HEADER GENE REGULATION 21-MAR-25 9QLM TITLE SOLUTION STRUCTURE OF THE TAF3-PHD BOUND TO A H3K4ME3Q5SER HISTONE TITLE 2 TAIL PEPTIDE WITH A SEROTONYLATED GLUTAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 140 KDA TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR,TBP- COMPND 5 ASSOCIATED FACTOR 3,TRANSCRIPTION INITIATION FACTOR TFIID 140 KDA COMPND 6 SUBUNIT,TAF(II)140,TAF140,TAFII-140,TAFII140; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: PLANT HOMEODOMAIN OF TAF3 WITH 2 ZINC IONS BOUND; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HISTONE H3.1; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 13 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 14 H3/L; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: TAF3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS SEROTONYLATION, METHYLATION, HISTONE H3, GENE REGULATION, TFIID EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.VAN INGEN,H.GIELINGH,L.PULIDO-CORTES,V.THIJSSEN,H.T.M.TIMMERS, AUTHOR 2 S.JONGKEES,R.V.HONORATO,A.M.J.J.BONVIN,M.LIU,R.YOSHISADA,L.R.SOARES REVDAT 2 23-JUL-25 9QLM 1 AUTHOR JRNL REVDAT 1 14-MAY-25 9QLM 0 JRNL AUTH L.PULIDO-CORTES,H.GIELINGH,V.THIJSSEN,M.LIU,R.YOSHISADA, JRNL AUTH 2 L.ROMAO SOARES,S.NIZAMUDDIN,F.FRIEDRICH,H.GRESCHIK,L.PENG, JRNL AUTH 3 R.VARGAS HONORATO,M.JUNG,A.M.J.J.BONVIN,M.L.BINIOSSEK, JRNL AUTH 4 R.SCHULE,S.JONGKEES,H.VAN INGEN,H.T.M.TIMMERS JRNL TITL MOLECULAR DETERMINANTS FOR RECOGNITION OF SEROTONYLATED JRNL TITL 2 CHROMATIN. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40637225 JRNL DOI 10.1093/NAR/GKAF612 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK REMARK 3 AUTHORS : BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9QLM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292146471. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 44 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.88 MM [U-13C; U-15N] TAF3-PHD, REMARK 210 0.88 MM H3K4ME3Q5SER, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 4 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM ZINC REMARK 210 CHLORIDE, 0.01 % W/V SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D F2-FILTERED NOESY; 2D F2 REMARK 210 -FILTERED TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; 2D 1H- REMARK 210 13C HSQC; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK, POKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 OD2 ASP A 921 H HIS A 924 1.51 REMARK 500 OD1 ASP A 889 HH21 ARG B 2 1.57 REMARK 500 OD2 ASP A 887 HZ3 LYS A 917 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 TYR A 857 37.70 -84.47 REMARK 500 1 PRO A 871 13.04 -69.94 REMARK 500 1 ASN A 874 37.08 70.28 REMARK 500 1 ASP A 889 -19.71 73.98 REMARK 500 1 LYS A 920 140.47 76.62 REMARK 500 1 LYS A 923 47.41 155.06 REMARK 500 2 TYR A 857 38.54 -82.56 REMARK 500 2 ASP A 887 -54.66 -132.28 REMARK 500 2 ASP A 889 -18.37 76.96 REMARK 500 2 PRO