HEADER TRANSCRIPTION REGULATOR 19-MAY-08 2K3Y TITLE SOLUTION STRUCTURE OF EAF3 CHROMO BARREL DOMAIN BOUND TO HISTONE H3 TITLE 2 WITH A DIMETHYLLYSINE ANALOG H3K36ME2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMATIN MODIFICATION-RELATED PROTEIN EAF3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1 TO 115; COMPND 5 SYNONYM: ESA1-ASSOCIATED FACTOR 3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: EAF3, YPR023C, YP9367.03C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PTEV KEYWDS EAF3, DIMETHYLATED HISTONE H3K36, EAF3-H3K36ME2 FUSION, CHROMO BARREL KEYWDS 2 DOMAIN, HISTONE DEACETYLASE, CHROMATIN REGULATOR, DNA DAMAGE, DNA KEYWDS 3 REPAIR, NUCLEUS, PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION KEYWDS 4 REGULATION, CHROMOSOMAL PROTEIN, DNA-BINDING, TRANSCRIPTION KEYWDS 5 REGULATOR EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.MER,C.XU REVDAT 7 06-NOV-24 2K3Y 1 REMARK REVDAT 6 15-NOV-23 2K3Y 1 ATOM REVDAT 5 16-MAR-22 2K3Y 1 REMARK SEQADV LINK REVDAT 4 09-JUN-09 2K3Y 1 REVDAT REVDAT 3 24-FEB-09 2K3Y 1 VERSN REVDAT 2 02-DEC-08 2K3Y 1 JRNL REVDAT 1 16-SEP-08 2K3Y 0 JRNL AUTH C.XU,G.CUI,M.V.BOTUYAN,G.MER JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION OF METHYLATED HISTONE JRNL TITL 2 H3K36 BY THE EAF3 SUBUNIT OF HISTONE DEACETYLASE COMPLEX JRNL TITL 3 RPD3S. JRNL REF STRUCTURE V. 16 1740 2008 JRNL REFN ISSN 0969-2126 JRNL PMID 18818090 JRNL DOI 10.1016/J.STR.2008.08.008 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, AMBER REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CASE, DARDEN, CHEATHAM, III, SIMMERLING, REMARK 3 WANG, DUKE, LUO, ... AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K3Y COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000100645. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4-1.5 MM [U-100% 15N] ENTITY, REMARK 210 20 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 1 MM EDTA, 2 MM REMARK 210 DTT, 93% H2O/7% D2O; 0.4-1.5 MM REMARK 210 [U-100% 13C; U-100% 15N] ENTITY, REMARK 210 20 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 1 MM EDTA, 2 MM REMARK 210 DTT, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N TOCSY; REMARK 210 3D 1H-15N NOESY; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HNCO; 3D HCACO; 3D CCH-COSY; 3D REMARK 210 CCH-TOCSY; 3D C(CO)NH; 3D H(CCO) REMARK 210 NH; 2D HBCGCDCEHE; 2D HBCGCDHD; REMARK 210 3D 1H-13C NOESY; 3D 1H-13C NOESY REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, SANE, SPARKY, CYANA 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 LOWEST REMARK 210 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 HIS A 0 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 OD1 ASP A 32 HG SER A 34 1.60 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 1 ALA A 9 CB - CA - C ANGL. DEV. = 9.1 DEGREES REMARK 500 5 TYR A 38 CB - CG - CD1 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 ARG A 132 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 7 TYR A 38 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 9 TYR A 38 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 10 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 16 ALA A 9 CB - CA - C ANGL. DEV. = 9.3 DEGREES REMARK 500 19 TYR A 38 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 20 ALA A 9 CB - CA - C ANGL. DEV. = 9.4 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 LEU A 28 -30.05 -158.01 REMARK 500 1 PRO A 42 46.20 -78.50 REMARK 500 1 ASP A 44 -169.17 -164.65 REMARK 500 1 GLU A 55 80.77 4.79 REMARK 500 1 PRO A 122 10.42 -61.01 REMARK 500 1 THR A 124 -30.97 73.17 REMARK 500 1 LYS A 129 94.68 19.63 REMARK 500 2 LEU A 4 -40.76 60.33 REMARK 500 2 LEU A 10 -3.14 -59.73 REMARK 500 2 LEU A 28 -25.21 -161.26 REMARK 500 2 PRO A 42 44.84 -74.29 REMARK 500 2 