HEADER TRANSCRIPTION 31-MAY-19 6K5W TITLE SOLUTION STRUCTURE OF THE CHROMODOMAIN OF YEAST EAF3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHROMATIN MODIFICATION-RELATED PROTEIN EAF3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ESA1-ASSOCIATED FACTOR 3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: EAF3, YPR023C, YP9367.03C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NUCLEAR PROTEIN, HISTONE ACETYL TRANSFERASE, HISTONE DEACETYLASE, KEYWDS 2 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.OKUDA,Y.NISHIMURA REVDAT 4 15-MAY-24 6K5W 1 REMARK REVDAT 3 14-JUN-23 6K5W 1 REMARK REVDAT 2 04-MAR-20 6K5W 1 JRNL REVDAT 1 26-FEB-20 6K5W 0 JRNL AUTH M.OKUDA,Y.NISHIMURA JRNL TITL THE EAF3 CHROMODOMAIN ACTS AS A PH SENSOR FOR GENE JRNL TITL 2 EXPRESSION BY ALTERING ITS BINDING AFFINITY FOR HISTONE JRNL TITL 3 METHYLATED-LYSINE RESIDUES. JRNL REF BIOSCI.REP. V. 40 2020 JRNL REFN ISSN 0144-8463 JRNL PMID 32031206 JRNL DOI 10.1042/BSR20191958 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6K5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012334. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 30 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.47 MM [U-13C,15N] EAF3, 90% REMARK 210 H2O/10% D2O; 1.47 MM [U-13C,15N] REMARK 210 EAF3, 100% D2O; 1.47 MM [U-15N] REMARK 210 EAF3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCANH; 3D CBCA(CO)NH; 3D REMARK 210 HNCA; 3D HN(CO)CA; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HBHA(CO)NH; 3D REMARK 210 CC(CO)NH; 3D H(CC)(CO)HN; 3D REMARK 210 HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 HNHA; 3D HNHB; 3D HN(CO)HB; 3D REMARK 210 HNCG; 3D HN(CO)CG; 2D CGCBH; 2D REMARK 210 CGCDH; 2D CGCEH; 2D HBCBCDHD; 2D REMARK 210 HBCBCGCEHE; 2D DQF-COSY; 2D 1H- REMARK 210 1H TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, NMRVIEW, MOLMOL, REMARK 210 PROCHECK / PROCHECK-NMR 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 -2 REMARK 465 SER 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 HE3 TRP A 31 HB3 TYR A 38 1.28 REMARK 500 OD1 ASP A 32 HG SER A 34 1.57 REMARK 500 O MET A 107 H LEU A 111 1.57 REMARK 500 HZ2 LYS A 29 OE1 GLU A 65 1.58 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 ALA A 9 -154.40 -151.95 REMARK 500 1 LEU A 10 105.35 -56.55 REMARK 500 1 LYS A 36 30.40 80.25 REMARK 500 1 ASN A 43 -64.35 -144.46 REMARK 500 1 SER A 50 -89.90 -162.26 REMARK 500 1 PRO A 58 105.20 -53.85 REMARK 500 1 SER A 66 108.05 -45.18 REMARK 500 1 LYS A 75 101.80 57.31 REMARK 500 1 TRP A 84 -107.32 -98.53 REMARK 500 1 LYS A 85 -175.30 -175.46 REMARK 500 2 GLU A 5 -6.19 -52.08 REMARK 500 2 ALA A 9 -157.35 -151.26 REMARK 500 2 LEU A 10 104.42 -56.00 REMARK 500 2 LYS A 36 34.30 77.68 REMARK 500 2 ASN A 43 -53.19 -158.94 REMARK 500 2 SER A 50 32.25 -91.26 REMARK 500 2 GLU A 55 84.35 53.28 REMARK 500 2 PRO A 58 109.01 -52.14 