HEADER RNA BINDING PROTEIN 06-APR-07 2YUD TITLE SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-CONTAINING PROTEIN TITLE 2 1 (PUTATIVE SPLICING FACTOR YT521) COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: YTH DOMAIN; COMPND 5 SYNONYM: PUTATIVE SPLICING FACTOR YT521; 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: YTHDC1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P060508-15; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS STRUCTURE GENOMICS, YTH DOMAIN, YTH DOMAIN-CONTAINING PROTEIN 1 KEYWDS 2 (PUTATIVE SPLICING FACTOR YT521), STRUCTURAL GENOMICS, NPPSFA, KEYWDS 3 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, KEYWDS 4 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, RNA BINDING KEYWDS 5 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.HE,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 2YUD 1 REMARK SEQADV REVDAT 2 24-FEB-09 2YUD 1 VERSN REVDAT 1 09-OCT-07 2YUD 0 JRNL AUTH F.HE,Y.MUTO,M.INOUE,T.KIGAWA,M.SHIROUZU,T.TARADA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH JRNL TITL 2 DOMAIN-CONTAINING PROTEIN 1 (PUTATIVE SPLICING FACTOR YT521) 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 2.1 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YUD 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_1000027145. 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 2.1 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 LYS A 13 70.09 -163.63 REMARK 500 1 TRP A 48 119.65 -168.37 REMARK 500 1 LEU A 51 162.40 -48.21 REMARK 500 1 ALA A 65 -169.78 -110.74 REMARK 500 1 ARG A 66 -74.56 -77.43 REMARK 500 1 ALA A 84 133.34 -172.81 REMARK 500 1 LEU A 86 106.61 -54.12 REMARK 500 1 GLU A 89 -170.11 -64.67 REMARK 500 1 HIS A 92 32.71 -151.46 REMARK 500 1 PRO A 102 -170.94 -69.73 REMARK 500 1 ARG A 121 45.95 -91.51 REMARK 500 1 LEU A 124 119.05 -161.90 REMARK 500 1 HIS A 131 -34.94 -174.44 REMARK 500 1 ASN A 137 -65.91 -179.08 REMARK 500 1 GLU A 138 35.71 -175.20 REMARK 500 1 GLU A 152 -170.76 -60.58 REMARK 500 2 SER A 2 83.40 58.67 REMARK 500 2 ARG A 12 140.65 -176.03 REMARK 500 2 LYS A 13 39.01 -172.16 REMARK 500 2 ASN A 35 121.83 -175.20 REMARK 500 2 TRP A 48 117.46 -167.10 REMARK 500 2 LEU A 51 162.50 -47.78 REMARK 500 2 ALA A 65 -169.81 -102.85 REMARK 500 2 ARG A 66 -74.51 -80.61 REMARK 500 2 GLU A 76 25.84 -161.58 REMARK 500 2 ALA A 84 134.40 -172.18 REMARK 500 2 LEU A 86 106.23 -52.76 REMARK 500 2 GLU A 89 -173.43 -62.40 REMARK 500 2 HIS A 92 26.03 -149.86 REMARK 500 2 PRO A 102 -176.18 -69.70 REMARK 500 2 TRP A 118 109.75 -53.17 REMARK 500 2 ARG A 121 39.99 -96.40 REMARK 500 2 LEU A 124 119.08 -161.95 REMARK 500 2 HIS A 131 -36.00 -172.68 REMARK 500 2 ASN A 137 -65.09 -178.77 REMARK 500 2 GLU A 138 35.37 -175.92 REMARK 500 2 GLU A 152 -169.88 -61.04 REMARK 500 3 ARG A 12 101.81 -177.32 