HEADER RNA BINDING PROTEIN 06-SEP-16 5GVQ TITLE SOLUTION STRUCTURE OF THE FIRST RRM DOMAIN OF HUMAN SPLICEOSOMAL TITLE 2 PROTEIN SF3B49 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPLICING FACTOR 3B SUBUNIT 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SPLICEOSOMAL PROTEIN SF3B49, PRE-MRNA-SPLICING FACTOR SF3B COMPND 5 49 KDA SUBUNIT,SPLICEOSOME-ASSOCIATED PROTEIN 49,SAP 49; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SF3B4, SAP49; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RRM, SF3B49, SF3B145, U2 SNRNP, RNA BINDING PROTEIN, STRUCTURAL KEYWDS 2 GENOMICS, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.KUWASAKO,N.NAMEKI,K.TSUDA,M.TAKAHASHI,A.SATO,N.TOCHIO,M.INOUE, AUTHOR 2 T.TERADA,T.KIGAWA,N.KOBAYASHI,M.SHIROUZU,T.ITO,T.SAKAMOTO, AUTHOR 3 K.WAKAMATSU,P.GUNTERT,S.TAKAHASHI,S.YOKOYAMA,Y.MUTO,RIKEN STRUCTURAL AUTHOR 4 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 1 12-APR-17 5GVQ 0 SPRSDE 12-APR-17 5GVQ 1X5U JRNL AUTH K.KUWASAKO,N.NAMEKI,K.TSUDA,M.TAKAHASHI,A.SATO,N.TOCHIO, JRNL AUTH 2 M.INOUE,T.TERADA,T.KIGAWA,N.KOBAYASHI,M.SHIROUZU,T.ITO, JRNL AUTH 3 T.SAKAMOTO,K.WAKAMATSU,P.GUNTERT,S.TAKAHASHI,S.YOKOYAMA, JRNL AUTH 4 Y.MUTO JRNL TITL SOLUTION STRUCTURE OF THE FIRST RNA RECOGNITION MOTIF DOMAIN JRNL TITL 2 OF HUMAN SPLICEOSOMAL PROTEIN SF3B49 AND ITS MODE OF JRNL TITL 3 INTERACTION WITH A SF3B145 FRAGMENT. JRNL REF PROTEIN SCI. V. 26 280 2017 JRNL REFN ESSN 1469-896X JRNL PMID 27862552 JRNL DOI 10.1002/PRO.3080 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 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 5GVQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001189. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 HUMAN SPLICEOSOMAL PROTEIN REMARK 210 SF3B49, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, KUJIRA, NMRVIEW, NMRPIPE 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: 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 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 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 88 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.5 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 VAL A 52 -37.36 -131.31 REMARK 500 1 LYS A 81 72.07 -104.64 REMARK 500 1 TYR A 83 28.69 46.44 REMARK 500 1 HIS A 95 -69.99 -120.49 REMARK 500 2 VAL A 52 -31.55 -135.01 REMARK 500 2 MET A 79 13.97 59.03 REMARK 500 2 LYS A 81 71.01 -113.70 REMARK 500 2 TYR A 83 28.55 46.89 REMARK 500 2 ALA A 94 75.76 40.64 REMARK 500 3 ASN A 13 98.19 -69.31 REMARK 500 3 VAL A 52 -37.88 -132.16 REMARK 500 3 MET A 79 