HEADER TRANSCRIPTION 22-FEB-08 2K17 TITLE SOLUTION STRUCTURE OF THE TAF3 PHD DOMAIN IN COMPLEX WITH A H3K4ME3 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: H3K4ME3 PEPTIDE; COMPND 3 CHAIN: P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 3; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: PLANTHOMEODOMAIN FINGER; COMPND 9 SYNONYM: TBP-ASSOCIATED FACTOR 3, TRANSCRIPTION INITIATION FACTOR COMPND 10 TFIID 140 KDA SUBUNIT, 140 KDA TATA BOX-BINDING PROTEIN-ASSOCIATED COMPND 11 FACTOR, TAF140, TAFII140; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 5 ORGANISM_COMMON: MOUSE; SOURCE 6 GENE: TAF3; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN, ALTERNATIVE SPLICING, METAL-BINDING, NUCLEUS, KEYWDS 2 PHOSPHOPROTEIN, TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC, ZINC- KEYWDS 3 FINGER EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.VAN INGEN,F.M.A.VAN SCHAIK,H.WIENK,M.TIMMERS,R.BOELENS REVDAT 4 14-JUN-23 2K17 1 REMARK REVDAT 3 19-FEB-20 2K17 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2K17 1 VERSN REVDAT 1 15-JUL-08 2K17 0 JRNL AUTH H.VAN INGEN,F.M.A.VAN SCHAIK,H.WIENK,J.BALLERING, JRNL AUTH 2 A.DESCHESNE,J.KRUIJZER,H.TIMMERS,R.BOELENS JRNL TITL RECOGNITION OF THE H3K4ME3 MARK BY THE TAF3-PHD FINGER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT IN EXPLICIT SOLVENT USING REMARK 3 RECOORD PROTOCOL REMARK 4 REMARK 4 2K17 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000100546. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-13C; U-15N] TAF3_PHD, REMARK 210 150 MM POTASSIUM CHLORIDE, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 0.01 MM REMARK 210 ZNCL2, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 750 MHZ; 700 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRPIPE, SPARKY 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: P, 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: 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 HIS A 852 99.05 -69.67 REMARK 500 1 MET A 853 -73.95 -126.07 REMARK 500 1 ALA A 854 89.04 178.97 REMARK 500 1 LYS A 919 -40.34 82.25 REMARK 500 1 LYS A 920 65.01 62.56 REMARK 500 2 ALA P 7 -87.51 -179.93 REMARK 500 2 ARG P 8 -51.62 -138.84 REMARK 500 2 MET A 853 -63.97 -105.69 REMARK 500 2 ALA A 854 -96.61 52.64 REMARK 500 2 ALA A 856 90.63 70.11 REMARK 500 2 ASN A 874 71.02 68.57 REMARK 500 2 ASP A 921 107.81 60.09 REMARK 500 2 LYS A 923 119.67 75.19 REMARK 500 3 THR P 6 -40.31 -152.86 REMARK 500 3 ALA P 7 -155.13 55.78 REMARK 500 3 ALA A 856 173.94 71.50 REMARK 500 3 TYR A 857 48.85 -84.64 REMARK 500 3 ASN A 874 12.34 81.23 REMARK 500 3 CYS A 885 -165.48 56.50 REMARK 500 3 LYS A 920 -176.41 62.22 REMARK 500 3 LYS A 922 174.73 70.42 REMARK 500 4 ALA P 7 151.06 65.08 REMARK 500 4 THR P 11 92.52 67.17 REMARK 500 4 MET A 855 19.29 -146.01 REMARK 500 4 ALA A 856 -158.99 67.72 REMARK 500 4 ASP A 889 69.07 66.22 REMARK 500 4 LYS A 922 98.92 64.80 REMARK 500 5 THR P 6 37.22 -92.56 REMARK 500 5 THR P 11 -74.39 -91.70 REMARK 500 5 ASN A 874 30.64 85.00 REMARK 500 5 PRO A 912 -9.63 -55.82 REMARK 500 5 LYS A 922 92.27 89.43 REMARK 500 6 GLN P 5 -58.69 -152.23 REMARK 500 6 THR P 6 76.87 57.94 REMARK 500 6 LYS P 9 -64.97 -156.98 REMARK 500 6 SER P 10 151.95 69.39 REMARK 500 6 ASN A 874 32.30 84.16 REMARK 500 6 CYS A 888 -84.85 -83.23 REMARK 500 6 ASP A 889 5.66 157.52 REMARK 500 6 LYS A 919 -45.74 -170.30 REMARK 500 6 LYS A 920 77.92 49.79 REMARK 500 7 ALA P 7 -171.24 -173.14 REMARK 500 7 ALA A 856 78.11 -66.98 REMARK 500 7 TYR A 857 -39.87 64.79 REMARK 500 7 ASP A 878 9.97 -168.54 REMARK 500 7 CYS A 888 -81.17 -77.90 REMARK 500 7 ASP A 889 -56.13 -148.13 REMARK 500 7 ASP A 921 -61.23 -100.48 REMARK 500 7 LYS A 922 85.04 43.52 REMARK 500 7 LYS A 923 -81.23 -170.27 REMARK 500 REMARK 500 THIS ENTRY HAS 139 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 16 ARG P 2 0.08 SIDE CHAIN REMARK 500 20 ARG P 8 0.10 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 A 941 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 870 SG REMARK 620 2 CYS A 873 SG 96.5 REMARK 620 3 HIS A 893 ND1 94.0 116.4 REMARK 620 4 CYS A 896 SG 98.5 120.8 119.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 940 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 885 SG REMARK 620 2 CYS A 888 SG 106.4 REMARK 620 3 CYS A 911 SG 111.1 112.4 REMARK 620 4 CYS A 914 SG 109.3 105.1 112.1 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 940 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 941 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K16 RELATED DB: PDB REMARK 900 RELATED ID: 15671 RELATED DB: BMRB DBREF 2K17 A 857 924 UNP Q5HZG4 TAF3_MOUSE 857 924 DBREF 2K17 P 1 13 PDB 2K17 2K17 1 13 SEQADV 2K17 GLY A 850 UNP Q5HZG4 EXPRESSION TAG SEQADV 2K17 SER A 851 UNP Q5HZG4 EXPRESSION TAG SEQADV 2K17 HIS A 852 UNP Q5HZG4 EXPRESSION TAG SEQADV 2K17 MET A 853 UNP Q5HZG4 EXPRESSION TAG SEQADV 2K17 ALA A 854 UNP Q5HZG4 EXPRESSION TAG SEQADV 2K17 MET A 855 UNP Q5HZG4 EXPRESSION TAG SEQADV 2K17 ALA A 856 UNP Q5HZG4 EXPRESSION TAG SEQRES 1 P 13 ALA ARG THR M3L GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 1 A 75 GLY SER HIS MET ALA MET ALA TYR VAL ILE ARG ASP GLU SEQRES 2 A 75 TRP GLY ASN GLN ILE TRP ILE CYS PRO GLY CYS ASN LYS SEQRES 3 A 75 PRO ASP ASP GLY SER PRO MET ILE GLY CYS ASP ASP CYS SEQRES 4 A 75 ASP ASP TRP TYR HIS TRP PRO CYS VAL GLY ILE MET ALA SEQRES 5 A 75 ALA PRO PRO GLU GLU MET GLN TRP PHE CYS PRO LYS CYS SEQRES 6 A 75 ALA ASN LYS ILE LYS LYS ASP LYS LYS HIS MODRES 2K17 M3L P 4 LYS N-TRIMETHYLLYSINE HET M3L P 4 31 HET ZN A 940 1 HET ZN A 941 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 1 M3L C9 H21 N2 O2 1+ FORMUL 3 ZN 2(ZN 2+) HELIX 1 1 TRP A 894 GLY A 898 1 5 HELIX 2 2 LYS A 913 LYS A 919 1 7 SHEET 1 A 3 ARG P 2 GLN P 5 0 SHEET 2 A 3 PRO A 881 GLY A 884 -1 O MET A 882 N M3L P 4 SHEET 3 A 3 TRP A 891 HIS A 893 -1 O TYR A 892 N ILE A 883 SHEET 1 B 2 VAL A 858 ARG A 860 0 SHEET 2 B 2 GLN A 866 TRP A 868 -1 O ILE A 867 N ILE A 859 LINK C THR P 3 N M3L P 4 1555 1555 1.31 LINK C M3L P 4 N GLN P 5 1555 1555 1.30 LINK SG CYS A 870 ZN ZN A 941 1555 1555 2.71 LINK SG CYS A 873 ZN ZN A 941 1555 1555 2.26 LINK SG CYS A 885 ZN ZN A 940 1555 1555 2.31 LINK SG CYS A 888 ZN ZN A 940 1555 1555 2.35 LINK ND1 HIS A 893 ZN ZN A 941 1555 1555 2.11 LINK SG CYS A 896 ZN ZN A 941 1555 1555 2.26 LINK SG CYS A 911 ZN ZN A 940 1555 1555 2.17 LINK SG CYS A 914 ZN ZN A 940 1555 1555 2.30 SITE 1 AC1 5 CYS A 885 ASP A 887 CYS A 888 PHE A 910 SITE 2 AC1 5 CYS A 911 SITE 1 AC2 4 ILE A 869 CYS A 870 CYS A 873 LYS A 875 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