HEADER PROTEIN BINDING 10-DEC-25 21EE TITLE CRYSTAL STRUCTURE OF HUMAN PHF20L1(1-80) IN COMPLEX WITH H3K36ME COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 20-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HISTONE H3.1T; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: H3/T,H3T,H3/G,HISTONE H3.4; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PHF20L1, CGI-72; 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 TUDOR DOMAIN, HISTONE BINDING, EPIGENETIC READER, METHYL LYSINE KEYWDS 2 RECOGNITION, PROTEIN PROTEIN INTERACTION, CHROMATIN REGULATION, KEYWDS 3 NUCLEAR PROTEIN, STRUCTURAL BIOLOGY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,X.HUANG,X.SHANG REVDAT 1 12-AUG-26 21EE 0 JRNL AUTH X.HUANG,Q.XIAO,X.LIU,X.SHANG,Z.WANG,H.HU,Y.ZHOU,Q.HUANG, JRNL AUTH 2 T.JIANG,S.QIN,Y.HUANG,J.B.LI,Y.LIU JRNL TITL A REVISED MODEL FOR PHF20L1 TUDOR FUNCTION: DNA BINDING JRNL TITL 2 OVERRIDES METHYLATION SELECTIVITY ON NUCLEOSOMES. JRNL REF J.BIOL.CHEM. V. 302 13181 2026 JRNL REFN ESSN 1083-351X JRNL PMID 42173250 JRNL DOI 10.1016/J.JBC.2026.113181 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34012 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.050 REMARK 3 FREE R VALUE TEST SET COUNT : 3417 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 24.5500 - 3.8600 0.99 1266 137 0.1834 0.2088 REMARK 3 2 3.8600 - 3.0700 1.00 1277 142 0.1718 0.1629 REMARK 3 3 3.0600 - 2.6800 1.00 1270 150 0.1812 0.2280 REMARK 3 4 2.6800 - 2.4300 1.00 1291 136 0.1903 0.1766 REMARK 3 5 2.4300 - 2.2600 1.00 1280 131 0.1688 0.2112 REMARK 3 6 2.2600 - 2.1300 1.00 1275 135 0.1577 0.2009 REMARK 3 7 2.1300 - 2.0200 1.00 1278 154 0.1561 0.1849 REMARK 3 8 2.0200 - 1.9300 1.00 1278 132 0.1640 0.1984 REMARK 3 9 1.9300 - 1.8600 1.00 1272 128 0.1704 0.1896 REMARK 3 10 1.8600 - 1.7900 1.00 1263 173 0.1688 0.2161 REMARK 3 11 1.7900 - 1.7400 1.00 1291 139 0.1802 0.2080 REMARK 3 12 1.7400 - 1.6900 1.00 1255 138 0.1842 0.2155 REMARK 3 13 1.6900 - 1.6400 1.00 1296 143 0.1865 0.2304 REMARK 3 14 1.6400 - 1.6000 1.00 1267 148 0.1997 0.2601 REMARK 3 15 1.6000 - 1.5700 1.00 1280 140 0.1946 0.2428 REMARK 3 16 1.5700 - 1.5300 1.00 1270 161 0.2043 0.2352 REMARK 3 17 1.5300 - 1.5000 1.00 1272 122 0.2237 0.2468 REMARK 3 18 1.5000 - 1.4700 1.00 1274 144 0.2286 0.2456 REMARK 3 19 1.4700 - 1.4500 1.00 1277 152 0.2557 0.2624 REMARK 3 20 1.4500 - 1.4200 1.00 1300 142 0.2616 0.2443 REMARK 3 21 1.4200 - 1.4000 1.00 1247 154 0.2640 0.2948 REMARK 3 22 1.4000 - 1.3800 1.00 1287 134 0.2911 0.2703 REMARK 3 23 1.3800 - 1.3600 1.00 1267 131 0.3321 0.3258 REMARK 3 24 1.3600 - 1.3400 0.99 1262 151 0.3761 0.3905 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 681 REMARK 3 ANGLE : 1.232 916 REMARK 3 CHIRALITY : 0.113 85 REMARK 3 PLANARITY : 0.012 116 REMARK 3 DIHEDRAL : 6.295 91 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 21EE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 18-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300067071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34026 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 24.