HEADER RNA BINDING PROTEIN/RNA 12-NOV-13 2RU3 TITLE SOLUTION STRUCTURE OF C.ELEGANS SUP-12 RRM IN COMPLEX WITH RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN SUP-12, ISOFORM A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA RECOGNITION MOTIF (RRM), UNP RESIDUES 20-121; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(*GP*UP*GP*UP*GP*C)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: SUP-12, CELE_T22B2.4, T22B2.4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET-15B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS SOLUTION STRUCTURE, PROTEIN-RNA COMPLEX, RRM (RNA RECOGNITION MOTIF), KEYWDS 2 RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.TAKAHASHI,K.KUWASAKO,S.UNZAI,K.TSUDA,S.YOSHIKAWA,F.HE,N.KOBAYASHI, AUTHOR 2 P.GUNTERT,M.SHIROUZU,T.ITO,A.TANAKA,S.YOKOYAMA,M.HAGIWARA, AUTHOR 3 H.KUROYANAGI,Y.MUTO REVDAT 3 14-JUN-23 2RU3 1 REMARK SEQADV REVDAT 2 18-MAR-15 2RU3 1 JRNL REVDAT 1 13-AUG-14 2RU3 0 JRNL AUTH K.KUWASAKO,M.TAKAHASHI,S.UNZAI,K.TSUDA,S.YOSHIKAWA,F.HE, JRNL AUTH 2 N.KOBAYASHI,P.GUNTERT,M.SHIROUZU,T.ITO,A.TANAKA,S.YOKOYAMA, JRNL AUTH 3 M.HAGIWARA,H.KUROYANAGI,Y.MUTO JRNL TITL RBFOX AND SUP-12 SANDWICH A G BASE TO COOPERATIVELY REGULATE JRNL TITL 2 TISSUE-SPECIFIC SPLICING JRNL REF NAT.STRUCT.MOL.BIOL. V. 21 778 2014 JRNL REFN ISSN 1545-9993 JRNL PMID 25132178 JRNL DOI 10.1038/NSMB.2870 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 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 2RU3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000150268. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5-7 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-100% 13C; U-100% 15N] REMARK 210 SUP-12-1, 0.72 MM RNA-2, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 2D 1H-13C HSQC; 3D HBHA(CO) REMARK 210 NH; 3D C(CO)NH; 3D H(CCO)NH; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 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 C B 12 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 2 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 86 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G B 9 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 3 C B 12 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 4 ARG A 86 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 G B 7 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 4 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 G B 11 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 5 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 6 G B 7 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 7 G B 7 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 G B 9 N3 - C4 - C5 ANGL. DEV. = -3.3 DEGREES REMARK 500 7 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 8 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 G B 7 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 8 U B 10 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 8 C B 12 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 C B 12 N3 - C2 - O2 ANGL. DEV. = -5.8 DEGREES REMARK 500 9 G B 9 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 10 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 G B 7 O4' - C1' - N9 ANGL. DEV. = 7.4 DEGREES REMARK 500 10 C B 12 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 C B 12 N3 - C2 - O2 ANGL. DEV. = -5.3 DEGREES REMARK 500 11 G B 7 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 11 G B 9 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES REMARK 500 11 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 12 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 G B 9 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 12 C B 12 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 13 ARG A 86 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 13 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 G B 7 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 13 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 13 U B 10 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 13 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 14 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 15 G B 9 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES REMARK 500 15 U B 10 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 15 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 16 