HEADER SPLICING/RNA 27-MAR-09 2KH9 TITLE SOLUTION STRUCTURE OF YEAST PRP24-RRM2 BOUND TO A FRAGMENT OF U6 RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: U4/U6 SNRNA-ASSOCIATED-SPLICING FACTOR PRP24; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 115-197; COMPND 5 SYNONYM: U4/U6 SNRNP PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(*AP*GP*AP*GP*AP*U)-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: PRP24, YMR268C, YM8156.10C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC RNA KEYWDS PROTEIN/RNA, RRM, SNRNP, SPLICING, MRNA PROCESSING, MRNA SPLICING, KEYWDS 2 NUCLEUS, PHOSPHOPROTEIN, RNA-BINDING, SPLICING-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.A.MARTIN-TUMASZ,S.E.BUTCHER REVDAT 4 22-MAY-24 2KH9 1 REMARK REVDAT 3 16-MAR-22 2KH9 1 REMARK SEQADV REVDAT 2 14-APR-10 2KH9 1 JRNL REVDAT 1 09-MAR-10 2KH9 0 JRNL AUTH S.MARTIN-TUMASZ,N.J.REITER,D.A.BROW,S.E.BUTCHER JRNL TITL STRUCTURE AND FUNCTIONAL IMPLICATIONS OF A COMPLEX JRNL TITL 2 CONTAINING A SEGMENT OF U6 RNA BOUND BY A DOMAIN OF PRP24. JRNL REF RNA V. 16 792 2010 JRNL REFN ISSN 1355-8382 JRNL PMID 20181740 JRNL DOI 10.1261/RNA.1913310 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, HADDOCK 2 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ..., AND KOLLM (AMBER), DOMINGUEZ, C., REMARK 3 BOELENS, R., BONVIN, A.M.M.J. (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000101118. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.15 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 300 UM PRP24-RRM2-1, 3 MM AGAGAU REMARK 210 -2, 10 MM [U-2H] TRIS-3, 50 MM REMARK 210 POTASSIUM CHLORIDE-4, 100% D2O; REMARK 210 500 UM [U-99% 15N] PRP24-RRM2-5, REMARK 210 5 MM AGAGAU-6, 10 MM [U-2H] TRIS- REMARK 210 7, 50 MM POTASSIUM CHLORIDE-8, REMARK 210 100% D2O; 500 MM [U-99% 13C; U- REMARK 210 99% 15N] PRP24-RRM2-9, 5 MM REMARK 210 AGAGAU-10, 10 MM TRIS-11, 50 MM REMARK 210 POTASSIUM CHLORIDE-12, 1 MM DTT- REMARK 210 13, 90% H2O/10% D2O; 500 UM [U- REMARK 210 99% 13C; U-99% 15N] PRP24-RRM2- REMARK 210 14, 5 MM AGAGAU-15, 10 MM TRIS- REMARK 210 16, 50 MM POTASSIUM CHLORIDE-17, REMARK 210 1 MM DTT-18, 10 UM DSS-19, 90% REMARK 210 H2O/10% D2O; 300 UM [U-99% 13C; REMARK 210 U-99% 15N] PRP24-RRM2-20, 3 MM REMARK 210 AGAGAU-21, 10 MM TRIS-22, 50 MM REMARK 210 POTASSIUM CHLORIDE-23, 1 MM DTT- REMARK 210 24, 6.5 % DMPC/DHPC 3:1-25, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCO; 3D HNCACB; 3D HBHA(CO)NH; REMARK 210 3D HCCH-TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 2D 1H-1H NOESY; REMARK 210 2D 1H-15N HSQC-IPAP; 3D J REMARK 210 MODULATED CHSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 900 MHZ; 800 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; DMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, NMRPIPE, NMRDRAW, REMARK 210 SPARKY, ATNOSCANDID, CNS, TALOS, REMARK 210 HADDOCK 2 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 202 REMARK 465 HIS A 203 REMARK 465 HIS A 204 REMARK 465 HIS A 205 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 H ARG A 148 O TYR A 162 1.55 REMARK 500 O THR A 118 HG SER A 193 1.59 REMARK 500 H1 MET A 114 OE1 GLU A 116 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 2 TYR A 162 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 A B 51 C3' - C2' - C1' ANGL. DEV. = -4.6 DEGREES REMARK 500 3 G B 52 C3' - C2' - C1' ANGL. DEV. = -7.5 DEGREES REMARK 500 7 A B 51 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 7 A B 51 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 8 TYR A 162 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 9 A B 51 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 9 A B 51 