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000 ,0.2 M MALONATE PH 6.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 19.48700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.70850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.70850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.48700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.20500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 TOTAL BURIED SURFACE AREA: 630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 70 REMARK 465 PRO A 71 REMARK 465 ALA A 72 REMARK 465 LEU A 73 REMARK 465 ARG A 74 REMARK 465 LYS A 75 REMARK 465 GLU A 76 REMARK 465 GLY A 77 REMARK 465 LEU A 78 REMARK 465 LYS A 79 REMARK 465 ASP A 80 REMARK 465 SER B 28 REMARK 465 ALA B 29 REMARK 465 PRO B 30 REMARK 465 ALA B 31 REMARK 465 THR B 32 REMARK 465 HIS B 39 REMARK 465 ARG B 40 REMARK 465 TYR B 41 REMARK 465 ARG B 42 DBREF 21EE A 1 80 UNP A8MW92 P20L1_HUMAN 1 80 DBREF 21EE B 28 42 UNP Q16695 H31T_HUMAN 29 43 SEQRES 1 A 80 MET SER LYS LYS PRO PRO ASN ARG PRO GLY ILE THR PHE SEQRES 2 A 80 GLU ILE GLY ALA ARG LEU GLU ALA LEU ASP TYR LEU GLN SEQRES 3 A 80 LYS TRP TYR PRO SER ARG ILE GLU LYS ILE ASP TYR GLU SEQRES 4 A 80 GLU GLY LYS MET LEU VAL HIS PHE GLU ARG TRP SER HIS SEQRES 5 A 80 ARG TYR ASP GLU TRP ILE TYR TRP ASP SER ASN ARG LEU SEQRES 6 A 80 ARG PRO LEU GLU ARG PRO ALA LEU ARG LYS GLU GLY LEU SEQRES 7 A 80 LYS ASP SEQRES 1 B 15 SER ALA PRO ALA THR GLY GLY VAL MLZ LYS PRO HIS ARG SEQRES 2 B 15 TYR ARG MODRES 21EE MLZ B 36 LYS MODIFIED RESIDUE HET MLZ B 36 10 HETNAM MLZ N-METHYL-LYSINE FORMUL 2 MLZ C7 H16 N2 O2 FORMUL 3 HOH *60(H2 O) HELIX 1 AA1 SER A 51 ASP A 55 5 5 SHEET 1 AA1 5 GLU A 56 TYR A 59 0 SHEET 2 AA1 5 LYS A 42 PHE A 47 -1 N VAL A 45 O GLU A 56 SHEET 3 AA1 5 TRP A 28 ASP A 37 -1 N GLU A 34 O LEU A 44 SHEET 4 AA1 5 ARG A 18 LEU A 22 -1 N LEU A 19 O SER A 31 SHEET 5 AA1 5 LEU A 65 ARG A 66 -1 O ARG A 66 N GLU A 20 LINK C VAL B 35 N MLZ B 36 1555 1555 1.32 LINK C MLZ B 36 N LYS B 37 1555 1555 1.33 CRYST1 38.974 42.410 47.417 90.00 90.00 90.00 P 21 21 21 4 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 0.025658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021089 0.00000 CONECT 628 633 CONECT 633 628 634 CONECT 634 633 635 641 CONECT 635 634 636 CONECT 636 635 637 CONECT 637 636 638 CONECT 638 637 639 CONECT 639 638 640 CONECT 640 639 CONECT 641 634 642 643 CONECT 642 641 CONECT 643 641 MASTER 242 0 1 1 5 0 0 6 709 2 12 9 END