A 904 109.55 -57.26 REMARK 500 2 PRO A 912 -7.85 -56.34 REMARK 500 2 LYS A 920 141.32 77.23 REMARK 500 2 LYS A 923 45.08 151.51 REMARK 500 2 GLU B 5 -86.01 -125.99 REMARK 500 2 ALA B 7 100.45 -53.11 REMARK 500 2 SER B 10 -110.27 -161.25 REMARK 500 2 THR B 11 23.92 -151.50 REMARK 500 3 SER A 851 41.21 -76.49 REMARK 500 3 ALA A 854 -156.88 -118.00 REMARK 500 3 TYR A 857 -61.52 68.62 REMARK 500 3 ASP A 861 -157.30 -98.81 REMARK 500 3 ASP A 878 -27.45 -176.47 REMARK 500 3 ASP A 886 32.67 -97.76 REMARK 500 3 ASP A 887 -52.81 -147.53 REMARK 500 3 CYS A 888 -95.87 -76.00 REMARK 500 3 ASP A 889 -73.74 -138.76 REMARK 500 3 ASP A 890 -149.86 -110.88 REMARK 500 3 ALA A 901 -175.16 -173.80 REMARK 500 3 ASP A 921 -72.90 -97.22 REMARK 500 3 LYS A 922 70.34 55.74 REMARK 500 3 LYS A 923 -75.12 -159.13 REMARK 500 3 THR B 6 52.30 -90.19 REMARK 500 3 SER B 10 107.23 -56.97 REMARK 500 3 THR B 11 29.25 -144.57 REMARK 500 4 SER A 851 42.68 -72.50 REMARK 500 4 ALA A 854 -156.44 -117.36 REMARK 500 4 TYR A 857 -63.91 70.01 REMARK 500 4 ASP A 861 -157.59 -96.83 REMARK 500 4 ASP A 878 68.36 -159.61 REMARK 500 4 ASP A 886 35.82 -98.63 REMARK 500 4 ASP A 887 -52.55 -152.87 REMARK 500 4 CYS A 888 -96.05 -73.07 REMARK 500 4 ASP A 889 -76.52 -139.90 REMARK 500 4 ASP A 890 -148.12 -106.66 REMARK 500 4 ALA A 901 -177.18 -173.00 REMARK 500 4 ASP A 921 -75.45 -96.10 REMARK 500 4 LYS A 923 -78.33 -156.53 REMARK 500 4 LYS B 9 54.03 -160.59 REMARK 500 5 ALA A 856 -107.25 47.44 REMARK 500 5 ASN A 874 54.04 71.56 REMARK 500 REMARK 500 THIS ENTRY HAS 227 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 870 SG REMARK 620 2 CYS A 873 SG 113.5 REMARK 620 3 HIS A 893 ND1 93.5 98.5 REMARK 620 4 CYS A 896 SG 123.7 104.5 120.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 885 SG REMARK 620 2 CYS A 888 SG 126.1 REMARK 620 3 CYS A 911 SG 117.5 109.1 REMARK 620 4 CYS A 914 SG 113.2 83.2 99.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K17 RELATED DB: PDB REMARK 900 COMPLEX OF TAF3-PHD AND H3K4ME3 PEPTIDE REMARK 900 RELATED ID: 34986 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE TAF3-PHD BOUND TO A H3K4ME3Q5SER HISTONE REMARK 900 TAIL PEPTIDE WITH A SEROTONYLATED GLUTAMINE DBREF 9QLM A 857 924 UNP Q5HZG4 TAF3_MOUSE 857 924 DBREF 9QLM B 1 12 UNP P68431 H31_HUMAN 2 13 SEQADV 9QLM GLY A 850 UNP Q5HZG4 EXPRESSION TAG SEQADV 9QLM SER A 851 UNP Q5HZG4 EXPRESSION TAG SEQADV 9QLM HIS A 852 UNP Q5HZG4 EXPRESSION TAG SEQADV 9QLM MET A 853 UNP Q5HZG4 EXPRESSION TAG SEQADV 9QLM ALA A 854 UNP Q5HZG4 EXPRESSION TAG SEQADV 9QLM MET A 855 UNP Q5HZG4 EXPRESSION TAG SEQADV 9QLM ALA A 856 UNP Q5HZG4 EXPRESSION TAG SEQADV 9QLM GLU B 5 UNP P68431 GLN 6 CONFLICT SEQRES 1 A 75 GLY SER HIS MET ALA MET ALA TYR VAL ILE ARG ASP GLU SEQRES 2 A 75 TRP GLY ASN GLN ILE TRP ILE CYS PRO GLY CYS ASN LYS SEQRES 3 A 75 PRO ASP ASP GLY SER PRO MET ILE GLY CYS ASP ASP CYS SEQRES 4 A 75 ASP ASP TRP