HEADER RNA BINDING PROTEIN 29-MAY-15 2N3H TITLE SOLUTION STRUCTURE OF DRB4 DSRBD2 (VIZ. DRB4(81-151)) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE-STRANDED RNA-BINDING PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DRBM 2 DOMAIN RESIDUES 81-151; COMPND 5 SYNONYM: DSRNA-BINDING PROTEIN 4, ATDRB4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: DBR4, AT3G62800, F26K9.230; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-30A KEYWDS RNAI, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.DESHMUKH,S.CHILIVERI REVDAT 6 15-MAY-24 2N3H 1 REMARK REVDAT 5 14-JUN-23 2N3H 1 REMARK REVDAT 4 14-FEB-18 2N3H 1 JRNL REVDAT 3 07-JUN-17 2N3H 1 JRNL REVDAT 2 09-NOV-16 2N3H 1 DBREF SEQRES REVDAT 1 07-SEP-16 2N3H 0 JRNL AUTH S.C.CHILIVERI,R.AUTE,U.RAI,M.V.DESHMUKH JRNL TITL DRB4 DSRBD1 DRIVES DSRNA RECOGNITION IN ARABIDOPSIS THALIANA JRNL TITL 2 TASI/SIRNA PATHWAY. JRNL REF NUCLEIC ACIDS RES. V. 45 8551 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28575480 JRNL DOI 10.1093/NAR/GKX481 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1.6, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000104374. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 500 UM [U-100% 15N] DRB4(81 REMARK 210 -151), 90% H2O/10% D2O; 500 UM REMARK 210 [U-100% 13C; U-100% 15N] DRB4(81- REMARK 210 151), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D H(CCO)NH-TOCSY; 3D (H) REMARK 210 C(CO)NH-TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 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 : TOPSPIN 2.1.6, CARA 1.8.4, REMARK 210 SPARKY, PROCHECKNMR 3.5.4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASP A 2 REMARK 465 HIS A 3 REMARK 465 VAL A 4 REMARK 465 TYR A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 7 REMARK 465 GLN A 8 REMARK 465 LEU A 9 REMARK 465 GLN A 10 REMARK 465 ALA A 11 REMARK 465 TYR A 12 REMARK 465 ALA A 13 REMARK 465 LEU A 14 REMARK 465 GLN A 15 REMARK 465 HIS A 16 REMARK 465 ASN A 17 REMARK 465 LEU A 18 REMARK 465 GLU A 19 REMARK 465 LEU A 20 REMARK 465 PRO A 21 REMARK 465 VAL A 22 REMARK 465 TYR A 23 REMARK 465 ALA A 24 REMARK 465 ASN A 25 REMARK 465 GLU A 26 REMARK 465 ARG A 27 REMARK 465 GLU A 28 REMARK 465 GLY A 29 REMARK 465 PRO A 30 REMARK 465 PRO A 31 REMARK 465 HIS A 32 REMARK 465 ALA A 33 REMARK 465 PRO A 34 REMARK 465 ARG A 35 REMARK 465 PHE A 36 REMARK 465 ARG A 37 REMARK 465 CYS A 38 REMARK 465 ASN A 39 REMARK 465 VAL A 40 REMARK 465 THR A 41 REMARK 465 PHE A 42 REMARK 465 CYS A 43 REMARK 465 GLY A 44 REMARK 465 GLN A 45 REMARK 465 THR A 46 REMARK 465 PHE A 47 REMARK 465 GLN A 48 REMARK 465 SER A 49 REMARK 465 SER A 50 REMARK 465 GLU A 51 REMARK 465 PHE A 52 REMARK 465 PHE A 53 REMARK 465 PRO A 54 REMARK 465 THR A 55 REMARK 465 LEU A 56 REMARK 465 LYS A 57 REMARK 465 SER A 58 REMARK 465 ALA A 59 REMARK 465 GLU A 60 REMARK 465 HIS A 61 REMARK 465 ALA A 62 REMARK 465 ALA A 63 REMARK 465 ALA A 64 REMARK 465 LYS A 65 REMARK 465 ILE A 66 REMARK 465 ALA A 67 REMARK 465 VAL A 68 REMARK 465 ALA A 69 REMARK 465 SER A 70 REMARK 465 LEU A 71 REMARK 465 THR A 72 REMARK 465 PRO A 73 REMARK 465 GLN A 74 REMARK 465 SER A 75 REMARK 465 PRO A 76 REMARK 465 GLU A 77 REMARK 465 GLY A 78 REMARK 465 ILE A 79 REMARK 465 ASP