HEADER TRANSCRIPTION 07-MAR-19 6O7G TITLE SOLUTION STRUCTURE OF MLL4 PHD6 DOMAIN IN COMPLEX WITH HISTONE H4K16AC TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE 2D; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: RESIDUES 1503-1562; COMPND 5 SYNONYM: LYSINE N-METHYLTRANSFERASE 2D,ALL1-RELATED PROTEIN, COMPND 6 MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 2; COMPND 7 EC: 2.1.1.43; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HISTONE H4; COMPND 11 CHAIN: A; 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 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS MLL4, PHD FINGER, H4K16AC, MOF, ACETYLATION, HISTONE, CHROMATIN, KEYWDS 2 TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Y.ZHANG,T.G.KUTATELADZE REVDAT 3 15-NOV-23 6O7G 1 ATOM REVDAT 2 12-JUN-19 6O7G 1 JRNL REVDAT 1 22-MAY-19 6O7G 0 JRNL AUTH Y.ZHANG,Y.JANG,J.E.LEE,J.AHN,L.XU,M.R.HOLDEN,E.M.CORNETT, JRNL AUTH 2 K.KRAJEWSKI,B.J.KLEIN,S.P.WANG,Y.DOU,R.G.ROEDER,B.D.STRAHL, JRNL AUTH 3 S.B.ROTHBART,X.SHI,K.GE,T.G.KUTATELADZE JRNL TITL SELECTIVE BINDING OF THE PHD6 FINGER OF MLL4 TO HISTONE JRNL TITL 2 H4K16AC LINKS MLL4 AND MOF. JRNL REF NAT COMMUN V. 10 2314 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31127101 JRNL DOI 10.1038/S41467-019-10324-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6O7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000236789. 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 : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.5 MM [U-13C; U-15N] MLL4 PHD6, REMARK 210 7.5 MM HISTONE H4K16AC (11-21) REMARK 210 PEPTIDE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 C(CO)NH; 3D HBHA(CO)NH; 3D H(CCO) REMARK 210 NH; 3D NOESY-HSQC; 3D FILTERED REMARK 210 NOESY; 2D FILTERED TOCSY 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 : NMRDRAW, CCPNMR ANALYSIS, X-PLOR REMARK 210 NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 APPLY THE FOLLOWING TO CHAINS: B, A 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 GLY B 1499 REMARK 465 SER B 1500 REMARK 465 HIS B 1501 REMARK 465 MET B 1502 REMARK 465 ACE A 10 REMARK 465 GLY A 11 REMARK 465 LYS A 20 REMARK 465 VAL A 21 REMARK 465 NH2 A 22 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-15 REMARK 470 RES CSSEQI ATOMS REMARK 470 LYS A 12 N CB CG CD CE NZ REMARK 470 ARG A 19 C O CB CG CD NE CZ REMARK 470 ARG A 19 NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG B1524 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 ARG B1524 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 ARG B1524 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG B1524 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 17 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES 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 LEU B1504 -43.16 -135.25 REMARK 500 1 VAL B1505 33.01 -79.83 REMARK 500 1 GLU B1527 -1.87 62.51 REMARK 500 1 SER B1536 19.37 58.07 REMARK 500 1 VAL B1560 33.65 -151.80 REMARK 500 2 LEU B1504 -48.88 -143.98 REMARK 500 2 VAL B1505 22.10 -78.73 REMARK 500 2 CYS B1553 -128.31 -93.15 REMARK 500 3 LEU B1504 -77.46 62.06 REMARK 500 3 GLU B1527 -2.07 63.69 REMARK 500 3 PHE B1538 -52.71 64.89 REMARK 500 3 VAL B1561 -34.23 -150.98 REMARK 500 3 ARG A 17 -44.63 -151.75 REMARK 500 3 HIS A 18 176.34 59.52 REMARK 500 4 THR B1506 23.98 -76.68 REMARK 500 4 CYS B1507 81.19 1.60 REMARK 500 4 CYS B1553 -135.77 -90.43 REMARK 500 4 TYR B1559 -76.27 -98.17 REMARK 500 4 ARG A 17 64.84 -151.07 REMARK 500 5 LEU B1504 -63.77 -142.46 REMARK 500 5 THR B1539 -172.80 61.16 REMARK 500 5 CYS B1553 -178.63 -68.91 REMARK 500 6 LEU B1504 -37.18 -135.31 REMARK 500 6 VAL B1515 102.57 54.64 REMARK 500 6 GLU B1517 -16.37 67.36 REMARK 500 6 GLU B1527 -1.65 62.43 REMARK 500 6 PHE B1551 75.35 54.61 REMARK 500 7 VAL B1505 -9.93 64.85 REMARK 500 7 TYR B1514 -170.67 58.24 REMARK 500 7 GLU B1517 8.40 59.47 REMARK 500 7 GLU B1527 -5.83 66.57 REMARK 500 8 LEU B1504 160.62 64.67 REMARK 500 8 VAL B1505 13.47 51.80 REMARK 500 8 SER B1536 19.71 59.34 REMARK 500 9 LEU B1504 -71.28 60.02 REMARK 500 10 GLU B1517 -5.80 62.48 REMARK 500 10 LEU B1519 151.12 59.97 REMARK 500 10 SER B1536 -37.97 -173.86 REMARK 500 10 CYS B1553 -179.67 -69.61 REMARK 500 10 VAL B1561 -25.55 -150.18 REMARK 500 11 VAL B1505 27.75 -75.14 REMARK 500 11 CYS B1510 -71.30 -84.87 REMARK 500 11 HIS B1511 -53.43 -157.45 REMARK 500 11 ALA B1512 -41.97 176.64 REMARK 500 11 GLU B1527 0.68 59.73 REMARK 500 12 LEU B1504 -39.97 -132.88 REMARK 500 12 CYS B1507 82.12 1.34 REMARK 500 12 VAL B1561 -35.34 -151.43 REMARK 500 13 VAL B1505 26.14 -78.16 REMARK 500 13 GLU B1527 7.92 59.86 REMARK 500 REMARK 500 THIS ENTRY HAS 60 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 13 ARG A 17 0.08 SIDE CHAIN 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 116.4 REMARK 620 3 HIS B1531 ND1 105.2 108.6 REMARK 620 4 CYS B1534 SG 108.2 113.0 104.5 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 108.3 REMARK 620 3 CYS B1553 SG 117.9 107.6 REMARK 620 4 CYS B1556 SG 108.7 107.9 106.1 REMARK 620 N 1 2 3 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30585 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF MLL4 PHD6 DOMAIN IN COMPLEX WITH HISTONE REMARK 900 H4K16AC PEPTIDE DBREF 6O7G B 1503 1562 UNP O14686 KMT2D_HUMAN 1503 1562 DBREF 6O7G A 10 22 PDB 6O7G 6O7G 10 22 SEQADV 6O7G GLY B 1499 UNP O14686 EXPRESSION TAG SEQADV 6O7G SER B 1500 UNP O14686 EXPRESSION TAG SEQADV 6O7G HIS B 1501 UNP O14686 EXPRESSION TAG SEQADV 6O7G MET B 1502 UNP O14686 EXPRESSION TAG SEQRES 1 B 64 GLY SER HIS MET SER LEU VAL THR CYS PRO ILE CYS HIS SEQRES 2 B 64 ALA PRO TYR VAL GLU GLU ASP LEU LEU ILE GLN CYS ARG SEQRES 3 B 64 HIS CYS GLU ARG TRP MET HIS ALA GLY CYS GLU SER LEU SEQRES 4 B 64 PHE THR GLU ASP ASP VAL GLU GLN ALA ALA ASP GLU GLY SEQRES 5 B 64 PHE ASP CYS VAL SER CYS GLN PRO TYR VAL VAL LYS SEQRES 1 A 13 ACE GLY LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL NH2 MODRES 6O7G ALY A 16 LYS MODIFIED RESIDUE HET ALY A 16 26 HET ZN B1601 1 HET ZN B1602 1 HETNAM ALY N(6)-ACETYLLYSINE HETNAM ZN ZINC ION FORMUL 2 ALY C8 H16 N2 O3 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 VAL B 1554 PRO B 1558 1 5 SHEET 1 AA1 3 TRP B1529 HIS B1531 0 SHEET 2 AA1 3 LEU B1520 GLN B1522 -1 N ILE B1521 O MET B1530 SHEET 3 AA1 3 ALA A 15 ALY A 16 -1 O ALY A 16 N LEU B1520 LINK C ALA A 15 N ALY A 16 1555 1555 1.34 LINK C ALY A 16 N ARG A 17 1555 1555 1.34 LINK SG CYS B1507 ZN ZN B1601 1555 1555 2.35 LINK SG CYS B1510 ZN ZN B1601 1555 1555 2.41 LINK SG CYS B1523 ZN ZN B1602 1555 1555 2.48 LINK SG CYS B1526 ZN ZN B1602 1555 1555 2.40 LINK ND1 HIS B1531 ZN ZN B1601 1555 1555 2.26 LINK SG CYS B1534 ZN ZN B1601 1555 1555 2.39 LINK SG CYS B1553 ZN ZN B1602 1555 1555 2.46 LINK SG CYS B1556 ZN ZN B1602 1555 1555 2.39 CISPEP 1 LYS A 12 GLY A 13 7 2.69 CISPEP 2 LYS A 12 GLY A 13 14 2.72 SITE 1 AC1 4 CYS B1507 CYS B1510 HIS B1531 CYS B1534 SITE 1 AC2 4 CYS B1523 CYS B1526 CYS B1553 CYS B1556 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