TYR HIS TRP PRO CYS VAL GLY ILE MET ALA SEQRES 5 A 75 ALA PRO PRO GLU GLU MET GLN TRP PHE CYS PRO LYS CYS SEQRES 6 A 75 ALA ASN LYS ILE LYS LYS ASP LYS LYS HIS SEQRES 1 B 12 ALA ARG THR M3L GLU THR ALA ARG LYS SER THR GLY MODRES 9QLM M3L B 4 LYS MODIFIED RESIDUE HET M3L B 4 31 HET ZN A1001 1 HET ZN A1002 1 HET SRO B 101 24 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION HETNAM SRO SEROTONIN HETSYN SRO 3-(2-AMINOETHYL)-1H-INDOL-5-OL FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN 2(ZN 2+) FORMUL 5 SRO C10 H12 N2 O HELIX 1 AA1 TRP A 894 GLY A 898 1 5 HELIX 2 AA2 LYS A 913 LYS A 920 1 8 SHEET 1 AA1 2 VAL A 858 ARG A 860 0 SHEET 2 AA1 2 GLN A 866 TRP A 868 -1 O ILE A 867 N ILE A 859 SHEET 1 AA2 3 TRP A 891 HIS A 893 0 SHEET 2 AA2 3 PRO A 881 GLY A 884 -1 N ILE A 883 O TYR A 892 SHEET 3 AA2 3 ARG B 2 GLU B 5 -1 O ARG B 2 N GLY A 884 LINK C THR B 3 N M3L B 4 1555 1555 1.33 LINK C M3L B 4 N GLU B 5 1555 1555 1.32 LINK CD GLU B 5 NZ SRO B 101 1555 1555 1.32 LINK SG CYS A 870 ZN ZN A1002 1555 1555 2.66 LINK SG CYS A 873 ZN ZN A1002 1555 1555 2.61 LINK SG CYS A 885 ZN ZN A1001 1555 1555 2.45 LINK SG CYS A 888 ZN ZN A1001 1555 1555 2.65 LINK ND1 HIS A 893 ZN ZN A1002 1555 1555 2.35 LINK SG CYS A 896 ZN ZN A1002 1555 1555 2.40 LINK SG CYS A 911 ZN ZN A1001 1555 1555 2.71 LINK SG CYS A 914 ZN ZN A1001 1555 1555 2.52 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 327 1344 CONECT 358 1344 CONECT 517 1343 CONECT 551 1343 CONECT 631 1344 CONECT 685 1344 CONECT 910 1343 CONECT 956 1343 CONECT 1183 1195 CONECT 1195 1183 1196 1207 CONECT 1196 1195 1197 1202 1208 CONECT 1197 1196 1198 1209 1210 CONECT 1198 1197 1199 1211 1212 CONECT 1199 1198 1200 1213 1214 CONECT 1200 1199 1201 1215 1216 CONECT 1201 1200 1204 1205 1206 CONECT 1202 1196 1203 1226 CONECT 1203 1202 CONECT 1204 1201 1217 1218 1219 CONECT 1205 1201 1220 1221 1222 CONECT 1206 1201 1223 1224 1225 CONECT 1207 1195 CONECT 1208 1196 CONECT 1209 1197 CONECT 1210 1197 CONECT 1211 1198 CONECT 1212 1198 CONECT 1213 1199 CONECT 1214 1199 CONECT 1215 1200 CONECT 1216 1200 CONECT 1217 1204 CONECT 1218 1204 CONECT 1219 1204 CONECT 1220 1205 CONECT 1221 1205 CONECT 1222 1205 CONECT 1223 1206 CONECT 1224 1206 CONECT 1225 1206 CONECT 1226 1202 CONECT 1232 1357 CONECT 1343 517 551 910 956 CONECT 1344 327 358 631 685 CONECT 1345 1346 1358 CONECT 1346 1345 1347 1354 CONECT 1347 1346 1348 1359 CONECT 1348 1347 1349 1360 CONECT 1349 1348 1350 1353 CONECT 1350 1349 1351 1361 CONECT 1351 1350 1352 1362 CONECT 1352 1351 1353 1355 CONECT 1353 1349 1352 1354 CONECT 1354 1346 1353 1363 CONECT 1355 1352 1356 1364 1365 CONECT 1356 1355 1357 1366 1367 CONECT 1357 1232 1356 1368 CONECT 1358 1345 CONECT 1359 1347 CONECT 1360 1348 CONECT 1361 1350 CONECT 1362 1351 CONECT 1363 1354 CONECT 1364 1355 CONECT 1365 1355 CONECT 1366 1356 CONECT 1367 1356 CONECT 1368 1357 MASTER 185 0 4 2 5 0 0 6 703 2 68 7 END