HEADER TRANSCRIPTION 04-OCT-12 4BD3 TITLE PHF19 LINKS METHYLATED LYSINE 36 OF HISTONE H3 TO REGULATION OF TITLE 2 POLYCOMB ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 19; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TUDOR DOMAIN, RESIDUES 38-95; COMPND 5 SYNONYM: POLYCOMB-LIKE PROTEIN 3, HPCL3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE H3; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: H3(31-41)K36ME3, RESIDUES 32-42; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-MCN; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS PHF-19, HISTONE RECOGNITION, H3K36ME3, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.LAPINAITE,B.SIMON,T.CARLOMAGNO REVDAT 4 14-JUN-23 4BD3 1 REMARK LINK REVDAT 3 19-DEC-12 4BD3 1 JRNL REVDAT 2 07-NOV-12 4BD3 1 JRNL ATOM REVDAT 1 31-OCT-12 4BD3 0 JRNL AUTH C.BALLARE,M.LANGE,A.LAPINAITE,G.MAS MARTIN,L.MOREY,G.PASCU, JRNL AUTH 2 R.LIEFKE,B.SIMON,Y.SHI,O.GOZANI,T.CARLOMAGNO,S.A.BENITAH, JRNL AUTH 3 L.DI CROCE JRNL TITL PHF19 LINKS METHYLATED LYS36 OF HISTONE H3 TO REGULATION OF JRNL TITL 2 POLYCOMB ACTIVITY JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 1257 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 23104054 JRNL DOI 10.1038/NSMB.2434 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4BD3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1290054272. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 200 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TRIPLE RESONANCE; NOESY; EDITED REMARK 210 -FILTERED REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW REMARK 210 METHOD USED : ARIA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 6 REMARK 210 REMARK 210 REMARK: NONE 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: PQS 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 PRO A 93 42.07 -77.56 REMARK 500 2 ASN A 77 -31.62 76.08 REMARK 500 3 LYS A 39 103.04 67.13 REMARK 500 3 PRO A 93 109.90 -54.54 REMARK 500 3 M3L B 36 78.69 60.06 REMARK 500 4 ASN A 77 -3.20 74.01 REMARK 500 4 THR B 32 -69.89 -107.13 REMARK 500 4 ARG B 40 179.44 68.68 REMARK 500 5 LYS A 39 81.95 65.44 REMARK 500 5 ASN A 77 -31.28 77.76 REMARK 500 6 VAL B 35 93.83 62.27 REMARK 500 7 LYS A 39 102.74 62.96 REMARK 500 7 THR B 32 -98.91 49.46 REMARK 500 8 ASN A 77 -1.03 72.22 REMARK 500 9 M3L B 36 114.53 -167.17 REMARK 500 9 ARG B 40 153.74 71.31 REMARK 500 10 ARG B 40 97.52 62.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B2T RELATED DB: PDB REMARK 900 TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONEH3 TAIL REMARK 900 CONTAINING TRIMETHYLLYSINE 4 AND PHOSPHOTHREONINE 3 REMARK 900 RELATED ID: 2B2U RELATED DB: PDB REMARK 900 TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONEH3 TAIL REMARK 900 CONTAINING TRIMETHYLLYSINE 4 AND DIMETHYLARGININE 2 REMARK 900 RELATED ID: 2B2V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF HUMAN CHD1 CHROMODOMAINS 1AND 2 BOUND REMARK 900 TO HISTONE H3 RESI 1-15 MEK4 REMARK 900 RELATED ID: 2B2W RELATED DB: PDB REMARK 900 TANDEM CHROMODOMAINS OF HUMAN CHD1 COMPLEXED WITH HISTONEH3 TAIL REMARK 900 CONTAINING TRIMETHYLLYSINE 4 REMARK 900 RELATED ID: 2C1J RELATED DB: PDB REMARK 900 MOLECULAR BASIS FOR THE RECOGNITION OF PHOSPHORYLATED AND REMARK 900 PHOSPHOACETYLATED HISTONE H3 BY 14-3-3 REMARK 900 RELATED ID: 2C1N RELATED DB: PDB REMARK 900 MOLECULAR BASIS FOR THE RECOGNITION OF PHOSPHORYLATED AND REMARK 900 PHOSPHOACETYLATED HISTONE H3 BY 14-3-3 REMARK 900 RELATED ID: 2CV5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NUCLEOSOME CORE PARTICLE REMARK 900 RELATED ID: 2UXN RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF HISTONE DEMETHYLATION BY LSD1 REVEALED BY REMARK 900 SUICIDE INACTIVATION REMARK 900 RELATED ID: 3ZVY RELATED DB: PDB REMARK 900 PHD FINGER OF HUMAN UHRF1 IN COMPLEX WITH UNMODIFIED HISTONE H3 N- REMARK 900 TERMINAL TAIL REMARK 900 RELATED ID: 4A0J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SURVIVIN BOUND TO THE PHOSPHORYLATED N- REMARK 900 TERMINAL TAIL OF HISTONE H3 REMARK 900 RELATED ID: 4A0N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SURVIVIN BOUND TO THE PHOSPHORYLATED N- REMARK 900 TERMINAL TAIL OF HISTONE H3 REMARK 900 RELATED ID: 4A7J RELATED DB: PDB REMARK 900 SYMMETRIC DIMETHYLATION OF H3 ARGININE 2 IS A NOVEL HISTONE MARK REMARK 900 THAT SUPPORTS EUCHROMATIN MAINTENANCE REMARK 900 RELATED ID: 18764 RELATED DB: BMRB DBREF 4BD3 A 38 95 UNP Q5T6S3 PHF19_HUMAN 38 95 DBREF 4BD3 B 31 41 UNP P68431 H31_HUMAN 32 42 SEQRES 1 A 58 SER LYS LEU THR GLU GLY GLN TYR VAL LEU CYS ARG TRP SEQRES 2 A 58 THR ASP GLY LEU TYR TYR LEU GLY LYS ILE LYS ARG VAL SEQRES 3 A 58 SER SER SER LYS GLN SER CYS LEU VAL THR PHE GLU ASP SEQRES 4 A 58 ASN SER LYS TYR TRP VAL LEU TRP LYS ASP ILE GLN HIS SEQRES 5 A 58 ALA GLY VAL PRO GLY GLU SEQRES 1 B 11 ALA THR GLY GLY VAL M3L LYS PRO HIS ARG TYR MODRES 4BD3 M3L B 36 LYS N-TRIMETHYLLYSINE HET M3L B 36 31 HETNAM M3L N-TRIMETHYLLYSINE FORMUL 2 M3L C9 H21 N2 O2 1+ SHEET 1 AA 4 LYS A 79 LEU A 83 0 SHEET 2 AA 4 SER A 69 PHE A 74 -1 O CYS A 70 N VAL A 82 SHEET 3 AA 4 TYR A 55 SER A 64 -1 O LYS A 59 N THR A 73 SHEET 4 AA 4 PRO B 38 HIS B 39 1 O HIS B 39 N TYR A 55 SHEET 1 AB 5 LYS A 79 LEU A 83 0 SHEET 2 AB 5 SER A 69 PHE A 74 -1 O CYS A 70 N VAL A 82 SHEET 3 AB 5 TYR A 55 SER A 64 -1 O LYS A 59 N THR A 73 SHEET 4 AB 5 TYR A 45 ARG A 49 -1 O VAL A 46 N GLY A 58 SHEET 5 AB 5 ILE A 87 HIS A 89 -1 O GLN A 88 N LEU A 47 SHEET 1 BA 2 PRO B 38 HIS B 39 0 SHEET 2 BA 2 TYR A 55 SER A 64 1 O TYR A 55 N HIS B 39 LINK C VAL B 35 N M3L B 36 1555 1555 1.32 LINK C M3L B 36 N LYS B 37 1555 1555 1.33 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 2 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