ASP A 44 -124.23 -160.89 REMARK 500 2 LYS A 54 -163.53 50.80 REMARK 500 2 SER A 66 118.47 -22.40 REMARK 500 2 ALA A 115 3.63 55.64 REMARK 500 2 SER A 120 77.13 -66.47 REMARK 500 3 ASP A 3 -60.84 -152.37 REMARK 500 3 PHE A 8 87.83 -59.26 REMARK 500 3 LEU A 28 -24.43 -160.53 REMARK 500 3 PRO A 42 41.73 -86.82 REMARK 500 3 SER A 49 17.85 53.98 REMARK 500 3 ALA A 52 75.54 -160.82 REMARK 500 3 THR A 53 -80.14 -112.50 REMARK 500 3 LYS A 54 -139.18 -148.14 REMARK 500 3 GLU A 55 107.53 -58.69 REMARK 500 3 ASP A 64 -29.88 -153.48 REMARK 500 3 GLU A 65 35.81 -82.08 REMARK 500 3 SER A 66 144.21 -32.73 REMARK 500 3 LYS A 129 94.49 30.48 REMARK 500 4 ASP A 3 -53.03 -150.03 REMARK 500 4 PHE A 8 83.51 -60.06 REMARK 500 4 LEU A 28 -28.37 -161.51 REMARK 500 4 PRO A 42 46.15 -78.32 REMARK 500 4 THR A 53 -82.09 -92.94 REMARK 500 4 LYS A 54 -154.74 -151.50 REMARK 500 4 ASP A 64 2.65 -160.32 REMARK 500 4 SER A 66 142.06 -33.05 REMARK 500 4 SER A 117 16.55 54.82 REMARK 500 4 SER A 120 16.68 -68.43 REMARK 500 4 ARG A 132 -38.35 126.75 REMARK 500 5 LEU A 4 12.63 58.32 REMARK 500 5 PHE A 8 82.60 -62.71 REMARK 500 5 LEU A 28 -35.06 -154.96 REMARK 500 5 LYS A 54 -153.41 49.66 REMARK 500 5 ASP A 64 -31.69 -152.07 REMARK 500 5 ALA A 115 0.62 54.80 REMARK 500 5 THR A 118 49.75 -75.90 REMARK 500 5 LYS A 129 97.56 28.03 REMARK 500 6 ASP A 3 -54.63 -162.35 REMARK 500 6 LEU A 10 -8.07 -58.77 REMARK 500 REMARK 500 THIS ENTRY HAS 193 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 1 PHE A 77 0.08 SIDE CHAIN REMARK 500 11 TYR A 23 0.09 SIDE CHAIN REMARK 500 12 TYR A 23 0.07 SIDE CHAIN REMARK 500 12 TYR A 94 0.08 SIDE CHAIN REMARK 500 13 TYR A 23 0.13 SIDE CHAIN REMARK 500 15 TYR A 23 0.18 SIDE CHAIN REMARK 500 16 TYR A 23 0.12 SIDE CHAIN REMARK 500 18 TYR A 94 0.10 SIDE CHAIN REMARK 500 19 TYR A 23 0.09 SIDE CHAIN REMARK 500 20 TYR A 94 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 HIS RESIDUES HAVE HYDROGENS ONLY ON THE EPSILON NITROGEN DBREF 2K3Y A 1 115 UNP Q12432 EAF3_YEAST 1 115 DBREF 2K3Y A 116 132 PDB 2K3Y 2K3Y 116 132 SEQADV 2K3Y GLY A -1 UNP Q12432 EXPRESSION TAG SEQADV 2K3Y HIS A 0 UNP Q12432 EXPRESSION TAG SEQADV 2K3Y VAL A 14 UNP Q12432 CYS 14 CONFLICT SEQADV 2K3Y SER A 76 UNP Q12432 CYS 76 CONFLICT SEQRES 1 A 136 GLY HIS MET VAL ASP LEU GLU GLN GLU PHE ALA LEU GLY SEQRES 2 A 136 GLY ARG VAL LEU ALA PHE HIS GLY PRO LEU MET TYR GLU SEQRES 3 A 136 ALA LYS ILE LEU LYS ILE TRP ASP PRO SER SER LYS MET SEQRES 4 A 136 TYR THR SER ILE PRO ASN ASP LYS PRO GLY GLY SER SER SEQRES 5 A 136 GLN ALA THR LYS GLU ILE LYS PRO GLN LYS LEU GLY GLU SEQRES 6 A 136 ASP GLU SER ILE PRO GLU GLU ILE ILE ASN GLY LYS SER SEQRES 7 A 136 PHE PHE ILE HIS TYR GLN GLY TRP LYS SER SER TRP ASP SEQRES 8 A 136 GLU TRP VAL GLY TYR ASP ARG ILE ARG ALA TYR ASN GLU SEQRES 9 A 136 GLU ASN ILE ALA MET LYS LYS ARG LEU ALA ASN GLU ALA SEQRES 10 A 136 GLY SER THR GLY SER ALA PRO ALA THR GLY GLY VAL M2L SEQRES 11 A 136 LYS PRO HIS ARG TYR ARG MODRES 2K3Y M2L A 128 LYS HET M2L A 128 26 HETNAM M2L (2R)-2-AMINO-3-(2-DIMETHYLAMINOETHYLSULFANYL)PROPANOIC HETNAM 2 M2L ACID FORMUL 1 M2L C7 H16 N2 O2 S HELIX 1 1 VAL A 2 GLU A 7 5 6 HELIX 2 2 PRO A 68 ASN A 73 1 6 HELIX 3 3 LYS A 85 ASP A 89 5 5 HELIX 4 4 ASN A 101 ALA A 115 1 15 SHEET 1 A 4 TYR A 38 SER A 40 0 SHEET 2 A 4 MET A 22 TRP A 31 -1 N ILE A 30 O THR A 39 SHEET 3 A 4 SER A 76 ILE A 79 -1 O PHE A 78 N LYS A 29 SHEET 4 A 4 GLU A 90 GLY A 93 -1 O GLU A 90 N ILE A 79 SHEET 1 B 4 TYR A 38 SER A 40 0 SHEET 2 B 4 MET A 22 TRP A 31 -1 N ILE A 30 O THR A 39 SHEET 3 B 4 ARG A 13 PHE A 17 -1 N VAL A 14 O ALA A 25 SHEET 4 B 4 ILE A 97 ALA A 99 -1 O ARG A 98 N LEU A 15 LINK C VAL A 127 N M2L A 128 1555 1555 1.33 LINK C M2L A 128 N LYS A 129 1555 1555 1.33 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