HEADER HYDROLASE 23-NOV-10 2L6M TITLE STRUCTURE OF C-TERMINAL DSRBD OF THE FISSION YEAST DICER (DCR1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN DICER; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1259-1358; COMPND 5 SYNONYM: CELL CYCLE CONTROL PROTEIN DCR1, RNA INTERFERENCE PATHWAY COMPND 6 PROTEIN DCR1, ENDORIBONUCLEASE DCR1, ATP-DEPENDENT HELICASE DCR1; COMPND 7 EC: 3.1.26.-, 3.6.4.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: DCR1, SPCC188.13C, SPCC584.10C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON-PLUS (RIL); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A+ KEYWDS DSRBD, DICER, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.BARRAUD,F.H.-T.ALLAIN REVDAT 4 14-JUN-23 2L6M 1 REMARK LINK REVDAT 3 05-FEB-20 2L6M 1 REMARK SEQADV REVDAT 2 26-OCT-11 2L6M 1 JRNL REVDAT 1 24-AUG-11 2L6M 0 JRNL AUTH P.BARRAUD,S.EMMERTH,Y.SHIMADA,H.R.HOTZ,F.H.ALLAIN,M.BUHLER JRNL TITL AN EXTENDED DSRBD WITH A NOVEL ZINC-BINDING MOTIF MEDIATES JRNL TITL 2 NUCLEAR RETENTION OF FISSION YEAST DICER. JRNL REF EMBO J. V. 30 4223 2011 JRNL REFN ISSN 0261-4189 JRNL PMID 21847092 JRNL DOI 10.1038/EMBOJ.2011.300 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, CNS REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L6M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000102022. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 DSRBD-1, 25 MM SODIUM PHOSPHATE- REMARK 210 2, 75 MM POTASSIUM CHLORIDE-3, 2 REMARK 210 MM DTT-4, 0.01 MM ZINC ION-5, 90% REMARK 210 H2O/10% D2O; 0.5 MM DSRBD-6, 25 REMARK 210 MM SODIUM PHOSPHATE-7, 75 MM REMARK 210 POTASSIUM CHLORIDE-8, 2 MM DTT-9, REMARK 210 0.01 MM ZINC ION-10, 100% D2O; REMARK 210 0.5 MM [U-100% 15N] DSRBD-11, 25 REMARK 210 MM SODIUM PHOSPHATE-12, 75 MM REMARK 210 POTASSIUM CHLORIDE-13, 2 MM DTT- REMARK 210 14, 0.01 MM ZINC ION-15, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D 1H-15N TOCSY; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 2D 1H-1H TOCSY; 2D 1H- REMARK 210 1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY, ATNOS/CANDID 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 OE1 GLU A 28 HZ1 LYS A 63 1.59 REMARK 500 HG1 THR A 36 OE1 GLU A 41 1.59 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 GLU A 41 96.08 -54.86 REMARK 500 1 ASN A 94 40.61 -105.18 REMARK 500 1 LYS A 96 -57.50 -134.18 REMARK 500 1 PHE A 97 -168.05 -160.90 REMARK 500 1 SER A 98 -167.22 -68.80 REMARK 500 2 LYS A 2 -78.90 -143.59 REMARK 500 2 SER A 33 37.81 -82.67 REMARK 500 2 ASN A 39 -80.09 -49.95 REMARK 500 2 THR A 40 -165.24 -106.24 REMARK 500 2 ASN A 94 73.40 -108.05 REMARK 500 2 LYS A 96 -47.81 -150.98 REMARK 500 3 PHE A 21 149.00 -170.34 REMARK 500 3 LYS A 31 106.38 -51.85 REMARK 500 3 ASN A 39 -75.64 -48.46 REMARK 500 3 GLU A 41 99.47 -55.11 REMARK 500 3 ASN A 94 69.33 -116.96 REMARK 500 3 LYS A 96 -48.42 -161.49 REMARK 500 4 SER A 32 -168.96 -129.83 REMARK 500 4 HIS A 34 99.32 -66.76 REMARK 500 4 LYS A 35 -45.42 -168.44 REMARK 500 4 LEU A 37 88.51 54.10 REMARK 500 4 THR A 40 -151.06 -111.82 REMARK 500 4 LEU A 42 -71.83 67.46 REMARK 500 4 HIS A 43 97.58 -170.30 REMARK 500 4 LYS A 96 -46.86 -150.46 REMARK 500 4 LYS A 99 48.59 72.12 REMARK 500 5 GLU A 41 101.29 -56.26 REMARK 500 5 THR A 45 97.06 -66.04 REMARK 500 5 LYS A 96 -44.48 -156.82 REMARK 500 5 SER A 98 148.86 