HEADER TRANSFERASE/PROTEIN BINDING 27-FEB-24 9ATN TITLE NMR STRUCTURE OF THE MLL4 PHD2/3 FINGERS IN COMPLEX WITH ASXL2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE 2D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSINE N-METHYLTRANSFERASE 2D,ALL1-RELATED PROTEIN, COMPND 5 MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 2; COMPND 6 EC: 2.1.1.364; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: POLYCOMB GROUP PROTEIN ASXL2; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: ADDITIONAL SEX COMBS-LIKE PROTEIN 2; COMPND 12 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: KMT2D, ALR, MLL2, MLL4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: ASXL2, ASXH2, KIAA1685; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MLL4, TRANSCRIPTION, PROTEIN BINDING, TRANSFERASE-PROTEIN BINDING KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Y.ZHANG,M.ZANDIAN,T.KUTATELADZE REVDAT 1 19-JUN-24 9ATN 0 JRNL AUTH Y.ZHANG,G.XIE,J.E.LEE,M.ZANDIAN,D.SUDARSHAN,B.ESTAVOYER, JRNL AUTH 2 C.BENZ,T.VIITA,G.ASGARITARGHI,C.LACHANCE,C.MESSMER, JRNL AUTH 3 L.SIMONETTI,V.K.SINHA,J.P.LAMBERT,Y.W.CHEN,S.P.WANG, JRNL AUTH 4 Y.IVARSSON,E.B.AFFAR,J.COTE,K.GE,T.G.KUTATELADZE JRNL TITL ASXLS BINDING TO THE PHD2/3 FINGERS OF MLL4 PROVIDES A JRNL TITL 2 MECHANISM FOR THE RECRUITMENT OF BAP1 TO ACTIVE ENHANCERS. JRNL REF NAT COMMUN V. 15 4883 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38849395 JRNL DOI 10.1038/S41467-024-49391-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9ATN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1000281731. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM 13C, 15N MLL4 PHD2,3, 25 REMARK 210 MM TRIS, 150 MM SODIUM CHLORIDE, REMARK 210 3 MM DTT, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D CBCA(CO)NH; 3D C(CO) REMARK 210 NH; 3D HBHA(CO)NH; 3D H(CCO)NH; REMARK 210 3D 1H-15N TOCSY; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, CCPNMR ANALYSIS, REMARK 210 NMRPIPE REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-15 REMARK 465 RES C SSSEQI REMARK 465 PRO A 223 REMARK 465 LEU A 224 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 ARG A 228 163.16 -42.94 REMARK 500 1 CYS A 232 -22.06 165.60 REMARK 500 1 GLU A 233 111.16 60.94 REMARK 500 1 CYS A 239 -43.32 -171.30 REMARK 500 1 CYS A 273 20.03 -144.59 REMARK 500 1 THR A 300 -9.67 -59.69 REMARK 500 1 CYS A 302 31.60 -170.21 REMARK 500 1 LYS A 304 -70.61 -49.15 REMARK 500 1 HIS A 313 -169.52 -109.26 REMARK 500 1 THR B 656 -97.46 -37.18 REMARK 500 2 ARG A 228 136.92 -23.42 REMARK 500 2 CYS A 232 -3.97 98.23 REMARK 500 2 GLU A 233 -179.47 53.30 REMARK 500 2 CYS A 244 101.01 -50.32 REMARK 500 2 CYS A 247 81.95 173.40 REMARK 500 2 TRP A 268 99.79 -62.83 REMARK 500 2 GLN A 269 -85.92 -56.69 REMARK 500 2 GLN A 277 33.87 -89.42 REMARK 500 2 ALA A 278 -48.65 -144.22 REMARK 500 2 ASP A 295 119.22 -32.72 REMARK 500 2 PHE A 301 12.59 -140.09 REMARK 500 2 CYS A 302 32.00 -172.24 REMARK 500 2 LYS A 316 177.96 177.97 REMARK 500 2 CYS A 317 161.42 -43.31 REMARK 500 2 THR B 656 -95.80 -37.19 REMARK 500 2 ILE B 660 -70.36 -59.86 REMARK 500 3 ALA A 227 69.59 64.63 REMARK 500 3 ARG A 228 153.24 -38.21 REMARK 500 3 CYS A 232 -5.05 100.06 REMARK 500 3 GLU A 233 -168.95 48.35 REMARK 500 3 CYS A 302 12.85 -165.89 REMARK 500 3 LEU A 303 174.90 -56.53 REMARK 500 3 TRP A 315 -86.46 -80.67 REMARK 500 3 LYS A 316 167.63 52.91 REMARK 500 3 ALA B 654 38.95 -90.36 REMARK 500 3 THR B 656 -97.45 -37.18 REMARK 500 4 ARG A 228 141.02 -27.50 REMARK 500 4 CYS A 232 -25.57 168.72 