HEADER GENE REGULATION 27-MAR-25 9NYA TITLE SOLUTION NMR STRUCTURE OF SET-9/26 PHD FINGER IN THE PEPTIDE TITLE 2 (H3K4ME3)-BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD-TYPE DOM; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD-TYPE ZINC FINGER, RESIDUES 780-866; COMPND 5 EC: 2.1.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: H3K4ME3 PEPTIDE; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: HISTONE H3.3C, HISTONE H3.5; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: SET-9, F15E6.1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: MODIFIED PGEX-6P; 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 TRANSGENERATIONAL EPIGENETIC INHERITANCE, TRANSCRIPTION, GENE KEYWDS 2 REGULATION EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR D.MONTEIRO,N.JONES,J.NI,W.BECKER,L.S.LAMBRECHTS,R.J.PAYNE,A.ASHE REVDAT 1 14-OCT-26 9NYA 0 JRNL AUTH D.MONTEIRO,N.JONES,J.NI,W.BECKER,L.S.LAMBRECHTS,R.J.PAYNE, JRNL AUTH 2 A.ASHE JRNL TITL SOLUTION NMR STRUCTURE OF SET-9/26 PHD FINGER IN THE PEPTIDE JRNL TITL 2 (H3K4ME3)-BOUND STATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9NYA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1000293931. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.08 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-98% 13C; U-98% 15N] REMARK 210 SET-9/26 PHD FINGER, 2.5 MM REMARK 210 H3K4ME3 (LYS4 IS TRI-METHYLATED), REMARK 210 1 MM TCEP.HCL, 50 MM SODIUM REMARK 210 CHLORIDE, 10 MM SODIUM PHOSPHATE, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(CA)CO; 3D HBHA(CO)NH; REMARK 210 HCCH-TOCSY; 3D HCCH-COSY; 15N- REMARK 210 RESOLVED [1H, 1H]-NOESY; 3D REMARK 210 13CALI-RESOLVED [1H, 1H]-NOESY; REMARK 210 3D 13CARO-RESOLVED [1H, 1H]-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.7, CARA 1.5.5, REMARK 210 NMRPIPE, CYANA 3.98, HADDOCK, REMARK 210 UNIO REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 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 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 1-4 REMARK 465 RES C SSSEQI REMARK 465 GLY A 775 REMARK 465 PRO A 776 REMARK 465 LEU A 777 REMARK 465 GLY A 778 REMARK 465 SER A 779 REMARK 465 ALA A 780 REMARK 465 ALA A 781 REMARK 465 GLN A 861 REMARK 465 LYS A 862 REMARK 465 ARG A 863 REMARK 465 LYS A 864 REMARK 465 SER A 865 REMARK 465 GLU A 866 REMARK 465 ARG B 8 REMARK 465 LYS B 9 REMARK 465 SER B 10 REMARK 465 THR B 11 REMARK 465 GLY B 12 REMARK 465 GLY B 13 REMARK 465 LYS B 14 REMARK 465 ALA B 15 REMARK 465 PRO B 16 REMARK 465 ARG B 17 REMARK 465 LYS B 18 REMARK 465 GLN B 19 REMARK 465 LYS B 20 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 ASP A 794 39.80 -92.46 REMARK 500 1 LYS A 820 48.76 -95.89 REMARK 500 1 ASN A 822 88.34 56.60 REMARK 500 1 LYS A 825 41.33 -109.34 REMARK 500 1 CYS A 828 -167.47 -100.14 REMARK 500 1 PRO A 833 102.54 -53.18 REMARK 500 2 ARG A 788 80.49 -151.52 REMARK 500 2 THR A 808 -159.63 -111.70 REMARK 500 2 LYS A 820 56.02 -116.62 REMARK 500 2 SER A 821 46.83 -143.86 REMARK 500 3 ASP A 794 41.83 -105.71 REMARK 500 3 LYS A 807 78.80 63.15 REMARK 500 3 LEU A 832 73.53 -152.27 REMARK 500 3 PRO A 833 109.09 -45.04 REMARK 500 4 ASP A 794 48.12 -109.90 REMARK 500 4 LYS A 807 70.65 64.88 REMARK 500 4 LYS A 820 46.76 -101.14 REMARK 500 4 SER A 821 46.76 -145.20 REMARK 500 4 ASN A 822 91.37 61.76 REMARK 500 4 LYS A 825 53.06 -99.64 REMARK 500 4 CYS A 828 -157.49 -97.84 REMARK 500 4 PRO A 833 104.62 -53.78 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 A 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 789 SG REMARK 620 2 CYS A 791 SG 109.6 REMARK 620 3 HIS A 811 ND1 106.6 112.0 REMARK 620 4 CYS A 814 SG 113.2 107.5 108.