HEADER PROTEIN BINDING 15-NOV-06 2JMI TITLE NMR SOLUTION STRUCTURE OF PHD FINGER FRAGMENT OF YEAST YNG1 PROTEIN IN TITLE 2 FREE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN YNG1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PHD FINGER; COMPND 5 SYNONYM: ING1 HOMOLOG 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: YNG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-4T KEYWDS PHD, HISTONE, RECOGNITION, YEAST, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.ILIN,S.D.TAVERNA,R.S.ROGERS,J.C.TANNY,H.LAVENDER,H.LI,L.BAKER, AUTHOR 2 J.BOYLE,L.P.BLAIR,B.T.CHAIT,D.J.PATEL,J.D.AITCHISON,A.J.TACKETT, AUTHOR 3 C.D.ALLIS REVDAT 4 20-DEC-23 2JMI 1 REMARK REVDAT 3 09-MAR-22 2JMI 1 REMARK SEQADV REVDAT 2 24-FEB-09 2JMI 1 VERSN REVDAT 1 03-JUL-07 2JMI 0 JRNL AUTH S.D.TAVERNA,S.ILIN,R.S.ROGERS,J.C.TANNY,H.LAVENDER,H.LI, JRNL AUTH 2 L.BAKER,J.BOYLE,L.P.BLAIR,B.T.CHAIT,D.J.PATEL,J.D.AITCHISON, JRNL AUTH 3 A.J.TACKETT,C.D.ALLIS JRNL TITL YNG1 PHD FINGER BINDING TO H3 TRIMETHYLATED AT K4 PROMOTES JRNL TITL 2 NUA3 HAT ACTIVITY AT K14 OF H3 AND TRANSCRIPTION AT A SUBSET JRNL TITL 3 OF TARGETED ORFS JRNL REF MOL.CELL V. 24 785 2006 JRNL REFN ISSN 1097-2765 JRNL PMID 17157260 JRNL DOI 10.1016/J.MOLCEL.2006.10.026 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JMI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000100018. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 20 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.54 MM [U-13C, U-15N] YNG1_PHD, REMARK 210 90% H2O, 10% D2O; 0.6 MM [U-15N] REMARK 210 YNG1_PHD, 90% H2O, 10% D2O; 0.54 REMARK 210 MM [U-13C, U-15N] YNG1_PHD, 100% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, TALOS, CARA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 85 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 4 REMARK 465 SER A 5 REMARK 465 HIS A 6 REMARK 465 MET A 7 REMARK 465 ALA A 8 REMARK 465 SER A 9 REMARK 465 GLU A 10 REMARK 465 PHE A 11 REMARK 465 ILE A 12 REMARK 465 ASN A 13 REMARK 465 GLN A 14 REMARK 465 GLY A 15 REMARK 465 ASP A 16 REMARK 465 VAL A 17 REMARK 465 THR A 18 REMARK 465 GLU A 19 REMARK 465 GLY A 20 REMARK 465 ASN A 21 REMARK 465 ASN A 22 REMARK 465 ASN A 23 REMARK 465 LYS A 84 REMARK 465 ARG A 85 REMARK 465 GLN A 86 REMARK 465 LYS A 87 REMARK 465 ARG A 88 REMARK 465 ARG A 89 REMARK 465 LYS A 90 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 SG CYS A 42 SG CYS A 47 0.92 REMARK 500 SG CYS A 29 SG CYS A 56 0.92 REMARK 500 SG CYS A 42 SG CYS A 73 0.97 REMARK 500 SG CYS A 47 SG CYS A 69 1.50 REMARK 500 O ASP A 72 H ILE A 76 1.56 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 GLU A 26 -125.55 -142.12 REMARK 500 1 VAL A 27 108.34 -164.41 REMARK 500 1 TYR A 28 -88.93 -103.13 REMARK 500 1 CYS A 29 156.04 -46.94 REMARK 500 1 PHE A 30 22.63 -68.87 REMARK 500 1 VAL A 34 -165.82 -126.57 REMARK 500 1 SER A 35 97.47 -64.79 REMARK 500 1 CYS A 42 90.07 -57.24 REMARK 500 1 ASP A 43 46.92 -72.00 REMARK 500 1 ALA A 46 -98.11 -76.86 REMARK 500 1 CYS A 47 102.18 44.36 REMARK 500 1 TRP A 51 117.12 -160.98 REMARK 500 1 VAL A 57 -140.04 -100.07 REMARK 500 1 LEU A 59 -177.67 172.08 REMARK 500 1 ALA A 62 86.38 55.40 REMARK 500 1 CYS A 69 -37.86 -23.62 REMARK 500 1 CYS A 73 -18.67 -44.43 REMARK 500 1 SER A 81 105.62 59.31 REMARK 500 2 VAL A 27 155.87 -48.60 REMARK 500 2 TYR A 28 -79.13 -134.72 REMARK 500 2 CYS A 29 21.90 -61.32 REMARK 500 2 PHE A 30 -5.26 62.56 REMARK 500 2 CYS A 31 6.14 -67.78 REMARK 500 2 SER A 35 98.02 -60.57 REMARK 500 2 CYS A 42 100.34 -48.23 REMARK 500 2 ASP A 43 38.84 -72.29 REMARK 500 2 CYS A 47 108.93 -2.50 REMARK 500 2 GLU A 50 31.75 -145.80 REMARK 500 2 VAL A 57 -138.79 -98.03 REMARK 500 2 LEU A 59 164.69 173.58 REMARK 500 2 GLN A 61 100.29 67.27 REMARK 500 2 ALA A 62 90.20 -18.41 REMARK 500 2 CYS A 69 -42.72 -22.58 REMARK 500 2 CYS A 73 -34.95 -37.28 REMARK 500 2 GLN A 79 156.33 64.86 REMARK 500 3 TYR A 28 -92.01 -116.13 REMARK 500 3 PHE A 30 -1.64 -56.43 REMARK 500 3 VAL A 34 167.26 -40.73 REMARK 500 3 TYR A 36 -98.69 -23.96 REMARK 500 3 PRO A 38 90.18 -53.18 REMARK 500 3 CYS A 42 100.46 -51.27 REMARK 500 3 ASP A 43 47.04 -82.19 REMARK 500 3 ALA A 46 -72.39 -98.47 REMARK 500 3 CYS A 47 99.08 18.72 REMARK 500 3 GLU A 50 33.92 -145.74 REMARK 500 3 VAL A 57 -142.19 -102.47 REMARK 500 3 LEU A 59 114.14 -177.81 REMARK 500 3 GLN A 61 117.47 72.04 REMARK 500 3 ALA A 62 106.20 -39.74 REMARK 500 3 CYS A 69 -35.92 -21.33 REMARK 500 REMARK 500 THIS ENTRY HAS 336 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 29 SG REMARK 620 2 CYS A 31 SG 34.9 REMARK 620 3 CYS A 56 SG 36.2 30.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 42 SG REMARK 620 2 CYS A 47 SG 35.2 REMARK 620 3 CYS A 69 SG 30.4 58.4 REMARK 620 4 CYS A 73 SG 42.4 37.2 40.2 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JMJ RELATED DB: PDB REMARK 900 PHD DOMAIN FROM THE YEAST YNG1 PROTEIN IN COMPLEX WITH H3(1-9)K4ME3 REMARK 900 PEPTIDE DBREF 2JMI A 12 90 UNP Q08465 YNG1_YEAST 141 219 SEQADV 2JMI GLY A 1 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI PRO A 2 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI LEU A 3 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI GLY A 4 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI SER A 5 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI HIS A 6 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI MET A 7 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI ALA A 8 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI SER A 9 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI GLU A 10 UNP Q08465 CLONING ARTIFACT SEQADV 2JMI PHE A 11 UNP Q08465 CLONING ARTIFACT SEQRES 1 A 90 GLY PRO LEU GLY SER HIS MET ALA SER GLU PHE ILE ASN SEQRES 2 A 90 GLN GLY ASP VAL THR GLU GLY ASN ASN ASN GLN GLU GLU SEQRES 3 A 90 VAL TYR CYS PHE CYS ARG ASN VAL SER TYR GLY PRO MET SEQRES 4 A 90 VAL ALA CYS ASP ASN PRO ALA CYS PRO PHE GLU TRP PHE SEQRES 5 A 90 HIS TYR GLY CYS VAL GLY LEU LYS GLN ALA PRO LYS GLY SEQRES 6 A 90 LYS TRP TYR CYS SER LYS ASP CYS LYS GLU ILE ALA ASN SEQRES 7 A 90 GLN ARG SER LYS SER LYS ARG GLN LYS ARG ARG LYS HET ZN A 201 1 HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 SER A 70 ARG A 80 1 11 SHEET 1 A 2 MET A 39 VAL A 40 0 SHEET 2 A 2 PHE A 52 HIS A 53 -1 O PHE A 52 N VAL A 40 SSBOND 1 CYS A 29 CYS A 31 1555 1555 0.90 SSBOND 2 CYS A 31 CYS A 56 1555 1555 0.72 SSBOND 3 CYS A 42 CYS A 69 1555 1555 0.76 SSBOND 4 CYS A 47 CYS A 73 1555 1555 0.95 SSBOND 5 CYS A 69 CYS A 73 1555 1555 0.97 LINK SG CYS A 29 ZN ZN A 401 1555 1555 1.55 LINK SG CYS A 31 ZN ZN A 401 1555 1555 1.42 LINK SG CYS A 42 ZN ZN A 201 1555 1555 1.40 LINK SG CYS A 47 ZN ZN A 201 1555 1555 1.58 LINK SG CYS A 56 ZN ZN A 401 1555 1555 1.27 LINK SG CYS A 69 ZN ZN A 201 1555 1555 1.49 LINK SG CYS A 73 ZN ZN A 201 1555 1555 1.27 SITE 1 AC1 4 CYS A 42 CYS A 47 CYS A 69 CYS A 73 SITE 1 AC2 4 CYS A 29 PHE A 30 CYS A 31 CYS A 56 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