HEADER TRANSCRIPTION / STRUCTURAL PROTEIN 12-SEP-16 5TBN TITLE SOLUTION NMR STRUCTURE OF PHF20 PHD DOMAIN IN COMPLEX WITH A HISTONE TITLE 2 H3K4ME2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHD FINGER PROTEIN 20; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 646-699; COMPND 5 SYNONYM: GLIOMA-EXPRESSED ANTIGEN 2,HEPATOCELLULAR CARCINOMA- COMPND 6 ASSOCIATED ANTIGEN 58,NOVEL ZINC FINGER PROTEIN,TRANSCRIPTION FACTOR COMPND 7 TZP; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HISTONE H3.1; COMPND 11 CHAIN: C; COMPND 12 FRAGMENT: RESIDUES 2-12; COMPND 13 SYNONYM: HISTONE H3/A,HISTONE H3/B,HISTONE H3/C,HISTONE H3/D,HISTONE COMPND 14 H3/F,HISTONE H3/H,HISTONE H3/I,HISTONE H3/J,HISTONE H3/K,HISTONE COMPND 15 H3/L; COMPND 16 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: PHF20, C20ORF104, GLEA2, HCA58, NZF, TZP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS PHD FINGER, METHYLATED LYSINE, TRANSCRIPTION - STRUCTURAL PROTEIN KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.CUI,M.V.BOTUYAN,G.MER REVDAT 4 04-DEC-19 5TBN 1 REMARK REVDAT 3 20-SEP-17 5TBN 1 COMPND REVDAT 2 02-NOV-16 5TBN 1 JRNL REVDAT 1 12-OCT-16 5TBN 0 JRNL AUTH B.J.KLEIN,X.WANG,G.CUI,C.YUAN,M.V.BOTUYAN,K.LIN,Y.LU,X.WANG, JRNL AUTH 2 Y.ZHAO,C.J.BRUNS,G.MER,X.SHI,T.G.KUTATELADZE JRNL TITL PHF20 READERS LINK METHYLATION OF HISTONE H3K4 AND P53 WITH JRNL TITL 2 H4K16 ACETYLATION. JRNL REF CELL REP V. 17 1158 2016 JRNL REFN ESSN 2211-1247 JRNL PMID 27760318 JRNL DOI 10.1016/J.CELREP.2016.09.056 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 14 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 5TBN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223981. 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 : 20 MM SODIUM PHOSPHATE REMARK 210 PRESSURE : 101325 PA REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-15N] PHF20 PHD DOMAIN, REMARK 210 6.0 MM H3K4ME2 PEPTIDE, 25 MM REMARK 210 SODIUM PHOSPHATE, 0.3 MM DSS, REMARK 210 1.5 MM SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O; 1.5 MM [U-13C; U-15N] PHF20 REMARK 210 PHD DOMAIN, 6.0 MM H3K4ME2 REMARK 210 PEPTIDE, 25 MM SODIUM PHOSPHATE, REMARK 210 0.3 MM DSS, 1.5 MM SODIUM AZIDE, REMARK 210 90% H2O/10% D2O; 2 MM H3K4ME2 REMARK 210 PEPTIDE, 25 MM SODIUM PHOSPHATE, REMARK 210 0.3 MM DSS, 1.5 MM SODIUM AZIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D NH(CA)CO; REMARK 210 3D HBHA(CO)NH; 3D CCH-TOCSY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D 13C,15N- REMARK 210 FILTERED, 13C/15N-EDITED NOESY; REMARK 210 2D 1H-1H NOESY; 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRDRAW, NMRPIPE, REMARK 210 NMRVIEW, SANE, CYANA, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: A, C 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: 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 CYS A 11 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 1 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 CYS A 11 CA - CB - SG ANGL. DEV. = 8.2 DEGREES REMARK 500 3 CYS A 11 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 