK 500 5 ARG A 200 -20.05 -147.15 REMARK 500 6 SER A 15 -167.85 57.07 REMARK 500 6 GLN A 56 -15.06 -140.43 REMARK 500 6 HIS A 58 -28.12 55.08 REMARK 500 6 GLN A 59 54.28 -164.17 REMARK 500 6 ARG A 200 -17.32 -142.59 REMARK 500 7 ASN A 26 53.24 -145.00 REMARK 500 7 ALA A 53 87.14 -150.65 REMARK 500 7 ALA A 57 -55.26 -159.91 REMARK 500 7 ASN A 61 68.61 39.70 REMARK 500 7 ARG A 200 -30.05 -146.60 REMARK 500 8 ASN A 26 48.22 -141.67 REMARK 500 8 GLN A 59 48.76 -157.60 REMARK 500 8 ASN A 159 71.91 45.70 REMARK 500 8 ARG A 189 38.71 -142.31 REMARK 500 9 PRO A 46 98.56 -67.97 REMARK 500 9 ALA A 53 87.45 -156.05 REMARK 500 9 ALA A 57 -32.67 -165.50 REMARK 500 9 ASN A 61 64.77 38.34 REMARK 500 9 ARG A 200 -20.27 -149.19 REMARK 500 10 ASN A 26 53.28 -145.81 REMARK 500 10 ALA A 53 87.38 -150.74 REMARK 500 10 ALA A 57 -41.83 64.20 REMARK 500 10 ARG A 200 -18.52 -146.86 REMARK 500 11 ASN A 26 56.95 -143.27 REMARK 500 11 ALA A 53 88.33 -150.62 REMARK 500 11 GLN A 59 62.88 -160.39 REMARK 500 11 ARG A 200 -9.16 -142.93 REMARK 500 12 ASN A 26 54.79 -146.83 REMARK 500 REMARK 500 THIS ENTRY HAS 99 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34104 RELATED DB: BMRB REMARK 900 STRUCTURE OF TRBP DSRBD 1 AND 2 IN COMPLEX WITH A 19 BP SIRNA REMARK 900 (COMPLEX A) DBREF 5N8M A 16 227 UNP Q15633 TRBP2_HUMAN 16 227 DBREF 5N8M B 1 21 PDB 5N8M 5N8M 1 21 DBREF 5N8M C 22 42 PDB 5N8M 5N8M 22 42 SEQADV 5N8M GLY A 13 UNP Q15633 EXPRESSION TAG SEQADV 5N8M GLY A 14 UNP Q15633 EXPRESSION TAG SEQADV 5N8M SER A 15 UNP Q15633 EXPRESSION TAG SEQRES 1 A 215 GLY GLY SER LEU PRO SER ILE GLU GLN MET LEU ALA ALA SEQRES 2 A 215 ASN PRO GLY LYS THR PRO ILE SER LEU LEU GLN GLU TYR SEQRES 3 A 215 GLY THR ARG ILE GLY LYS THR PRO VAL TYR ASP LEU LEU SEQRES 4 A 215 LYS ALA GLU GLY GLN ALA HIS GLN PRO ASN PHE THR PHE SEQRES 5 A 215 ARG VAL THR VAL GLY ASP THR SER CYS THR GLY GLN GLY SEQRES 6 A 215 PRO SER LYS LYS ALA ALA LYS HIS LYS ALA ALA GLU VAL SEQRES 7 A 215 ALA LEU LYS HIS LEU LYS GLY GLY SER MET LEU GLU PRO SEQRES 8 A 215 ALA LEU GLU ASP SER SER SER PHE SER PRO LEU ASP SER SEQRES 9 A 215 SER LEU PRO GLU ASP ILE PRO VAL PHE THR ALA ALA ALA SEQRES 10 A 215 ALA ALA THR PRO VAL PRO SER VAL VAL LEU THR ARG SER SEQRES 11 A 215 PRO PRO MET GLU LEU GLN PRO PRO VAL SER PRO GLN GLN SEQRES 12 A 215 SER GLU CYS ASN PRO VAL GLY ALA LEU GLN GLU LEU VAL SEQRES 13 A 215 VAL GLN LYS GLY TRP ARG LEU PRO GLU TYR THR VAL THR SEQRES 14 A 215 GLN GLU SER GLY PRO ALA HIS ARG LYS GLU PHE THR MET SEQRES 15 A 215 THR CYS ARG VAL GLU ARG PHE ILE GLU ILE GLY SER GLY SEQRES 16 A 215 THR SER LYS LYS LEU ALA LYS ARG ASN ALA ALA ALA LYS SEQRES 17 A 215 MET LEU LEU ARG VAL HIS THR SEQRES 1 B 21 U U A A U U A U C U A U U SEQRES 2 B 21 C C G U A C U U SEQRES 1 C 21 G U A C G G A A U A G A U SEQRES 2 C 21 A A U U A A U U HELIX 1 AA1 SER A 18 ASN A 26 1 9 HELIX 2 AA2 THR A 30 GLY A 43 1 14 HELIX 3 AA3 SER A 79 LYS A 96 1 18 HELIX 4 AA4 ASN A 159 LYS A 171 1 13 HELIX 5 AA5 PRO A 186 LYS A 190 5 5 HELIX 6 AA6 SER A 209 HIS A 226 1 18 SHEET 1 AA1 3 VAL A 47 GLU A 54 0 SHEET 2 AA1 3 ASN A 61 VAL A 68 -1 O ASN A 61 N GLU A 54 SHEET 3 AA1 3 THR A 71 GLY A 77 -1 O THR A 71 N VAL A 68 SHEET 1 AA2 3 GLU A 177 GLU A 183 0 SHEET 2 AA2 3 PHE A 192 ARG A 197 -1 O THR A 195 N THR A 179 SHEET 3 AA2 3 ILE A 202 GLY A 207 -1 O GLU A 203 N CYS A 196 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