HEADER RNA BINDING PROTEIN/RNA 29-APR-04 1T4L TITLE SOLUTION STRUCTURE OF DOUBLE-STRANDED RNA BINDING DOMAIN OF S. TITLE 2 CEREVISIAE RNASE III (RNT1P) IN COMPLEX WITH THE 5' TERMINAL RNA TITLE 3 HAIRPIN OF SNR47 PRECURSOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5' TERMINAL HAIRPIN OF SNR47 PRECURSOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AGAA TETRALOOP RNA HAIRPIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RIBONUCLEASE III; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: DOUBLE-STRANDED RNA BINDING DOMAIN; COMPND 10 SYNONYM: RNASE III; COMPND 11 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: 4932; SOURCE 7 GENE: RNT1, YMR239C, YM9408.01C, YM9959.21; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS DSRBD, RNASE III, AGNN TETRALOOP, PROTEIN-RNA COMPLEX, RNA BINDING KEYWDS 2 PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR H.WU,A.HENRAS,G.CHANFREAU,J.FEIGON REVDAT 4 02-MAR-22 1T4L 1 REMARK SEQADV REVDAT 3 24-FEB-09 1T4L 1 VERSN REVDAT 2 08-JUN-04 1T4L 1 JRNL REVDAT 1 01-JUN-04 1T4L 0 JRNL AUTH H.WU,A.HENRAS,G.CHANFREAU,J.FEIGON JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF THE AGNN TETRALOOP RNA JRNL TITL 2 FOLD BY THE DOUBLE-STRANDED RNA-BINDING DOMAIN OF RNT1P JRNL TITL 3 RNASE III. JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 8307 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15150409 JRNL DOI 10.1073/PNAS.0402627101 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 2359 DISTANCE RESTRAINTS REMARK 3 225 DIHEDRAL RESTRAINTS REMARK 3 43 RESIDUAL DIPOLAR COUPLINGS REMARK 4 REMARK 4 1T4L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022304. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20MM NAPI, 150 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 15N-LABELED RNT1P REMARK 210 DSRBD/UNLABELED SNR47H; REMARK 210 UNLABELED RNT1P DSRBD/UNLABELED REMARK 210 SNR47H; UNIFORMALLY 13C,15N- REMARK 210 LABELED RNT1P DSRBD/UNLABELED REMARK 210 SNR47H; UNIFORMALLY 13C,15N- REMARK 210 LABELED RNT1P DSRBD/UNLABELED REMARK 210 SNR47H; UNLABELED RNT1P DSRBD/ REMARK 210 13C,15N-A,U,G,C-SLECTIVELY REMARK 210 LABELED SNR47H SNR47H; UNLABELED REMARK 210 RNT1P DSRBD/UNIFORMALLY 13C,15N- REMARK 210 LABELED SNR47H SNR47H REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D REMARK 210 CBCA(CO)NH; 3D CBCANH; 3D REMARK 210 HBHA(CO)NH; 3D 15N-NOESY-HSQC; REMARK 210 3D 13C-NOESY-HMQC; 2D 13C- REMARK 210 FILTERED/EDITED NOESY; 3D HCCH- REMARK 210 TOCSY 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 : FELIX 2000, XWINNMR 2.6 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 O ASN B 419 H LYS B 421 1.39 REMARK 500 O VAL B 406 H GLY B 409 1.51 REMARK 500 O ASP B 434 H LEU B 438 1.60 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. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 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. = 3.7 DEGREES REMARK 500 1 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.6 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. = -2.7 DEGREES REMARK 500 1 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 18 N7 - C8 - N9 ANGL. DEV. = 3.7 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. = 3.7 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. = 4.4 DEGREES REMARK 500 1 