HEADER RNA BINDING PROTEIN 05-APR-07 2YU6 TITLE SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-CONTAINING PROTEIN TITLE 2 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: YTH DOMAIN; COMPND 5 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: YTHDC2; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P060508-16; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS YTH DOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.ENDO,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TARADA,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 16-MAR-22 2YU6 1 REMARK SEQADV REVDAT 2 24-FEB-09 2YU6 1 VERSN REVDAT 1 09-OCT-07 2YU6 0 JRNL AUTH R.ENDO,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TARADA, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH JRNL TITL 2 DOMAIN-CONTAINING PROTEIN 2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YU6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000027138. 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 : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0MM 13C, 15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL (PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY 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 : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9820, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS 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, TARGET REMARK 210 FUNCTION 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: 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 PRO A 34 3.56 -69.80 REMARK 500 1 SER A 59 134.30 -38.56 REMARK 500 1 GLN A 63 -19.90 -47.82 REMARK 500 1 ARG A 74 -38.58 -38.08 REMARK 500 1 GLN A 102 -36.68 -37.49 REMARK 500 1 PRO A 110 3.95 -69.68 REMARK 500 1 ASN A 114 49.44 32.96 REMARK 500 1 LYS A 116 142.62 -37.44 REMARK 500 1 GLN A 118 -39.37 -37.22 REMARK 500 1 ILE A 119 71.81 -68.40 REMARK 500 2 ASN A 20 -38.85 -38.28 REMARK 500 2 PRO A 34 4.32 -69.77 REMARK 500 2 PRO A 110 1.15 -69.74 REMARK 500 2 ASN A 114 33.06 37.19 REMARK 500 3 PRO A 34 3.49 -69.77 REMARK 500 3 GLN A 63 -19.46 -48.18 REMARK 500 3 GLN A 78 -61.06 -103.33 REMARK 500 3 PRO A 110 3.17 -69.75 REMARK 500 3 ASP A 113 46.56 74.85 REMARK 500 3 ASN A 114 34.07 34.21 REMARK 500 3 LYS A 116 147.30 -36.63 REMARK 500 3 GLN A 118 -31.95 -39.46 REMARK 500 4 PRO A 34 2.28 -69.79 REMARK 500 4 LYS A 39 -72.15 -64.23 REMARK 500 4 LEU A 40 -39.14 -39.84 REMARK 500 4 SER A 59 150.63 -34.39 REMARK 500 4 TRP A 80 137.29 -171.06 REMARK 500 4 ILE A 94 -61.87 -93.97 REMARK 500 4 GLN A 118 -39.78 -34.61 REMARK 500 5 SER A 5 156.77 -39.11 REMARK 500 5 SER A 6 106.12 -161.23 REMARK 500 5 PRO A 34 5.24 -69.79 REMARK 500 5 ARG A 38 -39.13 -34.23 REMARK 500 5 TRP A 80 136.80 -170.45 REMARK 500 5 ASN A 114 37.73 35.84 REMARK 500 5 ILE A 119 72.36 -66.70 REMARK 500 6 SER A 6 37.26 -99.32 REMARK 500 6 PRO A 34 2.81 -69.77 REMARK 500 6 LYS A 39 -72.98 -69.90 REMARK 500 6 SER A 59 141.03 -34.59 REMARK 500 6 ILE A 94 -60.87 -106.67 REMARK 500 6 GLN A 102 -34.67 -39.02 REMARK 500 6 ASN A 112 58.60 -102.66 REMARK 500 7 SER A 2 52.95 35.09 REMARK 500 7 SER A 5 83.48 -57.15 REMARK 500 7 PRO A 34 2.66 -69.75 REMARK 500 7 ARG A 38 -72.80 -43.73 REMARK 500 7 GLU A 75 119.48 -39.77 REMARK 500 7 ILE A 94 -60.11 -100.83 REMARK 500 7 PRO A 110 1.55 -69.74 REMARK 500 REMARK 500 THIS ENTRY HAS 147 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSS001001522.2 RELATED DB: TARGETDB DBREF 2YU6 A 8 141 UNP Q9H6S0 YTDC2_HUMAN 529 662 SEQADV 2YU6 GLY A 1 UNP Q9H6S0 EXPRESSION TAG SEQADV 2YU6 SER A 2 UNP Q9H6S0 EXPRESSION TAG SEQADV 2YU6 SER A 3 UNP Q9H6S0 EXPRESSION TAG SEQADV 2YU6 GLY A 4 UNP Q9H6S0 EXPRESSION TAG SEQADV 2YU6 SER A 5 UNP Q9H6S0 EXPRESSION TAG SEQADV 2YU6 SER A 6 UNP Q9H6S0 EXPRESSION TAG SEQADV 2YU6 GLY A 7 UNP Q9H6S0 EXPRESSION TAG SEQRES 1 A 141 GLY SER SER GLY SER SER GLY VAL ARG TYR PHE ILE MET SEQRES 2 A 141 LYS SER SER ASN LEU ARG ASN LEU GLU ILE SER GLN GLN SEQRES 3 A 141 LYS GLY ILE TRP SER THR THR PRO SER ASN GLU ARG LYS SEQRES 4 A 141 LEU ASN ARG ALA PHE TRP GLU SER SER ILE VAL TYR LEU SEQRES 5 A 141 VAL PHE SER VAL GLN GLY SER GLY HIS PHE GLN GLY PHE SEQRES 6 A 141 SER ARG MET SER SER GLU ILE GLY ARG GLU LYS SER GLN SEQRES 7 A 141 ASP TRP GLY SER ALA GLY LEU GLY GLY VAL PHE LYS VAL SEQRES 8 A 141 GLU TRP ILE ARG LYS GLU SER LEU PRO PHE GLN PHE ALA SEQRES 9 A 141 HIS HIS LEU LEU ASN PRO TRP ASN ASP ASN LYS LYS VAL SEQRES 10 A 141 GLN ILE SER ARG ASP GLY GLN GLU LEU GLU PRO GLN VAL SEQRES 11 A 141 GLY GLU GLN LEU LEU GLN LEU TRP GLU ARG LEU HELIX 1 1 ARG A 19 GLN A 26 1 8 HELIX 2 2 GLU A 37 GLU A 46 1 10 HELIX 3 3 PHE A 101 ALA A 104 1 4 HELIX 4 4 VAL A 130 ARG A 140 1 11 SHEET 1 A 6 ILE A 29 SER A 31 0 SHEET 2 A 6 VAL A 88 ARG A 95 -1 O PHE A 89 N TRP A 30 SHEET 3 A 6 GLY A 64 MET A 68 -1 N ARG A 67 O GLU A 92 SHEET 4 A 6 VAL A 50 VAL A 56 -1 N VAL A 50 O MET A 68 SHEET 5 A 6 ARG A 9 SER A 15 1 N SER A 15 O SER A 55 SHEET 6 A 6 GLN A 124 LEU A 126 -1 O LEU A 126 N TYR A 10 SHEET 1 B 2 HIS A 61 PHE A 62 0 SHEET 2 B 2 LEU A 99 PRO A 100 -1 O LEU A 99 N PHE A 62 SHEET 1 C 2 LEU A 108 ASN A 109 0 SHEET 2 C 2 LYS A 115 LYS A 116 -1 O LYS A 115 N ASN A 109 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