HEADER RNA BINDING PROTEIN 11-JUL-06 2DT6 TITLE SOLUTION STRUCTURE OF THE FIRST SURP DOMAIN OF HUMAN SPLICING FACTOR TITLE 2 SF3A120 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPLICING FACTOR 3 SUBUNIT 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SURP DOMAIN; COMPND 5 SYNONYM: SPLICEOSOME-ASSOCIATED PROTEIN 114, SAP 114, SF3A120; 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: SF3A120, SF3A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B-SF3A120 SURP1 KEYWDS STRUCTURE GENOMICS, SF3A120, SURP DOMAIN, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, RNA KEYWDS 4 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.KUWASAKO,F.HE,M.INOUE,A.TANAKA,S.SUGANO,P.GUENTERT,Y.MUTO, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 09-MAR-22 2DT6 1 REMARK SEQADV REVDAT 3 24-FEB-09 2DT6 1 VERSN REVDAT 2 02-JAN-07 2DT6 1 REMARK REVDAT 1 26-DEC-06 2DT6 0 JRNL AUTH K.KUWASAKO,F.HE,M.INOUE,A.TANAKA,S.SUGANO,P.GUENTERT,Y.MUTO, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURES OF THE SURP DOMAINS AND THE JRNL TITL 2 SUBUNIT-ASSEMBLY MECHANISM WITHIN THE SPLICING FACTOR SF3A JRNL TITL 3 COMPLEX IN 17S U2 SNRNP JRNL REF STRUCTURE V. 14 1677 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 17098193 JRNL DOI 10.1016/J.STR.2006.09.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, CYANA 2.1, OPALP 1.4 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA), KORADI, R. REMARK 3 (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DT6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000025815. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0MM U-15N, 13C PROTEIN; 20MM REMARK 210 SOLDIUM PHOSPHATE; 1MM D-DTT; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9321, CYANA 2.1, OPALP REMARK 210 1.4 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINTED ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST 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: 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: 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 6 ARG A 70 CD - NE - CZ ANGL. DEV. = 10.4 DEGREES REMARK 500 6 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 70 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 ARG A 70 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 70 NE - CZ - NH2 ANGL. DEV. = -4.0 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 2 GLU A 48 -51.44 -144.16 REMARK 500 4 GLU A 48 -58.89 -144.26 REMARK 500 5 GLU A 48 -51.81 -168.57 REMARK 500 6 GLU A 48 -56.99 -153.35 REMARK 500 7 GLU A 48 -51.01 -172.47 REMARK 500 8 GLU A 48 -58.11 -156.10 REMARK 500 9 GLU A 48 -63.29 -146.42 REMARK 500 10 GLU A 48 -49.73 -162.24 REMARK 500 10 ILE A 76 -5.45 -57.45 REMARK 500 13 GLU A 48 -60.76 -15.36 REMARK 500 15 GLU A 48 -55.21 -149.02 REMARK 500 15 ASN A 77 49.29 -99.74 REMARK 500 17 GLU A 48 -52.97 -149.29 REMARK 500 19 GLU A 48 -51.85 -128.69 REMARK 500 20 GLU A 48 -44.75 -147.19 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 TYR A 90 0.08 SIDE CHAIN REMARK 500 4 TYR A 94 0.07 SIDE CHAIN REMARK 500 7 ARG A 62 0.10 SIDE CHAIN REMARK 500 8 ARG A 50 0.13 SIDE CHAIN REMARK 500 9 TYR A 90 0.09 SIDE CHAIN REMARK 500 9 TYR A 94 0.06 SIDE CHAIN REMARK 500 13 ARG A 50 0.08 SIDE CHAIN REMARK 500 15 TYR A 90 0.08 SIDE CHAIN REMARK 500 15 ARG A 95 0.09 SIDE CHAIN REMARK 500 17 TYR A 90 0.07 SIDE CHAIN REMARK 500 17 ARG A 95 0.12 SIDE CHAIN REMARK 500 20 ARG A 50 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DT7 RELATED DB: PDB REMARK 900 RELATED ID: HSO003016611.1 RELATED DB: TARGETDB DBREF 2DT6 A 48 110 UNP Q15459 SF3A1_HUMAN 48 110 SEQADV 2DT6 GLY A 47 UNP Q15459 CLONING ARTIFACT SEQRES 1 A 64 GLY GLU VAL ARG ASN ILE VAL ASP LYS THR ALA SER PHE SEQRES 2 A 64 VAL ALA ARG ASN GLY PRO GLU PHE GLU ALA ARG ILE ARG SEQRES 3 A 64 GLN ASN GLU ILE ASN ASN PRO LYS PHE ASN PHE LEU ASN SEQRES 4 A 64 PRO ASN ASP PRO TYR HIS ALA TYR TYR ARG HIS LYS VAL SEQRES 5 A 64 SER GLU PHE LYS GLU GLY LYS ALA GLN GLU PRO SER HELIX 1 1 GLY A 47 GLY A 64 1 18 HELIX 2 2 PRO A 65 GLU A 75 1 11 HELIX 3 3 ASN A 78 ASN A 85 5 8 HELIX 4 4 TYR A 90 GLY A 104 1 15 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