11.81 59.88 REMARK 500 3 LYS A 81 70.52 -108.86 REMARK 500 4 GLN A 14 -40.79 -145.78 REMARK 500 4 VAL A 52 -37.48 -131.36 REMARK 500 4 LYS A 81 71.23 -118.83 REMARK 500 4 TYR A 83 27.58 46.27 REMARK 500 4 LYS A 97 44.63 -81.98 REMARK 500 5 VAL A 52 -37.94 -132.06 REMARK 500 5 MET A 79 9.58 58.26 REMARK 500 5 TYR A 83 27.18 45.97 REMARK 500 5 LEU A 99 -45.94 -152.72 REMARK 500 5 SER A 103 169.40 62.00 REMARK 500 6 ARG A 12 -94.55 48.64 REMARK 500 6 VAL A 52 -38.79 -131.40 REMARK 500 6 LYS A 81 70.54 -100.61 REMARK 500 6 TYR A 83 27.44 45.85 REMARK 500 6 ALA A 94 46.13 -78.38 REMARK 500 7 GLU A 11 -28.93 58.63 REMARK 500 7 ASN A 13 27.88 46.10 REMARK 500 7 VAL A 52 -31.53 -135.54 REMARK 500 7 LYS A 81 69.52 -119.90 REMARK 500 7 TYR A 83 27.37 46.17 REMARK 500 8 ARG A 12 -136.68 45.35 REMARK 500 8 VAL A 52 -38.56 -131.51 REMARK 500 8 LYS A 81 71.52 -117.91 REMARK 500 8 TYR A 83 29.90 45.82 REMARK 500 9 VAL A 52 -40.30 -132.91 REMARK 500 9 MET A 79 13.38 58.21 REMARK 500 9 LYS A 81 71.42 -113.28 REMARK 500 9 TYR A 83 28.61 47.01 REMARK 500 9 LYS A 97 166.89 60.97 REMARK 500 10 SER A 6 13.53 59.31 REMARK 500 10 ASN A 13 43.09 -75.46 REMARK 500 10 VAL A 52 -37.44 -132.13 REMARK 500 10 MET A 79 9.59 59.61 REMARK 500 10 LYS A 81 70.21 -112.78 REMARK 500 10 TYR A 83 28.77 46.00 REMARK 500 10 HIS A 95 38.86 -89.00 REMARK 500 10 ASN A 96 47.59 -76.41 REMARK 500 REMARK 500 THIS ENTRY HAS 99 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X5U RELATED DB: PDB REMARK 900 RELATED ID: 36018 RELATED DB: BMRB DBREF 5GVQ A 1 105 PDB 5GVQ 5GVQ 1 105 SEQRES 1 A 105 GLY SER SER GLY SER SER GLY PRO ILE SER GLU ARG ASN SEQRES 2 A 105 GLN ASP ALA THR VAL TYR VAL GLY GLY LEU ASP GLU LYS SEQRES 3 A 105 VAL SER GLU PRO LEU LEU TRP GLU LEU PHE LEU GLN ALA SEQRES 4 A 105 GLY PRO VAL VAL ASN THR HIS MET PRO LYS ASP ARG VAL SEQRES 5 A 105 THR GLY GLN HIS GLN GLY TYR GLY PHE VAL GLU PHE LEU SEQRES 6 A 105 SER GLU GLU ASP ALA ASP TYR ALA ILE LYS ILE MET ASP SEQRES 7 A 105 MET ILE LYS LEU TYR GLY LYS PRO ILE ARG VAL ASN LYS SEQRES 8 A 105 ALA SER ALA HIS ASN LYS ASN LEU SER GLY PRO SER SER SEQRES 9 A 105 GLY HELIX 1 AA1 GLY A 1 SER A 5 5 5 HELIX 2 AA2 SER A 28 LEU A 37 1 10 HELIX 3 AA3 SER A 66 ASP A 78 1 13 SHEET 1 AA1 4 VAL A 42 HIS A 46 0 SHEET 2 AA1 4 TYR A 59 PHE A 64 -1 O GLU A 63 N VAL A 43 SHEET 3 AA1 4 THR A 17 GLY A 21 -1 N VAL A 18 O VAL A 62 SHEET 4 AA1 4 ARG A 88 LYS A 91 -1 O ASN A 90 N TYR A 19 SHEET 1 AA2 2 LYS A 81 LEU A 82 0 SHEET 2 AA2 2 LYS A 85 PRO A 86 -1 O LYS A 85 N LEU A 82 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