A 80 REMARK 465 ASN A 152 REMARK 465 SER A 153 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 TYR A 83 -16.37 -45.41 REMARK 500 1 LYS A 131 33.65 -90.90 REMARK 500 2 TYR A 83 -15.50 -47.43 REMARK 500 2 SER A 95 9.03 55.06 REMARK 500 2 SER A 96 -130.82 -59.89 REMARK 500 2 LEU A 98 151.29 -44.94 REMARK 500 2 LYS A 131 35.31 -85.83 REMARK 500 3 TYR A 83 -16.09 -46.46 REMARK 500 3 LEU A 98 152.92 -44.81 REMARK 500 3 LYS A 131 33.07 -88.97 REMARK 500 4 TYR A 83 -16.35 -47.58 REMARK 500 4 LYS A 131 31.09 -90.49 REMARK 500 5 TYR A 83 -15.75 -47.07 REMARK 500 5 SER A 96 -114.73 -79.56 REMARK 500 5 LYS A 131 32.33 -88.19 REMARK 500 6 TYR A 83 -15.29 -46.55 REMARK 500 6 SER A 96 -124.82 -73.08 REMARK 500 6 LEU A 98 152.25 -44.77 REMARK 500 6 LYS A 131 33.38 -93.30 REMARK 500 7 TYR A 83 -16.58 -48.02 REMARK 500 7 SER A 95 47.15 39.49 REMARK 500 7 SER A 96 44.70 -100.48 REMARK 500 7 LEU A 97 93.17 64.66 REMARK 500 7 LYS A 131 32.84 -89.71 REMARK 500 8 TYR A 83 -15.77 -48.56 REMARK 500 8 ALA A 121 19.05 53.32 REMARK 500 8 LYS A 131 35.36 -86.12 REMARK 500 9 TYR A 83 -15.89 -46.05 REMARK 500 9 SER A 95 40.84 39.24 REMARK 500 9 SER A 96 33.26 -87.47 REMARK 500 9 LEU A 97 100.58 76.93 REMARK 500 9 LEU A 98 152.02 -44.21 REMARK 500 9 LYS A 131 33.56 -86.65 REMARK 500 9 ASN A 150 -103.75 41.12 REMARK 500 10 TYR A 83 -15.87 -46.13 REMARK 500 10 SER A 96 -117.40 -80.43 REMARK 500 10 LYS A 131 36.13 -86.28 REMARK 500 11 TYR A 83 -16.36 -46.49 REMARK 500 11 LYS A 131 33.03 -88.84 REMARK 500 12 TYR A 83 -16.38 -47.01 REMARK 500 12 LEU A 98 155.01 -45.47 REMARK 500 12 LYS A 131 32.64 -88.39 REMARK 500 13 TYR A 83 -15.79 -47.01 REMARK 500 13 SER A 96 -127.85 -61.86 REMARK 500 13 LYS A 131 35.20 -86.12 REMARK 500 14 TYR A 83 -16.46 -48.26 REMARK 500 14 SER A 95 81.36 41.33 REMARK 500 14 LEU A 97 93.98 79.59 REMARK 500 14 ALA A 121 19.37 52.89 REMARK 500 14 LYS A 131 33.99 -88.61 REMARK 500 REMARK 500 THIS ENTRY HAS 70 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25138 RELATED DB: BMRB REMARK 900 RELATED ID: 2N3F RELATED DB: PDB REMARK 900 RELATED ID: 2N3G RELATED DB: PDB DBREF 2N3H A 81 151 UNP Q8H1D4 DRB4_ARATH 81 151 SEQRES 1 A 153 MET ASP HIS VAL TYR LYS GLY GLN LEU GLN ALA TYR ALA SEQRES 2 A 153 LEU GLN HIS ASN LEU GLU LEU PRO VAL TYR ALA ASN GLU SEQRES 3 A 153 ARG GLU GLY PRO PRO HIS ALA PRO ARG PHE ARG CYS ASN SEQRES 4 A 153 VAL THR PHE CYS GLY GLN THR PHE GLN SER SER GLU PHE SEQRES 5 A 153 PHE PRO THR LEU LYS SER ALA GLU HIS ALA ALA ALA LYS SEQRES 6 A 153 ILE ALA VAL ALA SER LEU THR PRO GLN SER PRO GLU GLY SEQRES 7 A 153 ILE ASP VAL ALA TYR LYS ASN LEU LEU GLN GLU ILE ALA SEQRES 8 A 153 GLN LYS GLU SER SER LEU LEU PRO PHE TYR ALA THR ALA SEQRES 9 A 153 THR SER GLY PRO SER HIS ALA PRO THR PHE THR SER THR SEQRES 10 A 153 VAL GLU PHE ALA GLY LYS VAL PHE SER GLY GLU GLU ALA SEQRES 11 A 153 LYS THR LYS LYS LEU ALA GLU MET SER ALA ALA LYS VAL SEQRES 12 A 153 ALA PHE MET SER ILE LYS ASN GLY ASN SER HELIX 1 1 ALA A 82 SER A 95 1 14 HELIX 2 2 THR A 132 ASN A 150 1 19 SHEET 1 A 3 PHE A 100 SER A 106 0 SHEET 2 A 3 THR A 113 PHE A 120 -1 O THR A 117 N ALA A 102 SHEET 3 A 3 LYS A 123 SER A 126 -1 O LYS A 123 N PHE A 120 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