HEADER GENE REGULATION 06-SEP-23 8U2Y TITLE SOLUTION STRUCTURE OF THE PHD6 FINGER OF MLL4 BOUND TO TET3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLCYTOSINE DIOXYGENASE TET3; COMPND 3 CHAIN: A; COMPND 4 EC: 1.14.11.80; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE 2D; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: LYSINE N-METHYLTRANSFERASE 2D,ALL1-RELATED PROTEIN, COMPND 10 MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 2; COMPND 11 EC: 2.1.1.364; 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: TET3, KIAA0401; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: KMT2D, ALR, MLL2, MLL4; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS KMT2D, TET3, CHROMATIN, EPIGENETICS, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.A.MOHID,M.ZANDIAN,Y.ZHANG,T.G.KUTATELADZE REVDAT 1 19-JUN-24 8U2Y 0 JRNL AUTH D.C.BECHT,S.A.MOHID,J.E.LEE,M.ZANDIAN,C.BENZ,S.BISWAS, JRNL AUTH 2 V.K.SINHA,Y.IVARSSON,K.GE,Y.ZHANG,T.G.KUTATELADZE JRNL TITL MLL4 BINDS TET3. JRNL REF STRUCTURE V. 32 706 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38579707 JRNL DOI 10.1016/J.STR.2024.03.005 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 8U2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000277205. 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 : 2.0 MM [U-13C; U-15N] PROTEIN, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 CC(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 H(CCO)NH; 3D 1H-13C NOESY; 3D 1H- REMARK 210 15N NOESY; 3D HCCH-TOCSY; 2D 1H- REMARK 210 13C HSQC; 2D 1H-15N HSQC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 1D 1H 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 : CCPNMR ANALYSIS, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 VAL B1505 -38.52 -155.84 REMARK 500 1 HIS B1511 78.88 -65.27 REMARK 500 1 GLU B1516 102.21 -48.23 REMARK 500 1 GLU B1517 -172.22 -171.60 REMARK 500 1 ASP B1518 171.98 56.43 REMARK 500 2 SER A1455 172.56 179.40 REMARK 500 2 LEU B1504 41.99 -85.87 REMARK 500 2 VAL B1505 -24.51 177.53 REMARK 500 2 VAL B1515 34.06 39.53 REMARK 500 2 GLU B1517 -41.32 -145.62 REMARK 500 2 PHE B1538 -72.05 -83.34 REMARK 500 2 PHE B1551 133.99 61.74 REMARK 500 3 VAL B1505 -6.23 73.43 REMARK 500 3 GLU B1517 -41.11 164.84 REMARK 500 4 TYR B1514 67.57 73.93 REMARK 500 4 GLU B1517 25.60 -140.55 REMARK 500 5 VAL A1452 73.15 48.68 REMARK 500 5 LEU B1504 108.64 59.38 REMARK 500 5 VAL B1505 -15.72 80.65 REMARK 500 5 ALA B1512 -54.41 178.34 REMARK 500 5 THR B1539 128.83 76.08 REMARK 500 6 VAL B1505 -2.50 72.04 REMARK 500 6 VAL B1515 -72.17 -90.32 REMARK 500 6 GLU B1516 -169.40 -174.71 REMARK 500 7 LEU B1504 -73.65 68.55 REMARK 500 7 HIS B1511 45.52 38.45 REMARK 500 7 GLU B1516 109.57 -48.14 REMARK 500 7 GLU B1517 -158.52 -177.75 REMARK 500 7 ASP B1518 -159.94 48.34 REMARK 500 7 PHE B1538 -63.71 -93.05 REMARK 500 8 VAL B1505 -64.57 72.83 REMARK 500 8 PRO B1508 38.26 -81.52 REMARK 500 8 ILE B1509 -78.69 -141.42 REMARK 500 9 LEU B1504 161.00 59.50 REMARK 500 9 VAL B1505 -71.19 69.74 REMARK 500 9 HIS B1511 -1.11 71.19 REMARK 500 9 ALA B1512 -53.33 178.40 REMARK 500 9 GLU B1517 70.63 -176.52 REMARK 500 9 PHE B1551 150.93 63.04 REMARK 500 10 PRO B1508 47.10 -82.19 REMARK 500 10 ILE B1509 -67.20 -144.91 REMARK 500 10 HIS B1511 -10.18 75.27 REMARK 500 10 ALA B1512 -50.81 -177.71 REMARK 500 10 GLU B1535 33.93 -95.62 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 B1601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1507 SG REMARK 620 2 CYS B1510 SG 108.9 REMARK 620 3 HIS B1531 ND1 109.8 109.0 REMARK 620 4 CYS B1534 SG 108.9 109.5 110.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B1523 SG REMARK 620 2 CYS B1526 SG 110.4 REMARK 620 3 CYS B1553 SG 110.0 109.2 REMARK 620 4 CYS B1556 SG 109.3 109.0 108.9 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31105 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF TET3/MLL4-PHD6 DBREF 8U2Y A 1451 1459 UNP O43151 TET3_HUMAN 1451 1459 DBREF 8U2Y B 1503 1562 UNP O14686 KMT2D_HUMAN 1503 1562 SEQRES 1 A 9 GLY VAL GLY GLY SER TRP GLY VAL PHE SEQRES 1 B 60 SER LEU VAL THR CYS PRO ILE CYS HIS ALA PRO TYR VAL SEQRES 2 B 60 GLU GLU ASP LEU LEU ILE GLN CYS ARG HIS CYS GLU ARG SEQRES 3 B 60 TRP MET HIS ALA GLY CYS GLU SER LEU PHE THR GLU ASP SEQRES 4 B 60 ASP VAL GLU GLN ALA ALA ASP GLU GLY PHE ASP CYS VAL SEQRES 5 B 60 SER CYS GLN PRO TYR VAL VAL LYS HET ZN B1601 1 HET ZN B1602 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 ALA B 1532 GLU B 1535 5 4 HELIX 2 AA2 GLU B 1540 GLU B 1549 1 10 HELIX 3 AA3 SER B 1555 VAL B 1560 1 6 SHEET 1 AA1 3 GLU B1527 HIS B1531 0 SHEET 2 AA1 3 LEU B1520 CYS B1523 -1 N ILE B1521 O MET B1530 SHEET 3 AA1 3 SER A1455 GLY A1457 -1 O SER A1455 N LEU B1520 LINK SG CYS B1507 ZN ZN B1601 1555 1555 2.30 LINK SG CYS B1510 ZN ZN B1601 1555 1555 2.30 LINK SG CYS B1523 ZN ZN B1602 1555 1555 2.32 LINK SG CYS B1526 ZN ZN B1602 1555 1555 2.30 LINK ND1 HIS B1531 ZN ZN B1601 1555 1555 2.33 LINK SG CYS B1534 ZN ZN B1601 1555 1555 2.32 LINK SG CYS B1553 ZN ZN B1602 1555 1555 2.30 LINK SG CYS B1556 ZN ZN B1602 1555 1555 2.29 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