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 25 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 G A 26 N7 - C8 - N9 ANGL. DEV. = 4.7 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. = 3.7 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 6 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 9 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.7 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. = -2.6 DEGREES REMARK 500 2 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.7 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. = 3.7 DEGREES REMARK 500 2 A A 21 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 G A 23 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 23 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 25 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 25 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 400 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 ALA B 370 -79.28 -54.86 REMARK 500 1 LYS B 371 -45.15 -29.33 REMARK 500 1 LEU B 374 -80.90 -68.29 REMARK 500 1 SER B 376 -31.57 -135.92 REMARK 500 1 ILE B 378 -62.50 -129.50 REMARK 500 1 SER B 382 45.26 79.13 REMARK 500 1 ARG B 384 -6.16 84.56 REMARK 500 1 LEU B 385 129.50 -36.02 REMARK 500 1 LYS B 391 56.23 95.68 REMARK 500 1 LYS B 392 107.41 -31.21 REMARK 500 1 PRO B 393 159.53 -44.98 REMARK 500 1 ASP B 397 61.56 166.45 REMARK 500 1 ASN B 399 127.21 -30.67 REMARK 500 1 ILE B 420 -46.09 48.79 REMARK 500 1 ALA B 447 -78.00 -72.58 REMARK 500 1 ILE B 448 103.90 -0.39 REMARK 500 1 SER B 451 -177.36 -176.57 REMARK 500 2 ALA B 370 -74.26 -68.54 REMARK 500 2 LEU B 374 -72.79 -64.69 REMARK 500 2 ILE B 378 -121.05 -141.99 REMARK 500 2 ALA B 381 34.56 155.28 REMARK 500 2 SER B 382 16.95 -151.98 REMARK 500 2 ARG B 384 41.28 36.79 REMARK 500 2 LYS B 391 55.97 80.82 REMARK 500 2 LYS B 392 131.33 -33.88 REMARK 500 2 PRO B 393 174.42 -53.74 REMARK 500 2 ASP B 397 63.19 179.18 REMARK 500 2 ASN B 399 116.60 7.71 REMARK 500 2 ILE B 420 -41.88 98.14 REMARK 500 2 ILE B 448 133.03 -39.01 REMARK 500 2 PRO B 449 -164.44 -50.06 REMARK 500 3 SER B 365 56.93 36.67 REMARK 500 3 ALA B 370 -75.28 -62.33 REMARK 500 3 LEU B 374 -71.09 -67.66 REMARK 500 3 ILE B 378 33.58 -142.07 REMARK 500 3 SER B 382 44.94 90.42 REMARK 500 3 ARG B 384 -8.95 81.78 REMARK 500 3 LYS B 391 62.60 85.99 REMARK 500 3 LYS B 392 125.92 -29.47 REMARK 500 3 ASP B 397 54.63 163.82 REMARK 500 3 ASN B 399 148.41 -30.99 REMARK 500 3 ARG B 405 -156.68 -145.59 REMARK 500 3 THR B 414 155.30 176.09 REMARK 500 3 ILE B 420 -45.93 48.33 REMARK 500 3 ALA B 447 57.11 -117.06 REMARK 500 3 PRO B 449 -146.55 -59.51 REMARK 500 3 ARG B 450 -169.95 -54.76 REMARK 500 4 ALA B 370 -78.83 -61.35 REMARK 500 4 ILE B 378 -151.42 -126.91 REMARK 500 4 ALA B 381 71.36 160.15 REMARK 500 REMARK 500 THIS ENTRY HAS 247 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1T4L B 366 453 UNP Q02555 RNT1_YEAST 366 453 DBREF 1T4L A 1 32 PDB 1T4L 1T4L 1 32 SEQADV 1T4L GLY B 364 UNP Q02555 CLONING ARTIFACT SEQADV 1T4L SER B 365 UNP Q02555 CLONING ARTIFACT 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 ILE B 378 1 13 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 HIS B 386 VAL B 390 0 SHEET 2 A 3 SER B 400 VAL B 406 -1 O ARG B 405 N HIS B 386 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