REMARK 500 3 LYS A 13 -171.02 -173.96 REMARK 500 3 GLN A 15 -37.68 -174.01 REMARK 500 3 TRP A 48 118.92 -168.06 REMARK 500 3 LEU A 51 162.42 -47.96 REMARK 500 3 ALA A 65 -169.89 -104.60 REMARK 500 3 ARG A 66 -74.56 -80.22 REMARK 500 3 ALA A 84 138.64 -174.09 REMARK 500 3 LEU A 86 106.87 -53.62 REMARK 500 3 SER A 90 178.05 -57.27 REMARK 500 3 PRO A 102 -171.01 -69.80 REMARK 500 3 ARG A 121 46.57 -93.03 REMARK 500 3 LEU A 124 119.08 -162.12 REMARK 500 REMARK 500 THIS ENTRY HAS 397 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002101933.2 RELATED DB: TARGETDB DBREF 2YUD A 8 180 UNP Q96MU7 YTDC1_HUMAN 337 509 SEQADV 2YUD GLY A 1 UNP Q96MU7 EXPRESSION TAG SEQADV 2YUD SER A 2 UNP Q96MU7 EXPRESSION TAG SEQADV 2YUD SER A 3 UNP Q96MU7 EXPRESSION TAG SEQADV 2YUD GLY A 4 UNP Q96MU7 EXPRESSION TAG SEQADV 2YUD SER A 5 UNP Q96MU7 EXPRESSION TAG SEQADV 2YUD SER A 6 UNP Q96MU7 EXPRESSION TAG SEQADV 2YUD GLY A 7 UNP Q96MU7 EXPRESSION TAG SEQRES 1 A 180 GLY SER SER GLY SER SER GLY VAL ARG ALA VAL ARG LYS SEQRES 2 A 180 ASP GLN THR SER LYS LEU LYS TYR VAL LEU GLN ASP ALA SEQRES 3 A 180 ARG PHE PHE LEU ILE LYS SER ASN ASN HIS GLU ASN VAL SEQRES 4 A 180 SER LEU ALA LYS ALA LYS GLY VAL TRP SER THR LEU PRO SEQRES 5 A 180 VAL ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SER ALA SEQRES 6 A 180 ARG SER VAL ILE LEU ILE PHE SER VAL ARG GLU SER GLY SEQRES 7 A 180 LYS PHE GLN GLY PHE ALA ARG LEU SER SER GLU SER HIS SEQRES 8 A 180 HIS GLY GLY SER PRO ILE HIS TRP VAL LEU PRO ALA GLY SEQRES 9 A 180 MET SER ALA LYS MET LEU GLY GLY VAL PHE LYS ILE ASP SEQRES 10 A 180 TRP ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SER ALA SEQRES 11 A 180 HIS LEU THR ASN PRO TRP ASN GLU HIS LYS PRO VAL LYS SEQRES 12 A 180 ILE GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU CYS GLY SEQRES 13 A 180 THR GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SER ILE SEQRES 14 A 180 ASP LEU TYR GLN VAL ILE HIS LYS MET ARG HIS HELIX 1 1 THR A 16 VAL A 22 1 7 HELIX 2 2 HIS A 36 LYS A 45 1 10 HELIX 3 3 PRO A 52 SER A 64 1 13 HELIX 4 4 ALA A 107 LEU A 110 5 4 HELIX 5 5 PHE A 126 SER A 129 1 4 HELIX 6 6 LEU A 153 LEU A 162 1 10 HELIX 7 7 TYR A 172 ARG A 179 1 8 SHEET 1 A 4 VAL A 47 TRP A 48 0 SHEET 2 A 4 VAL A 113 CYS A 120 -1 O PHE A 114 N TRP A 48 SHEET 3 A 4 LYS A 79 HIS A 91 -1 N SER A 87 O LYS A 115 SHEET 4 A 4 LEU A 124 PRO A 125 -1 O LEU A 124 N PHE A 80 SHEET 1 B 6 VAL A 47 TRP A 48 0 SHEET 2 B 6 VAL A 113 CYS A 120 -1 O PHE A 114 N TRP A 48 SHEET 3 B 6 LYS A 79 HIS A 91 -1 N SER A 87 O LYS A 115 SHEET 4 B 6 VAL A 68 VAL A 74 -1 N VAL A 68 O LEU A 86 SHEET 5 B 6 ARG A 27 SER A 33 1 N PHE A 29 O ILE A 69 SHEET 6 B 6 GLN A 149 ILE A 151 -1 O GLN A 149 N LEU A 30 SHEET 1 C 2 THR A 133 ASN A 134 0 SHEET 2 C 2 LYS A 140 PRO A 141 -1 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