HEADER TRANSFERASE 03-APR-07 2YSM TITLE SOLUTION STRUCTURE OF THE SECOND AND THIRD PHD DOMAIN FROM HISTONE- TITLE 2 LYSINE N-METHYLTRANSFERASE 2C (KMT2C/MLL3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 3 COMPND 3 HOMOLOG; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PHD DOMAIN; COMPND 6 SYNONYM: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC COMPND 7 MLL3, HOMOLOGOUS TO ALR PROTEIN; COMPND 8 EC: 2.1.1.43; 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: MLL3, HALR, KIAA1506; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE PROTEIN SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P070115-52 KEYWDS PHD DOMAIN, MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN, KEYWDS 2 HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-4 SPECIFIC MLL3, KEYWDS 3 HOMOLOGOUS TO ALR PROTEIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL KEYWDS 4 PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 5 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR X.R.QIN,F.HAYASHI,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS AUTHOR 2 INITIATIVE (RSGI) REVDAT 3 21-MAR-18 2YSM 1 TITLE SOURCE REMARK REVDAT 2 24-FEB-09 2YSM 1 VERSN REVDAT 1 09-OCT-07 2YSM 0 JRNL AUTH X.R.QIN,F.HAYASHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FIRST AND SECOND PHD DOMAIN FROM JRNL TITL 2 MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 3 HOMOLOG JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YSM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000027082. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.94MM 13C, 15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL(PH7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; REMARK 210 0.05MM ZNCL2+1MM IDA; 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9820, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY,TARGET REMARK 210 FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SPECTROMETER_ID 1 FOR 3D_15N_SEPARAED_NOESY; REMARK 210 SPECTROMETER_ID 2 FOR 3D_13C_SEPARAED_NOESY; 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ASN A 9 170.21 -58.18 REMARK 500 1 ASP A 14 47.23 73.90 REMARK 500 1 GLU A 65 49.39 -78.68 REMARK 500 1 LYS A 68 41.49 -83.50 REMARK 500 1 THR A 74 -71.85 -112.50 REMARK 500 1 ASP A 76 46.83 72.13 REMARK 500 1 LYS A 89 -38.44 -35.20 REMARK 500 1 ILE A 103 113.41 -38.55 REMARK 500 1 PRO A 108 88.13 -69.77 REMARK 500 2 CYS A 25 154.21 -46.28 REMARK 500 2 VAL A 41 103.76 -44.96 REMARK 500 2 PRO A 43 2.54 -69.74 REMARK 500 2 ALA A 47 107.77 -56.81 REMARK 500 2 THR A 74 -63.48 -94.66 REMARK 500 2 ASN A 100 -36.70 -36.17 REMARK 500 2 ILE A 103 135.97 -33.68 REMARK 500 2 PRO A 108 93.00 -69.76 REMARK 500 3 VAL A 41 109.48 -49.44 REMARK 500 3 PRO A 43 4.61 -69.77 REMARK 500 3 GLU A 65 89.22 -61.39 REMARK 500 3 THR A 74 -62.48 -96.41 REMARK 500 3 PRO A 92 2.35 -69.78 REMARK 500 3 THR A 93 36.84 30.26 REMARK 500 3 ASN A 94 105.77 -173.32 REMARK 500 3 ASN A 100 -26.06 -38.45 REMARK 500 4 ALA A 8 97.91 -69.65 REMARK 500 4 ASP A 14 44.30 32.24 REMARK 500 4 THR A 27 -70.18 -79.11 REMARK 500 4 ASP A 38 40.50 72.82 REMARK 500 4 VAL A 41 101.90 -58.67 REMARK 500 4 PRO A 43 3.09 -69.80 REMARK 500 4 ARG A 46 -38.97 -36.61 REMARK 500 4 CYS A 54 -53.66 -125.82 REMARK 500 4 LYS A 55 143.80 -29.96 REMARK 500 4 LYS A 68 46.25 -87.79 REMARK 500 4 LEU A 70 98.10 -68.42 REMARK 500 4 CYS A 72 159.05 -48.21 REMARK 500 4 LYS A 77 -71.35 -97.23 REMARK 500 4 PRO A 86 -177.69 -69.78 REMARK 500 4 LYS A 89 -39.16 -38.95 REMARK 500 4 PRO A 92 -174.62 -69.77 REMARK 500 4 PRO A 108 6.35 -69.72 REMARK 500 4 SER A 109 117.36 -27.18 REMARK 500 5 SER A 2 41.72 39.93 REMARK 500 5 ASP A 14 47.18 74.32 REMARK 500 5 CYS A 54 -51.00 -122.69 REMARK 500 5 LYS A 55 147.75 -31.96 REMARK 500 5 GLU A 65 99.23 -63.80 REMARK 500 5 SER A 106 116.88 -35.11 REMARK 500 6 PRO A 43 4.29 -69.74 REMARK 500 REMARK 500 THIS ENTRY HAS 182 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 10 SG REMARK 620 2 CYS A 13 SG 103.3 REMARK 620 3 HIS A 33 ND1 107.1 105.8 REMARK 620 4 CYS A 36 SG 112.6 107.8 119.0 REMARK 620 N 1 2 3 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 25 SG REMARK 620 2 CYS A 28 SG 107.7 REMARK 620 3 CYS A 51 SG 109.5 117.3 REMARK 620 4 CYS A 54 SG 114.2 103.6 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 57 SG REMARK 620 2 CYS A 60 SG 104.1 REMARK 620 3 HIS A 80 ND1 104.0 107.5 REMARK 620 4 CYS A 83 SG 110.8 114.8 114.