REMARK 500 4 GLU A 233 96.39 52.51 REMARK 500 4 SER A 246 -45.94 -143.81 REMARK 500 4 THR A 261 -169.42 -169.60 REMARK 500 4 ALA A 262 -164.86 43.26 REMARK 500 4 ASP A 295 127.38 -23.04 REMARK 500 4 LYS A 296 145.98 -178.08 REMARK 500 4 CYS A 302 30.70 -171.08 REMARK 500 4 HIS A 313 -168.02 -120.00 REMARK 500 4 THR B 656 -97.65 -33.55 REMARK 500 5 ARG A 228 104.38 41.42 REMARK 500 5 VAL A 231 60.41 -107.87 REMARK 500 5 CYS A 232 -35.11 -172.09 REMARK 500 REMARK 500 THIS ENTRY HAS 186 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 A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 229 SG REMARK 620 2 CYS A 232 SG 109.5 REMARK 620 3 HIS A 252 ND1 109.5 108.9 REMARK 620 4 CYS A 255 SG 108.9 110.5 109.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 244 SG REMARK 620 2 CYS A 247 SG 109.5 REMARK 620 3 CYS A 270 SG 109.3 109.4 REMARK 620 4 CYS A 273 SG 109.7 109.6 109.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 276 SG REMARK 620 2 CYS A 279 SG 109.4 REMARK 620 3 HIS A 299 ND1 109.4 108.4 REMARK 620 4 CYS A 302 SG 109.7 110.0 109.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 291 SG REMARK 620 2 CYS A 294 SG 109.3 REMARK 620 3 CYS A 317 SG 108.4 110.1 REMARK 620 4 CYS A 320 SG 110.4 108.8 109.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31041 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF THE MLL4 PHD2/3 FINGERS IN COMPLEX WITH ASXL2 DBREF 9ATN A 227 322 UNP O14686 KMT2D_HUMAN 227 322 DBREF 9ATN B 652 670 UNP Q76L83 ASXL2_HUMAN 652 670 SEQADV 9ATN PRO A 223 UNP O14686 EXPRESSION TAG SEQADV 9ATN LEU A 224 UNP O14686 EXPRESSION TAG SEQADV 9ATN GLY A 225 UNP O14686 EXPRESSION TAG SEQADV 9ATN SER A 226 UNP O14686 EXPRESSION TAG SEQRES 1 A 100 PRO LEU GLY SER ALA ARG CYS ALA VAL CYS GLU GLY PRO SEQRES 2 A 100 GLY GLU LEU CYS ASP LEU PHE PHE CYS THR SER CYS GLY SEQRES 3 A 100 HIS HIS TYR HIS GLY ALA CYS LEU ASP THR ALA LEU THR SEQRES 4 A 100 ALA ARG LYS ARG ALA GLY TRP GLN CYS PRO GLU CYS LYS SEQRES 5 A 100 VAL CYS GLN ALA CYS ARG LYS PRO GLY ASN ASP SER LYS SEQRES 6 A 100 MET LEU VAL CYS GLU THR CYS ASP LYS GLY TYR HIS THR SEQRES 7 A 100 PHE CYS LEU LYS PRO PRO MET GLU GLU LEU PRO ALA HIS SEQRES 8 A 100 SER TRP LYS CYS LYS ALA CYS ARG VAL SEQRES 1 B 19 THR GLY ALA ARG THR LEU ALA ASP ILE LYS ALA LYS ALA SEQRES 2 B 19 GLN LEU VAL LYS ALA GLN HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HETNAM ZN ZINC ION FORMUL 3 ZN 4(ZN 2+) HELIX 1 AA1 HIS A 252 ASP A 257 1 6 HELIX 2 AA2 THR A 261 ALA A 266 1 6 HELIX 3 AA3 CYS A 317 VAL A 322 1 6 HELIX 4 AA4 ALA B 654 GLN B 670 1 17 SHEET 1 AA1 2 PHE A 242 PHE A 243 0 SHEET 2 AA1 2 HIS A 250 TYR A 251 -1 O TYR A 251 N PHE A 242 SHEET 1 AA2 2 MET A 288 VAL A 290 0 SHEET 2 AA2 2 GLY A 297 HIS A 299 -1 O TYR A 298 N LEU A 289 LINK SG CYS A 229 ZN ZN A 501 1555 1555 2.30 LINK SG CYS A 232 ZN ZN A 501 1555 1555 2.31 LINK SG CYS A 244 ZN ZN A 502 1555 1555 2.30 LINK SG CYS A 247 ZN ZN A 502 1555 1555 2.30 LINK ND1 HIS A 252 ZN ZN A 501 1555 1555 2.30 LINK SG CYS A 255 ZN ZN A 501 1555 1555 2.31 LINK SG CYS A 270 ZN ZN A 502 1555 1555 2.30 LINK SG CYS A 273 ZN ZN A 502 1555 1555 2.30 LINK SG CYS A 276 ZN ZN A 503 1555 1555 2.31 LINK SG CYS A 279 ZN ZN A 503 1555 1555 2.30 LINK SG CYS A 291 ZN ZN A 504 1555 1555 2.30 LINK SG CYS A 294 ZN ZN A 504 1555 1555 2.30 LINK ND1 HIS A 299 ZN ZN A 503 1555 1555 2.30 LINK SG CYS A 302 ZN ZN A 503 1555 1555 2.32 LINK SG CYS A 317 ZN ZN A 504 1555 1555 2.30 LINK SG CYS A 320 ZN ZN A 504 1555 1555 2.31 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