HEADER RNA BINDING PROTEIN 15-JAN-20 6LR2 TITLE SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-2 CONTAINING TITLE 2 PROTEIN 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN CONTAINING PROTEIN 2 (YTHDC2); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: CELL-FREE GATEWAY CLONING VECTOR N-TERM 8XHIS SOURCE 6 EGFP PCELLFREE_G03; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1508207; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P060508-16 KEYWDS RNA BINDING PROTEIN, MEIOSIS RELATED PROTEIN, STRUCTURAL GENOMICS, KEYWDS 2 PSI-2, PROTEIN STRUCTURE INITIATIVE, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.MUTO,N.KOBAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 15-MAY-24 6LR2 1 REMARK REVDAT 2 14-JUN-23 6LR2 1 REMARK REVDAT 1 20-JAN-21 6LR2 0 JRNL AUTH R.ENDO,F.HE,M.INOUE,Y.MUTO,T.KIGAWA,M.SHIROUZU,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 : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 3191 NOE REMARK 3 -DERIVED DISTANCE CONTRRAINS, 71 MAIN CHAIN DIHEDRAL ANGLE REMARK 3 CONSTRAINTS BASED ON TALOS PROGRAM AND 51 SIDE CHAIN DIHEDRAL REMARK 3 CONSTRAINTS BASED ON NOE PATTERN. REMARK 4 REMARK 4 6LR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1300015064. 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 : 1.0 MG/ML [U-99% 13C; U-99% 15N] REMARK 210 HELICASE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C,15N-SEPARATED_NOESY REMARK 210 SPECTRA 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 2.0.17, KUJIRA 0.9820, REMARK 210 NMRVIEW 5.0.4 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 FAVORABLE NON REMARK 210 -BOND 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: 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 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 ARG A 74 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 13 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 15 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 ARG A 95 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 16 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 17 ARG A 38 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 17 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 18 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 18 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 20 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 20 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 20 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 20 ARG A 74 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER A 5 -174.08 58.24 REMARK 500 1 ASN A 112 -74.66 -98.70 REMARK 500 1 ASP A 113 13.88 -157.24 REMARK 500 1 ASP A 122 96.09 -56.82 REMARK 500 2 SER A 6 -148.49 57.00 REMARK 500 2 GLN A 63 38.19 -82.84 REMARK 500 2 ASN A 112 -80.77 -92.04 REMARK 500 2 ASP A 113 36.01 -164.97 REMARK 500 2 ILE A 119 47.40 -90.46 REMARK 500 3 GLN A 63 35.00 -85.53 REMARK 500 3 ASN A 112 -81.65 -90.86 REMARK 500 3 ASP A 113 40.92 -165.08 REMARK 500 4 SER A 3 42.54 -77.26 REMARK 500 4 ASN A 112 -79.55 -96.38 REMARK 500 4 ASP A 113 34.18 -161.89 REMARK 500 4 ASN A 114 16.35 59.74 REMARK 500 4 ASP A 122 105.02 -59.81 REMARK 500 5 ASN A 112 -82.09 -79.07 REMARK 500 5 ASP A 113 32.34 -154.47 REMARK 500 5 ASP A 122 92.21 -59.00 REMARK 500 6 SER A 6 19.72 55.34 REMARK 500 6 GLN A 63 34.92 -90.46 REMARK 500 6 ASN A 112 -73.37 -115.34 REMARK 500 6 ASP A 113 39.99 -156.57 REMARK 500 7 SER A 5 130.80 65.93 REMARK 500 7 ASN A 112 -74.14 -102.06 REMARK 500 7 ASP A 113 11.29 -157.91 REMARK 500 8 GLN A 63 29.56 -78.36 REMARK 500 8 ASN A 112 -77.00 -83.45 REMARK 500 8 ASP A 113 36.17 -165.99 REMARK 500 8 ILE A 119 49.02 -83.95 REMARK 500 8 ASP A 122 97.77 -61.06 REMARK 500 9 GLN A 63 35.97 -78.65 REMARK 500 9 ASN A 112 -79.61 -91.68 REMARK 500 9 ASP A 113 32.86 -164.40 REMARK 500 9 ASN A 114 17.11 58.34 REMARK 500 9 ILE A 119 45.63 -84.60 REMARK 500 9 ASP A 122 99.56 -58.50 REMARK 500 10 SER A 3 -36.16 -153.06 REMARK 500 10 GLN A 63 37.23 -83.09 REMARK 500 10 ASN A 112 -76.22 -94.05 REMARK 500 10 ASP A 113 16.68 -162.73 REMARK 500 10 ILE A 119 49.28 -87.12 REMARK 500 11 GLN A 63 20.48 -73.85 REMARK 500 11 ASN A 112 -80.04 -89.34 REMARK 500 11 ASP A 113 34.85 -165.14 REMARK 500 11 ASN A 114 15.98 58.78 REMARK 500 11 ILE A 119 44.35 -93.60 REMARK 500 12 LYS A 76 48.00 -143.99 REMARK 500 12 ASN A 112 -90.34 -97.87 REMARK 500 REMARK 500 THIS ENTRY HAS 75 RAMACHANDRAN OUTLIERS. 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 4 ARG A 42 0.08 SIDE CHAIN REMARK 500 8 ARG A 42 0.09 SIDE CHAIN REMARK 500 10 ARG A 42 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36310 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE YTH DOMAIN IN YTH DOMAIN-2 CONTAINING REMARK 900 PROTEIN 2 REMARK 900 RELATED ID: P060508-16 RELATED DB: TARGETTRACK REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT 6L2R HAS A MUTATION, L129Q BASED RS1132529 IN REMARK 999 DBSNP DATABASE. DBREF 6LR2 A 8 141 UNP Q6ZMY0 Q6ZMY0_HUMAN 1198 1331 SEQADV 6LR2 GLY A 1 UNP Q6ZMY0 EXPRESSION TAG SEQADV 6LR2 SER A 2 UNP Q6ZMY0 EXPRESSION TAG SEQADV 6LR2 SER A 3 UNP Q6ZMY0 EXPRESSION TAG SEQADV 6LR2 GLY A 4 UNP Q6ZMY0 EXPRESSION TAG SEQADV 6LR2 SER A 5 UNP Q6ZMY0 EXPRESSION TAG SEQADV 6LR2 SER A 6 UNP Q6ZMY0 EXPRESSION TAG SEQADV 6LR2 GLY A 7 UNP Q6ZMY0 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 AA1 ASN A 17 GLY A 28 1 12 HELIX 2 AA2 THR A 33 SER A 47 1 15 HELIX 3 AA3 GLN A 102 HIS A 105 5 4 HELIX 4 AA4 GLU A 127 GLN A 136 1 10 HELIX 5 AA5 LEU A 137 LEU A 141 5 5 SHEET 1 AA1 6 ILE A 29 SER A 31 0 SHEET 2 AA1 6 VAL A 88 ARG A 95 -1 O PHE A 89 N TRP A 30 SHEET 3 AA1 6 GLY A 64 MET A 68 -1 N ARG A 67 O GLU A 92 SHEET 4 AA1 6 ILE A 49 PHE A 54 -1 N LEU A 52 O SER A 66 SHEET 5 AA1 6 VAL A 8 ILE A 12 1 N ARG A 9 O TYR A 51 SHEET 6 AA1 6 GLN A 124 LEU A 126 -1 O GLN A 124 N ILE A 12 SHEET 1 AA2 2 HIS A 61 PHE A 62 0 SHEET 2 AA2 2 LEU A 99 PRO A 100 -1 O LEU A 99 N PHE A 62 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