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES 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 THR A 115 -7.51 -140.74 REMARK 500 1 GLU A 116 -155.32 -105.44 REMARK 500 1 CYS A 117 -12.97 160.50 REMARK 500 1 ASN A 123 110.32 43.47 REMARK 500 1 PHE A 124 138.65 171.96 REMARK 500 1 PRO A 126 13.11 -68.15 REMARK 500 1 VAL A 142 112.46 77.95 REMARK 500 1 VAL A 143 115.89 11.29 REMARK 500 1 LEU A 152 -1.43 102.30 REMARK 500 1 ASN A 155 -175.46 -179.60 REMARK 500 1 ARG A 159 0.25 -51.07 REMARK 500 1 SER A 167 -53.15 -158.77 REMARK 500 1 LYS A 168 -38.89 162.86 REMARK 500 1 VAL A 189 68.86 -111.79 REMARK 500 2 THR A 115 23.58 -140.95 REMARK 500 2 GLU A 116 -89.31 -130.12 REMARK 500 2 CYS A 117 -24.17 57.84 REMARK 500 2 ASN A 123 107.93 45.17 REMARK 500 2 PHE A 124 130.55 171.81 REMARK 500 2 VAL A 142 108.02 47.45 REMARK 500 2 VAL A 143 110.31 23.58 REMARK 500 2 LEU A 152 -32.37 116.91 REMARK 500 2 ASN A 155 166.87 178.32 REMARK 500 2 THR A 156 13.14 -65.23 REMARK 500 2 SER A 157 -98.33 -49.33 REMARK 500 2 ARG A 159 4.66 -48.06 REMARK 500 2 PHE A 160 158.53 -44.94 REMARK 500 2 SER A 167 -67.58 -170.91 REMARK 500 2 LYS A 168 -40.60 178.78 REMARK 500 2 GLU A 184 19.80 59.52 REMARK 500 2 VAL A 189 71.96 -111.33 REMARK 500 2 LEU A 196 -48.24 -131.64 REMARK 500 3 THR A 115 15.40 -149.45 REMARK 500 3 CYS A 117 2.38 33.83 REMARK 500 3 ASN A 123 109.71 47.00 REMARK 500 3 PHE A 124 134.82 173.62 REMARK 500 3 VAL A 142 109.63 73.91 REMARK 500 3 VAL A 143 115.22 15.81 REMARK 500 3 LEU A 152 13.09 90.56 REMARK 500 3 PHE A 154 -50.18 -155.87 REMARK 500 3 SER A 157 -78.54 -147.96 REMARK 500 3 ARG A 159 11.13 -64.80 REMARK 500 3 PHE A 160 151.63 -45.93 REMARK 500 3 SER A 167 -65.82 -163.34 REMARK 500 3 LYS A 168 -37.43 169.35 REMARK 500 3 VAL A 189 73.99 -111.21 REMARK 500 4 THR A 115 -2.64 -155.37 REMARK 500 4 CYS A 117 -24.67 52.91 REMARK 500 4 ASN A 123 111.24 47.53 REMARK 500 4 PHE A 124 139.46 176.14 REMARK 500 REMARK 500 THIS ENTRY HAS 162 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 3 A B 53 0.09 SIDE CHAIN REMARK 500 7 A B 53 0.07 SIDE CHAIN REMARK 500 9 A B 53 0.06 SIDE CHAIN REMARK 500 9 U B 54 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7070 RELATED DB: BMRB DBREF 2KH9 A 115 197 UNP P49960 PRP24_YEAST 115 197 DBREF 2KH9 B 49 54 PDB 2KH9 2KH9 49 54 SEQADV 2KH9 MET A 114 UNP P49960 EXPRESSION TAG SEQADV 2KH9 LEU A 198 UNP P49960 EXPRESSION TAG SEQADV 2KH9 GLU A 199 UNP P49960 EXPRESSION TAG SEQADV 2KH9 HIS A 200 UNP P49960 EXPRESSION TAG SEQADV 2KH9 HIS A 201 UNP P49960 EXPRESSION TAG SEQADV 2KH9 HIS A 202 UNP P49960 EXPRESSION TAG SEQADV 2KH9 HIS A 203 UNP P49960 EXPRESSION TAG SEQADV 2KH9 HIS A 204 UNP P49960 EXPRESSION TAG SEQADV 2KH9 HIS A 205 UNP P49960 EXPRESSION TAG SEQRES 1 A 92 MET THR GLU CYS THR LEU TRP MET THR ASN PHE PRO PRO SEQRES 2 A 92 SER TYR THR GLN ARG ASN ILE ARG ASP LEU LEU GLN ASP SEQRES 3 A 92 ILE ASN VAL VAL ALA LEU SER ILE ARG LEU PRO SER LEU SEQRES 4 A 92 ARG PHE ASN THR SER ARG ARG PHE ALA TYR ILE ASP VAL SEQRES 5 A 92 THR SER LYS GLU ASP ALA ARG TYR CYS VAL GLU LYS LEU SEQRES 6 A 92 ASN GLY LEU LYS ILE GLU GLY TYR THR LEU VAL THR LYS SEQRES 7 A 92 VAL SER ASN PRO LEU GLU LEU GLU HIS HIS HIS HIS HIS SEQRES 8 A 92 HIS SEQRES 1 B 6 A G A G A U HELIX 1 1 THR A 129 ILE A 140 1 12 HELIX 2 2 LYS A 168 ASN A 179 1 12 SHEET 1 A 4 ALA A 144 ARG A 148 0 SHEET 2 A 4 ALA A 161 VAL A 165 -1 O TYR A 162 N ARG A 148 SHEET 3 A 4 THR A 118 THR A 122 -1 N MET A 121 O ALA A 161 SHEET 4 A 4 VAL A 189 VAL A 192 -1 O LYS A 191 N TRP A 120 SHEET 1 B 2 LYS A 182 ILE A 183 0 SHEET 2 B 2 TYR A 186 THR A 187 -1 O TYR A 186 N ILE A 183 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