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 72 SG REMARK 620 2 CYS A 75 SG 109.7 REMARK 620 3 CYS A 98 SG 115.8 109.6 REMARK 620 4 CYS A 101 SG 108.6 108.0 104.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002102485.2 RELATED DB: TARGETDB DBREF 2YSM A 8 105 UNP Q8NEZ4 MLL3_HUMAN 342 439 SEQADV 2YSM GLY A 1 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM SER A 2 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM SER A 3 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM GLY A 4 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM SER A 5 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM SER A 6 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM GLY A 7 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM SER A 106 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM GLY A 107 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM PRO A 108 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM SER A 109 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM SER A 110 UNP Q8NEZ4 EXPRESSION TAG SEQADV 2YSM GLY A 111 UNP Q8NEZ4 EXPRESSION TAG SEQRES 1 A 111 GLY SER SER GLY SER SER GLY ALA ASN CYS ALA VAL CYS SEQRES 2 A 111 ASP SER PRO GLY ASP LEU LEU ASP GLN PHE PHE CYS THR SEQRES 3 A 111 THR CYS GLY GLN HIS TYR HIS GLY MET CYS LEU ASP ILE SEQRES 4 A 111 ALA VAL THR PRO LEU LYS ARG ALA GLY TRP GLN CYS PRO SEQRES 5 A 111 GLU CYS LYS VAL CYS GLN ASN CYS LYS GLN SER GLY GLU SEQRES 6 A 111 ASP SER LYS MET LEU VAL CYS ASP THR CYS ASP LYS GLY SEQRES 7 A 111 TYR HIS THR PHE CYS LEU GLN PRO VAL MET LYS SER VAL SEQRES 8 A 111 PRO THR ASN GLY TRP LYS CYS LYS ASN CYS ARG ILE CYS SEQRES 9 A 111 ILE SER GLY PRO SER SER GLY HET ZN A 301 1 HET ZN A 501 1 HET ZN A 701 1 HET ZN A 901 1 HETNAM ZN ZINC ION FORMUL 2 ZN 4(ZN 2+) HELIX 1 1 PHE A 82 LEU A 84 5 3 HELIX 2 2 CYS A 98 ILE A 103 1 6 SHEET 1 A 2 PHE A 23 PHE A 24 0 SHEET 2 A 2 HIS A 31 TYR A 32 -1 O TYR A 32 N PHE A 23 SHEET 1 B 2 MET A 69 VAL A 71 0 SHEET 2 B 2 GLY A 78 HIS A 80 -1 O TYR A 79 N LEU A 70 LINK SG CYS A 10 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 13 ZN ZN A 301 1555 1555 2.36 LINK SG CYS A 25 ZN ZN A 501 1555 1555 2.24 LINK SG CYS A 28 ZN ZN A 501 1555 1555 2.30 LINK ND1 HIS A 33 ZN ZN A 301 1555 1555 2.04 LINK SG CYS A 36 ZN ZN A 301 1555 1555 2.24 LINK SG CYS A 51 ZN ZN A 501 1555 1555 2.22 LINK SG CYS A 54 ZN ZN A 501 1555 1555 2.37 LINK SG CYS A 57 ZN ZN A 701 1555 1555 2.36 LINK SG CYS A 60 ZN ZN A 701 1555 1555 2.26 LINK SG CYS A 72 ZN ZN A 901 1555 1555 2.32 LINK SG CYS A 75 ZN ZN A 901 1555 1555 2.25 LINK ND1 HIS A 80 ZN ZN A 701 1555 1555 2.06 LINK SG CYS A 83 ZN ZN A 701 1555 1555 2.32 LINK SG CYS A 98 ZN ZN A 901 1555 1555 2.24 LINK SG CYS A 101 ZN ZN A 901 1555 1555 2.36 CISPEP 1 GLN A 85 PRO A 86 1 -0.03 CISPEP 2 GLN A 85 PRO A 86 2 0.01 CISPEP 3 GLN A 85 PRO A 86 3 -0.04 CISPEP 4 GLN A 85 PRO A 86 4 -0.05 CISPEP 5 GLN A 85 PRO A 86 5 0.01 CISPEP 6 GLN A 85 PRO A 86 6 0.09 CISPEP 7 GLN A 85 PRO A 86 7 0.05 CISPEP 8 GLN A 85 PRO A 86 8 -0.05 CISPEP 9 GLN A 85 PRO A 86 9 0.01 CISPEP 10 GLN A 85 PRO A 86 10 0.03 CISPEP 11 GLN A 85 PRO A 86 11 0.02 CISPEP 12 GLN A 85 PRO A 86 12 -0.03 CISPEP 13 GLN A 85 PRO A 86 13 -0.02 CISPEP 14 GLN A 85 PRO A 86 14 0.01 CISPEP 15 GLN A 85 PRO A 86 15 -0.04 CISPEP 16 GLN A 85 PRO A 86 16 -0.03 CISPEP 17 GLN A 85 PRO A 86 17 0.04 CISPEP 18 GLN A 85 PRO A 86 18 -0.10 CISPEP 19 GLN A 85 PRO A 86 19 0.01 CISPEP 20 GLN A 85 PRO A 86 20 -0.03 SITE 1 AC1 4 CYS A 10 CYS A 13 HIS A 33 CYS A 36 SITE 1 AC2 4 CYS A 25 CYS A 28 CYS A 51 CYS A 54 SITE 1 AC3 4 CYS A 57 CYS A 60 HIS A 80 CYS A 83 SITE 1 AC4 4 CYS A 72 CYS A 75 CYS A 98 CYS A 101 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