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
(ATOM LINES ARE NOT SHOWN.)
END