3 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 CYS A 11 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 4 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 CYS A 11 CA - CB - SG ANGL. DEV. = 7.9 DEGREES REMARK 500 6 CYS A 11 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 6 ARG C 2 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 CYS A 11 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 7 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 CYS A 11 CA - CB - SG ANGL. DEV. = 8.2 DEGREES REMARK 500 8 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 CYS A 11 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 9 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 CYS A 11 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 11 CYS A 11 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 11 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 CYS A 11 CA - CB - SG ANGL. DEV. = 8.0 DEGREES REMARK 500 12 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 13 CYS A 11 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 13 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 CYS A 11 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 14 ARG C 2 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 15 CYS A 11 CA - CB - SG ANGL. DEV. = 7.9 DEGREES REMARK 500 15 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 CYS A 11 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 17 CYS A 11 CA - CB - SG ANGL. DEV. = 8.3 DEGREES REMARK 500 17 ARG C 8 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 18 CYS A 11 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 19 CYS A 11 CA - CB - SG ANGL. DEV. = 8.2 DEGREES REMARK 500 20 CYS A 11 CA - CB - SG ANGL. DEV. = 8.3 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 ASP A 0 13.96 53.03 REMARK 500 1 CYS A 51 -62.71 -94.45 REMARK 500 1 ALA C 7 -37.36 -154.11 REMARK 500 2 ASP A 0 11.91 51.53 REMARK 500 2 CYS A 51 -60.90 -91.24 REMARK 500 2 ARG C 8 149.81 65.82 REMARK 500 3 ASP A 0 14.63 50.57 REMARK 500 3 ARG A 1 -3.05 59.22 REMARK 500 3 CYS A 51 -63.26 -93.85 REMARK 500 3 GLN C 5 16.95 53.11 REMARK 500 4 ASP A 0 12.22 47.97 REMARK 500 4 ARG A 1 10.00 57.97 REMARK 500 4 TYR A 49 -39.01 -36.95 REMARK 500 4 CYS A 51 -61.46 -96.67 REMARK 500 5 ASP A 0 13.90 50.68 REMARK 500 5 ARG A 1 8.99 58.89 REMARK 500 5 CYS A 51 -63.02 -94.23 REMARK 500 5 MLY C 4 -31.60 -133.34 REMARK 500 5 THR C 6 18.98 51.35 REMARK 500 5 ALA C 7 19.96 54.34 REMARK 500 5 LYS C 9 -165.20 -77.94 REMARK 500 6 ASP A 0 10.92 49.98 REMARK 500 6 ARG A 1 -1.17 59.05 REMARK 500 6 TYR A 49 -38.09 -37.53 REMARK 500 6 CYS A 51 -62.07 -96.33 REMARK 500 6 ARG C 2 -73.95 56.90 REMARK 500 6 THR C 3 155.00 56.02 REMARK 500 6 MLY C 4 -29.66 -141.96 REMARK 500 7 ASP A 0 10.70 49.74 REMARK 500 7 ARG A 1 14.84 53.15 REMARK 500 7 CYS A 51 -60.23 -91.31 REMARK 500 7 ARG C 2 -70.03 44.67 REMARK 500 7 THR C 3 149.85 57.77 REMARK 500 8 ASP A 0 16.80 55.16 REMARK 500 8 CYS A 51 -63.27 -95.43 REMARK 500 8 ARG C 2 -69.89 50.35 