177.75 REMARK 500 5 LYS A 99 -36.65 72.07 REMARK 500 6 LYS A 2 116.10 74.96 REMARK 500 6 LYS A 31 -165.88 -177.13 REMARK 500 6 HIS A 34 45.52 -83.29 REMARK 500 6 LEU A 37 93.30 58.55 REMARK 500 6 LEU A 38 -150.56 -144.40 REMARK 500 6 THR A 45 107.16 -58.72 REMARK 500 6 ASN A 94 66.33 -113.39 REMARK 500 6 LYS A 96 -45.66 -158.07 REMARK 500 7 ASP A 20 76.65 -159.27 REMARK 500 7 PHE A 21 147.54 -171.34 REMARK 500 7 SER A 33 -168.67 -108.88 REMARK 500 7 LEU A 38 -163.26 -122.80 REMARK 500 7 ASN A 39 -70.22 -44.97 REMARK 500 7 THR A 40 -151.58 -118.10 REMARK 500 7 HIS A 43 98.57 -67.40 REMARK 500 7 ASN A 94 68.02 -108.79 REMARK 500 8 HIS A 34 30.05 71.91 REMARK 500 8 LEU A 38 -69.26 -140.29 REMARK 500 8 ASN A 39 -75.84 -145.30 REMARK 500 REMARK 500 THIS ENTRY HAS 130 RAMACHANDRAN OUTLIERS. 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 HIS A 55 NE2 110.4 REMARK 620 3 CYS A 93 SG 109.2 107.2 REMARK 620 4 CYS A 95 SG 112.0 106.3 111.6 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 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17315 RELATED DB: BMRB DBREF 2L6M A 2 101 UNP Q09884 DCR1_SCHPO 1259 1358 SEQADV 2L6M MET A -19 UNP Q09884 EXPRESSION TAG SEQADV 2L6M GLY A -18 UNP Q09884 EXPRESSION TAG SEQADV 2L6M SER A -17 UNP Q09884 EXPRESSION TAG SEQADV 2L6M SER A -16 UNP Q09884 EXPRESSION TAG SEQADV 2L6M HIS A -15 UNP Q09884 EXPRESSION TAG SEQADV 2L6M HIS A -14 UNP Q09884 EXPRESSION TAG SEQADV 2L6M HIS A -13 UNP Q09884 EXPRESSION TAG SEQADV 2L6M HIS A -12 UNP Q09884 EXPRESSION TAG SEQADV 2L6M HIS A -11 UNP Q09884 EXPRESSION TAG SEQADV 2L6M HIS A -10 UNP Q09884 EXPRESSION TAG SEQADV 2L6M SER A -9 UNP Q09884 EXPRESSION TAG SEQADV 2L6M SER A -8 UNP Q09884 EXPRESSION TAG SEQADV 2L6M GLY A -7 UNP Q09884 EXPRESSION TAG SEQADV 2L6M LEU A -6 UNP Q09884 EXPRESSION TAG SEQADV 2L6M VAL A -5 UNP Q09884 EXPRESSION TAG SEQADV 2L6M PRO A -4 UNP Q09884 EXPRESSION TAG SEQADV 2L6M ARG A -3 UNP Q09884 EXPRESSION TAG SEQADV 2L6M GLY A -2 UNP Q09884 EXPRESSION TAG SEQADV 2L6M SER A -1 UNP Q09884 EXPRESSION TAG SEQADV 2L6M HIS A 0 UNP Q09884 EXPRESSION TAG SEQADV 2L6M MET A 1 UNP Q09884 EXPRESSION TAG SEQRES 1 A 121 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 121 LEU VAL PRO ARG GLY SER HIS MET LYS GLY ASP ILE GLU SEQRES 3 A 121 HIS LYS VAL TYR GLN LEU LEU LYS ASP GLN GLY CYS GLU SEQRES 4 A 121 ASP PHE GLY THR LYS CYS VAL ILE GLU GLU VAL LYS SER SEQRES 5 A 121 SER HIS LYS THR LEU LEU ASN THR GLU LEU HIS LEU THR SEQRES 6 A 121 LYS TYR TYR GLY PHE SER PHE PHE ARG HIS GLY ASN ILE SEQRES 7 A 121 VAL ALA TYR GLY LYS SER ARG LYS VAL ALA ASN ALA LYS SEQRES 8 A 121 TYR ILE MET LYS GLN ARG LEU LEU LYS LEU LEU GLU ASP SEQRES 9 A 121 LYS SER ASN LEU LEU LEU TYR SER CYS ASN CYS LYS PHE SEQRES 10 A 121 SER LYS LYS LYS HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASP A 4 LYS A 14 1 11 HELIX 2 2 LYS A 66 LYS A 85 1 20 HELIX 3 3 SER A 86 TYR A 91 1 6 SHEET 1 A 3 PHE A 21 GLU A 29 0 SHEET 2 A 3 LYS A 46 ARG A 54 -1 O PHE A 53 N GLY A 22 SHEET 3 A 3 ASN A 57 SER A 64 -1 O SER A 64 N TYR A 48 LINK SG CYS A 18 ZN ZN A 201 1555 1555 2.33 LINK NE2 HIS A 55 ZN ZN A 201 1555 1555 2.05 LINK SG CYS A 93 ZN ZN A 201 1555 1555 2.31 LINK SG CYS A 95 ZN ZN A 201 1555 1555 2.32 SITE 1 AC1 4 CYS A 18 HIS A 55 CYS A 93 CYS A 95 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