REMARK 500 2 GLU A 63 23.73 -75.82 REMARK 500 2 GLU A 65 -76.84 -118.38 REMARK 500 2 SER A 66 99.02 62.26 REMARK 500 2 LYS A 75 104.68 56.99 REMARK 500 2 TYR A 81 124.96 -38.93 REMARK 500 2 TRP A 84 -168.87 -117.47 REMARK 500 2 TYR A 94 -9.07 -55.97 REMARK 500 2 ALA A 118 -156.51 -115.35 REMARK 500 2 LYS A 119 66.75 -153.37 REMARK 500 3 ALA A 9 -150.83 -151.92 REMARK 500 3 LYS A 36 32.21 75.17 REMARK 500 3 ASN A 43 -53.61 -174.24 REMARK 500 3 GLN A 51 38.35 -88.96 REMARK 500 3 ALA A 52 49.32 -149.84 REMARK 500 3 LYS A 54 -63.92 67.96 REMARK 500 3 PRO A 58 105.27 -56.23 REMARK 500 3 LYS A 75 105.51 58.68 REMARK 500 3 TYR A 100 98.62 -52.83 REMARK 500 4 ASP A 3 44.22 -67.54 REMARK 500 4 PHE A 8 60.02 -114.39 REMARK 500 4 ALA A 9 -155.32 -149.04 REMARK 500 4 LEU A 10 101.80 -54.17 REMARK 500 4 LYS A 36 28.54 81.05 REMARK 500 4 ASP A 44 78.84 56.11 REMARK 500 4 SER A 49 -174.32 64.12 REMARK 500 4 THR A 53 -76.77 71.41 REMARK 500 4 LYS A 54 -68.34 63.15 REMARK 500 4 PRO A 58 107.63 -54.03 REMARK 500 4 LYS A 75 105.97 55.19 REMARK 500 4 LYS A 85 -167.41 -108.96 REMARK 500 4 LYS A 119 21.43 -152.90 REMARK 500 5 ASP A 3 21.04 -143.47 REMARK 500 REMARK 500 THIS ENTRY HAS 252 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36261 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE CHROMODOMAIN OF YEAST EAF3 DBREF 6K5W A 1 120 UNP Q12432 EAF3_YEAST 1 120 SEQADV 6K5W GLY A -2 UNP Q12432 EXPRESSION TAG SEQADV 6K5W SER A -1 UNP Q12432 EXPRESSION TAG SEQADV 6K5W HIS A 0 UNP Q12432 EXPRESSION TAG SEQRES 1 A 123 GLY SER HIS MET VAL ASP LEU GLU GLN GLU PHE ALA LEU SEQRES 2 A 123 GLY GLY ARG CYS LEU ALA PHE HIS GLY PRO LEU MET TYR SEQRES 3 A 123 GLU ALA LYS ILE LEU LYS ILE TRP ASP PRO SER SER LYS SEQRES 4 A 123 MET TYR THR SER ILE PRO ASN ASP LYS PRO GLY GLY SER SEQRES 5 A 123 SER GLN ALA THR LYS GLU ILE LYS PRO GLN LYS LEU GLY SEQRES 6 A 123 GLU ASP GLU SER ILE PRO GLU GLU ILE ILE ASN GLY LYS SEQRES 7 A 123 CYS PHE PHE ILE HIS TYR GLN GLY TRP LYS SER SER TRP SEQRES 8 A 123 ASP GLU TRP VAL GLY TYR ASP ARG ILE ARG ALA TYR ASN SEQRES 9 A 123 GLU GLU ASN ILE ALA MET LYS LYS ARG LEU ALA ASN GLU SEQRES 10 A 123 ALA LYS GLU ALA LYS LYS HELIX 1 AA1 ASP A 3 GLU A 7 5 5 HELIX 2 AA2 PRO A 68 ASN A 73 1 6 HELIX 3 AA3 LYS A 85 SER A 87 5 3 HELIX 4 AA4 GLU A 103 ALA A 115 1 13 SHEET 1 AA1 5 GLN A 59 LYS A 60 0 SHEET 2 AA1 5 MET A 37 SER A 40 -1 N TYR A 38 O GLN A 59 SHEET 3 AA1 5 LEU A 21 TRP A 31 -1 N ILE A 30 O THR A 39 SHEET 4 AA1 5 CYS A 76 TYR A 81 -1 O PHE A 78 N LYS A 29 SHEET 5 AA1 5 ASP A 89 GLY A 93 -1 O VAL A 92 N PHE A 77 SHEET 1 AA2 5 GLN A 59 LYS A 60 0 SHEET 2 AA2 5 MET A 37 SER A 40 -1 N TYR A 38 O GLN A 59 SHEET 3 AA2 5 LEU A 21 TRP A 31 -1 N ILE A 30 O THR A 39 SHEET 4 AA2 5 ARG A 13 HIS A 18 -1 N HIS A 18 O LEU A 21 SHEET 5 AA2 5 ILE A 97 ALA A 99 -1 O ARG A 98 N LEU A 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