HEADER RNA BINDING PROTEIN/RNA 19-JUN-12 2LUP TITLE RDC REFINED SOLUTION STRUCTURE OF DOUBLE-STRANDED RNA BINDING DOMAIN TITLE 2 OF S. CEREVISIAE RNASE III (RNT1P) IN COMPLEX WITH THE TERMINAL RNA TITLE 3 HAIRPIN OF SNR47 PRECURSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (32-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RIBONUCLEASE 3; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: RIBONUCLEASE III, RNASE III; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 5 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 6 ORGANISM_TAXID: 559292; SOURCE 7 STRAIN: ATCC 204508 / S288C; SOURCE 8 VARIANT: YMR239C; SOURCE 9 GENE: RNT1, YM9408.01C, YM9959.21, YMR239C; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS DSRBD, RNT1P, SNR47, DOUBLE STRAND RNA BINDING, RNA BINDING PROTEIN- KEYWDS 2 RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR Z.WANG,J.FEIGON REVDAT 2 14-JUN-23 2LUP 1 REMARK SEQADV REVDAT 1 04-JUL-12 2LUP 0 JRNL AUTH Z.WANG,E.HARTMAN,K.ROY,G.CHANFREAU,J.FEIGON JRNL TITL STRUCTURE OF A YEAST RNASE III DSRBD COMPLEX WITH A JRNL TITL 2 NONCANONICAL RNA SUBSTRATE PROVIDES NEW INSIGHTS INTO JRNL TITL 3 BINDING SPECIFICITY OF DSRBDS. JRNL REF STRUCTURE V. 19 999 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21742266 JRNL DOI 10.1016/J.STR.2011.03.022 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.WU,A.HENRAS,G.CHANFREAU,J.FEIGON REMARK 1 TITL STRUCTURAL BASIS FOR RECOGNITION OF THE AGNN TETRALOOP RNA REMARK 1 TITL 2 FOLD BY THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF RNT1P REMARK 1 TITL 3 RNASE III. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 101 8307 2004 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 15150409 REMARK 1 DOI 10.1073/PNAS.0402627101 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, 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: THIS STRUCTURE IS AN RDC REFINED REMARK 3 STRUCTURE OF PDB ENTRY 1T4L USING THE SAME RESTRAINTS PLUS REMARK 3 ADDITIONAL RDCS [81 RDCS (REFINED) VS 43 RDCS (1T4L)]. REMARK 4 REMARK 4 2LUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000102856. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 90 % H2O, 10 % [U-100% REMARK 210 2H] D2O, 20 MM SODIUM PHOSPHATE, REMARK 210 150 MM SODIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 90 % [U-100% 2H] REMARK 210 D2O, 10 % SODIUM CHLORIDE, 150 REMARK 210 MM SODIUM PHOSPHATE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HNCO; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, TALOS, X-PLOR REMARK 210 NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 HO2' G A 11 O4' U A 12 1.40 REMARK 500 O ASN B 419 H LYS B 421 1.46 REMARK 500 O2' C A 30 H5' U A 31 1.56 REMARK 500 H THR B 414 OD1 ASN B 430 1.57 REMARK 500 O ASP B 434 H LEU B 438 1.58 REMARK 500 O LYS B 421 H ILE B 425 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 1 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 19 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 G A 23 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 G A 25 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 25 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 26 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 28 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 19 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 19 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 G A 23 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 25 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 429 ANGLE DEVIATIONS. 