REMARK 500 8 THR C 3 149.57 57.64 REMARK 500 9 ASP A 0 17.56 47.41 REMARK 500 9 ARG A 1 16.60 51.11 REMARK 500 9 CYS A 51 -61.10 -91.93 REMARK 500 9 THR C 6 28.72 -140.37 REMARK 500 10 ASP A 0 17.52 49.84 REMARK 500 10 ARG A 1 15.29 51.94 REMARK 500 10 CYS A 51 -63.43 -93.83 REMARK 500 10 ARG C 2 -70.68 47.67 REMARK 500 10 THR C 3 150.78 57.53 REMARK 500 10 SER C 10 175.87 62.42 REMARK 500 11 ASP A 0 19.03 48.28 REMARK 500 11 ARG A 1 16.94 50.30 REMARK 500 11 CYS A 51 -62.88 -94.21 REMARK 500 REMARK 500 THIS ENTRY HAS 96 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 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 CYS A 11 SG 110.0 REMARK 620 3 HIS A 31 ND1 107.2 116.4 REMARK 620 4 CYS A 34 SG 106.7 105.5 110.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 800 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 23 SG REMARK 620 2 CYS A 26 SG 111.3 REMARK 620 3 CYS A 48 SG 106.9 110.3 REMARK 620 4 CYS A 51 SG 112.4 104.2 111.7 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 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 801 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30177 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF PHF20 PHD DOMAIN IN COMPLEX WITH A REMARK 900 HISTONE H3K4ME2 PEPTIDE DBREF 5TBN A 0 53 UNP Q9BVI0 PHF20_HUMAN 646 699 DBREF 5TBN C 1 11 UNP P68431 H31_HUMAN 2 12 SEQADV 5TBN GLY A -3 UNP Q9BVI0 EXPRESSION TAG SEQADV 5TBN HIS A -2 UNP Q9BVI0 EXPRESSION TAG SEQADV 5TBN MET A -1 UNP Q9BVI0 EXPRESSION TAG SEQADV 5TBN NH2 C 12 UNP P68431 AMIDATION SEQRES 1 A 57 GLY HIS MET ASP ARG TYR ASP PHE GLU VAL VAL ARG CYS SEQRES 2 A 57 ILE CYS GLU VAL GLN GLU GLU ASN ASP PHE MET ILE GLN SEQRES 3 A 57 CYS GLU GLU CYS GLN CYS TRP GLN HIS GLY VAL CYS MET SEQRES 4 A 57 GLY LEU LEU GLU GLU ASN VAL PRO GLU LYS TYR THR CYS SEQRES 5 A 57 TYR VAL CYS GLN ASP SEQRES 1 C 12 ALA ARG THR MLY GLN THR ALA ARG LYS SER THR NH2 MODRES 5TBN MLY C 4 LYS MODIFIED RESIDUE HET MLY C 4 28 HET NH2 C 12 3 HET ZN A 800 1 HET ZN A 801 1 HETNAM MLY N-DIMETHYL-LYSINE HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 2 MLY C8 H18 N2 O2 FORMUL 2 NH2 H2 N FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 HIS A 31 GLY A 36 1 6 SHEET 1 AA1 4 VAL A 6 VAL A 7 0 SHEET 2 AA1 4 CYS A 28 GLN A 30 1 O TRP A 29 N VAL A 6 SHEET 3 AA1 4 PHE A 19 GLN A 22 -1 N ILE A 21 O GLN A 30 SHEET 4 AA1 4 THR C 3 GLN C 5 -1 O MLY C 4 N MET A 20 LINK SG CYS A 9 ZN ZN A 801 1555 1555 2.35 LINK SG CYS A 11 ZN ZN A 801 1555 1555 2.35 LINK SG CYS A 23 ZN ZN A 800 1555 1555 2.35 LINK SG CYS A 26 ZN ZN A 800 1555 1555 2.35 LINK ND1 HIS A 31 ZN ZN A 801 1555 1555 2.05 LINK SG CYS A 34 ZN ZN A 801 1555 1555 2.34 LINK SG CYS A 48 ZN ZN A 800 1555 1555 2.35 LINK SG CYS A 51 ZN ZN A 800 1555 1555 2.35 LINK C THR C 3 N MLY C 4 1555 1555 1.34 LINK C MLY C 4 N GLN C 5 1555 1555 1.34 LINK C THR C 11 N NH2 C 12 1555 1555 1.25 SITE 1 AC1 5 CYS A 23 CYS A 26 CYS A 28 CYS A 48 SITE 2 AC1 5 CYS A 51 SITE 1 AC2 4 CYS A 9 CYS A 11 HIS A 31 CYS A 34 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