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 17 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 17 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 17 G B 7 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 17 C B 12 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 56 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 SER A 20 -19.97 -144.84 REMARK 500 1 ARG A 30 -2.79 73.90 REMARK 500 1 THR A 32 -44.00 68.21 REMARK 500 1 THR A 35 -20.05 -141.38 REMARK 500 1 GLN A 73 17.11 58.80 REMARK 500 1 ASP A 101 19.07 58.48 REMARK 500 1 LYS A 104 99.54 -65.77 REMARK 500 1 ALA A 110 -72.36 -24.33 REMARK 500 1 TYR A 111 0.53 -34.37 REMARK 500 2 PRO A 25 18.03 -61.75 REMARK 500 2 VAL A 27 12.85 54.53 REMARK 500 2 THR A 35 -23.17 -140.28 REMARK 500 2 ASP A 69 134.32 -39.37 REMARK 500 2 ALA A 110 -84.43 -38.88 REMARK 500 2 TYR A 111 1.67 -24.88 REMARK 500 2 LEU A 112 -74.30 -87.16 REMARK 500 3 THR A 21 -50.54 -137.15 REMARK 500 3 VAL A 26 123.14 73.93 REMARK 500 3 THR A 32 -28.98 67.79 REMARK 500 3 THR A 35 -25.31 -143.31 REMARK 500 3 GLN A 73 10.55 59.98 REMARK 500 3 ALA A 110 -86.69 -45.80 REMARK 500 3 TYR A 111 3.64 -27.09 REMARK 500 3 LEU A 112 -74.23 -89.26 REMARK 500 3 ARG A 117 17.29 -159.93 REMARK 500 4 SER A 29 -39.24 -169.02 REMARK 500 4 THR A 32 -27.21 67.05 REMARK 500 4 ALA A 110 -82.94 -41.53 REMARK 500 4 TYR A 111 2.54 -29.01 REMARK 500 4 LEU A 112 -71.63 -87.37 REMARK 500 5 ALA A 23 -38.98 -166.49 REMARK 500 5 THR A 32 -46.93 -142.77 REMARK 500 5 ALA A 110 -84.93 -42.18 REMARK 500 5 TYR A 111 2.66 -26.17 REMARK 500 5 LEU A 112 -74.68 -87.69 REMARK 500 5 ASN A 119 -54.63 -161.47 REMARK 500 6 ALA A 110 -92.81 -46.90 REMARK 500 6 TYR A 111 5.25 -27.29 REMARK 500 6 LEU A 112 -74.34 -89.62 REMARK 500 7 PRO A 25 39.80 -65.60 REMARK 500 7 VAL A 26 42.26 -78.22 REMARK 500 7 ARG A 70 1.53 -68.58 REMARK 500 7 ALA A 110 -79.53 -39.16 REMARK 500 7 TYR A 111 0.26 -30.81 REMARK 500 8 THR A 35 -19.21 -143.34 REMARK 500 8 GLN A 73 11.55 59.99 REMARK 500 8 ILE A 99 60.74 65.43 REMARK 500 8 ALA A 110 -75.13 -19.39 REMARK 500 8 TYR A 111 2.50 -34.88 REMARK 500 8 VAL A 120 121.09 76.03 REMARK 500 REMARK 500 THIS ENTRY HAS 123 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 U B 8 0.06 SIDE CHAIN REMARK 500 3 U B 8 0.06 SIDE CHAIN REMARK 500 4 U B 8 0.09 SIDE CHAIN REMARK 500 6 U B 8 0.10 SIDE CHAIN REMARK 500 7 U B 8 0.07 SIDE CHAIN REMARK 500 8 ARG A 103 0.09 SIDE CHAIN REMARK 500 8 U B 8 0.07 SIDE CHAIN REMARK 500 8 G B 9 0.09 SIDE CHAIN REMARK 500 8 U B 10 0.06 SIDE CHAIN REMARK 500 9 G B 7 0.06 SIDE CHAIN REMARK 500 9 U B 8 0.06 SIDE CHAIN REMARK 500 10 U B 8 0.08 SIDE CHAIN REMARK 500 11 U B 8 0.07 SIDE CHAIN REMARK 500 12 U B 8 0.07 SIDE CHAIN REMARK 500 13 U B 8 0.07 SIDE CHAIN REMARK 500 13 U B 10 0.09 SIDE CHAIN REMARK 500 13 C B 12 0.10 SIDE CHAIN REMARK 500 14 U B 8 0.08 SIDE CHAIN REMARK 500 14 C B 12 0.10 SIDE CHAIN REMARK 500 15 U B 8 0.06 SIDE CHAIN REMARK 500 15 C B 12 0.08 SIDE CHAIN REMARK 500 16 ARG A 70 0.10 SIDE CHAIN REMARK 500 16 U B 8 0.07 SIDE CHAIN REMARK 500 16 G B 11 0.07 SIDE CHAIN REMARK 500 17 U B 8 0.07 SIDE CHAIN REMARK 500 18 U B 8 0.07 SIDE CHAIN REMARK 500 19 U B 8 0.09 SIDE CHAIN REMARK 500 19 C B 12 0.09 SIDE CHAIN REMARK 500 20 U B 8 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11541 RELATED DB: BMRB REMARK 900 RELATED ID: 2MGZ RELATED DB: PDB DBREF 2RU3 A 20 121 UNP O45189 O45189_CAEEL 20 121 DBREF 2RU3 B 7 12 PDB 2RU3 2RU3 7 12 SEQADV 2RU3 GLY A 19 UNP O45189 EXPRESSION TAG SEQRES 1 A 103 GLY SER THR ASN ALA GLU PRO VAL VAL GLY SER ARG ASP SEQRES 2 A 103 THR MET PHE THR LYS ILE PHE VAL GLY GLY LEU PRO TYR SEQRES 3 A 103 HIS THR SER ASP LYS THR LEU HIS GLU TYR PHE GLU GLN SEQRES 4 A 103 PHE GLY ASP ILE GLU GLU ALA VAL VAL ILE THR ASP ARG SEQRES 5 A 103 ASN THR GLN LYS SER ARG GLY TYR GLY PHE VAL THR MET SEQRES 6 A 103 LYS ASP ARG ALA SER ALA GLU ARG ALA CYS LYS ASP PRO SEQRES 7 A 103 ASN PRO ILE ILE ASP GLY ARG LYS ALA ASN VAL ASN LEU SEQRES 8 A 103 ALA TYR LEU GLY ALA LYS PRO ARG THR ASN VAL GLN SEQRES 1 B 6 G U G U G C HELIX 1 1 SER A 47 GLU A 56 1 10 HELIX 2 2 ASP A 85 LYS A 94 1 10 SHEET 1 A 4 ILE A 61 THR A 68 0 SHEET 2 A 4 SER A 75 MET A 83 -1 O THR A 82 N GLU A 63 SHEET 3 A 4 LYS A 36 GLY A 40 -1 N VAL A 39 O GLY A 79 SHEET 4 A 4 ASN A 106 LEU A 109 -1 O ASN A 106 N GLY A 40 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