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 ASP B 367 -96.60 26.12 REMARK 500 1 ALA B 370 -72.15 -62.59 REMARK 500 1 LYS B 371 -38.18 -39.15 REMARK 500 1 SER B 382 -10.93 94.33 REMARK 500 1 ARG B 384 64.76 67.33 REMARK 500 1 HIS B 386 72.65 -158.67 REMARK 500 1 LYS B 391 21.87 87.30 REMARK 500 1 LYS B 392 122.41 -8.72 REMARK 500 1 ASP B 397 63.12 163.51 REMARK 500 1 ASN B 399 123.36 -6.75 REMARK 500 1 ILE B 420 -44.97 53.44 REMARK 500 1 ARG B 426 -32.16 -36.32 REMARK 500 1 ASP B 434 71.71 -109.25 REMARK 500 1 ALA B 447 -72.07 -70.31 REMARK 500 1 ILE B 448 100.23 27.87 REMARK 500 1 PRO B 449 -169.05 -71.57 REMARK 500 1 SER B 451 67.30 60.33 REMARK 500 2 ASP B 367 -71.88 -45.67 REMARK 500 2 MET B 368 -35.48 -38.58 REMARK 500 2 LEU B 374 -70.18 -59.72 REMARK 500 2 SER B 382 -3.66 87.78 REMARK 500 2 ARG B 384 74.09 69.84 REMARK 500 2 LYS B 391 21.06 94.65 REMARK 500 2 LYS B 392 118.94 4.24 REMARK 500 2 ASP B 397 56.24 179.25 REMARK 500 2 PRO B 398 -35.75 -38.57 REMARK 500 2 ASN B 399 134.30 -30.51 REMARK 500 2 ASP B 408 27.10 -167.08 REMARK 500 2 ILE B 420 -42.57 55.99 REMARK 500 2 ALA B 447 -71.46 -72.64 REMARK 500 2 ILE B 448 116.02 -15.14 REMARK 500 2 SER B 451 158.39 -48.37 REMARK 500 2 GLU B 452 32.35 -148.15 REMARK 500 3 ALA B 370 -71.70 -61.36 REMARK 500 3 LEU B 374 -73.24 -46.79 REMARK 500 3 LEU B 377 -35.85 -144.51 REMARK 500 3 ALA B 381 -14.75 158.04 REMARK 500 3 LYS B 391 19.83 94.00 REMARK 500 3 LYS B 392 108.32 -6.27 REMARK 500 3 PRO B 393 157.14 -47.51 REMARK 500 3 ASP B 397 56.82 172.56 REMARK 500 3 ASN B 399 137.04 -22.72 REMARK 500 3 ASN B 419 37.08 -99.99 REMARK 500 3 ILE B 420 -46.47 48.27 REMARK 500 3 ARG B 426 -32.93 -39.02 REMARK 500 3 ILE B 448 105.51 -29.77 REMARK 500 3 PRO B 449 -167.39 -51.62 REMARK 500 3 ARG B 450 -50.53 -177.37 REMARK 500 3 SER B 451 -175.78 179.86 REMARK 500 3 GLU B 452 76.40 65.26 REMARK 500 REMARK 500 THIS ENTRY HAS 275 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18534 RELATED DB: BMRB REMARK 900 RELATED ID: 2LUQ RELATED DB: PDB REMARK 900 RELATED ID: 1T4L RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF DOUBLE-STRANDED RNA BINDING DOMAIN OF S. REMARK 900 CEREVISIAE RNASE III (RNT1P) IN COMPLEX WITH THE 5' TERMINAL RNA REMARK 900 HAIRPIN OF SNR47 PRECURSOR DBREF 2LUP B 366 453 UNP Q02555 RNT1_YEAST 366 453 DBREF 2LUP A 1 32 PDB 2LUP 2LUP 1 32 SEQADV 2LUP GLY B 364 UNP Q02555 EXPRESSION TAG SEQADV 2LUP SER B 365 UNP Q02555 EXPRESSION TAG SEQRES 1 A 32 G G G A U A C C A U G U U SEQRES 2 A 32 C A G A A G A A C G U G G SEQRES 3 A 32 U A U C U C SEQRES 1 B 90 GLY SER LEU ASP MET ASN ALA LYS ARG GLN LEU TYR SER SEQRES 2 B 90 LEU ILE GLY TYR ALA SER LEU ARG LEU HIS TYR VAL THR SEQRES 3 B 90 VAL LYS LYS PRO THR ALA VAL ASP PRO ASN SER ILE VAL SEQRES 4 B 90 GLU CYS ARG VAL GLY ASP GLY THR VAL LEU GLY THR GLY SEQRES 5 B 90 VAL GLY ARG ASN ILE LYS ILE ALA GLY ILE ARG ALA ALA SEQRES 6 B 90 GLU ASN ALA LEU ARG ASP LYS LYS MET LEU ASP PHE TYR SEQRES 7 B 90 ALA LYS GLN ARG ALA ALA ILE PRO ARG SER GLU SER HELIX 1 1 LEU B 366 GLY B 379 1 14 HELIX 2 2 ILE B 420 LEU B 432 1 13 HELIX 3 3 ASP B 434 ILE B 448 1 15 SHEET 1 A 3 LEU B 385 VAL B 390 0 SHEET 2 A 3 SER B 400 VAL B 406 -1 O GLU B 403 N VAL B 388 SHEET 3 A 3 THR B 410 GLY B 417 -1 O GLY B 415 N VAL B 402 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