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 220 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 803 SG REMARK 620 2 CYS A 806 SG 107.4 REMARK 620 3 CYS A 828 SG 116.3 106.1 REMARK 620 4 CYS A 831 SG 110.5 110.4 106.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 52907 RELATED DB: BMRB DBREF 9NYA A 780 866 UNP O44498 SET9_CAEEL 780 866 DBREF 9NYA B 1 19 UNP Q6NXT2 H3C_HUMAN 2 20 SEQADV 9NYA GLY A 775 UNP O44498 EXPRESSION TAG SEQADV 9NYA PRO A 776 UNP O44498 EXPRESSION TAG SEQADV 9NYA LEU A 777 UNP O44498 EXPRESSION TAG SEQADV 9NYA GLY A 778 UNP O44498 EXPRESSION TAG SEQADV 9NYA SER A 779 UNP O44498 EXPRESSION TAG SEQADV 9NYA LYS B 20 UNP Q6NXT2 CLONING ARTIFACT SEQRES 1 A 92 GLY PRO LEU GLY SER ALA ALA GLU GLU SER TRP THR MET SEQRES 2 A 92 ARG CYS HIS CYS GLY MET ASP HIS GLY ASP GLY ASP THR SEQRES 3 A 92 ILE GLU CYS GLU GLY CYS LYS THR TRP GLN HIS MET ALA SEQRES 4 A 92 CYS MET GLY LEU THR LEU LYS SER ASN THR SER LYS TYR SEQRES 5 A 92 LYS CYS GLU MET CYS LEU PRO ARG ARG LEU PRO VAL SER SEQRES 6 A 92 LYS ALA GLU ALA ALA ARG GLU GLN GLU ARG ILE LEU ASN SEQRES 7 A 92 ARG LEU ARG ALA ALA ALA ARG LYS GLN LYS ARG LYS SER SEQRES 8 A 92 GLU SEQRES 1 B 20 ALA ARG THR M3L GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 B 20 LYS ALA PRO ARG LYS GLN LYS MODRES 9NYA M3L B 4 LYS MODIFIED RESIDUE HET M3L B 4 31 HET ZN A 200 1 HET ZN A 220 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 2 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 HIS A 811 GLY A 816 1 6 HELIX 2 AA2 SER A 839 LYS A 860 1 22 SHEET 1 AA1 3 TRP A 809 GLN A 810 0 SHEET 2 AA1 3 GLY A 798 GLU A 802 -1 N ILE A 801 O GLN A 810 SHEET 3 AA1 3 THR B 3 THR B 6 -1 O M3L B 4 N THR A 800 LINK C THR B 3 N M3L B 4 1555 1555 1.37 LINK C M3L B 4 N GLN B 5 1555 1555 1.37 LINK ZN ZN A 200 SG CYS A 789 1555 1555 2.25 LINK ZN ZN A 200 SG CYS A 791 1555 1555 2.28 LINK ZN ZN A 200 ND1 HIS A 811 1555 1555 1.90 LINK ZN ZN A 200 SG CYS A 814 1555 1555 2.26 LINK ZN ZN A 220 SG CYS A 803 1555 1555 2.28 LINK ZN ZN A 220 SG CYS A 806 1555 1555 2.28 LINK ZN ZN A 220 SG CYS A 828 1555 1555 2.28 LINK ZN ZN A 220 SG CYS A 831 1555 1555 2.30 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 CONECT 126 1359 CONECT 154 1359 CONECT 304 1360 CONECT 336 1360 CONECT 424 1359 CONECT 467 1359 CONECT 690 1360 CONECT 732 1360 CONECT 1274 1286 CONECT 1286 1274 1287 1298 CONECT 1287 1286 1288 1293 1299 CONECT 1288 1287 1289 1300 1301 CONECT 1289 1288 1290 1302 1303 CONECT 1290 1289 1291 1304 1305 CONECT 1291 1290 1292 1306 1307 CONECT 1292 1291 1295 1296 1297 CONECT 1293 1287 1294 1317 CONECT 1294 1293 CONECT 1295 1292 1308 1309 1310 CONECT 1296 1292 1311 1312 1313 CONECT 1297 1292 1314 1315 1316 CONECT 1298 1286 CONECT 1299 1287 CONECT 1300 1288 CONECT 1301 1288 CONECT 1302 1289 CONECT 1303 1289 CONECT 1304 1290 CONECT 1305 1290 CONECT 1306 1291 CONECT 1307 1291 CONECT 1308 1295 CONECT 1309 1295 CONECT 1310 1295 CONECT 1311 1296 CONECT 1312 1296 CONECT 1313 1296 CONECT 1314 1297 CONECT 1315 1297 CONECT 1316 1297 CONECT 1317 1293 CONECT 1359 126 154 424 467 CONECT 1360 304 336 690 732 MASTER 176 0 3 2 3 0 0 6 681 2 43 10 END