Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TAF14 YEATS DOMAIN IN COMPLEX WITH HISTONE H3K9CR
 
Authors :  F. H. Andrews, T. G. Kuateladze
Date :  08 Mar 16  (Deposition) - 20 Apr 16  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.22
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Crotonylation, Crotonyllysine, Epigenetics, Reader, Histone H3, H3K9Cr, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. H. Andrews, S. A. Shinsky, E. K. Shanle, J. B. Bridgers, A. Gest, I. K. Tsun, K. Krajewski, X. Shi, B. D. Strahl, T. G. Kutateladze
The Taf14 Yeats Domain Is A Reader Of Histone Crotonylation
Nat. Chem. Biol. V. 12 396 2016
PubMed-ID: 27089029  |  Reference-DOI: 10.1038/NCHEMBIO.2065

(-) Compounds

Molecule 1 - TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 14
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: ACTIN NON-COMPLEMENTING MUTANT 1,CHROMOSOME STABILITY PROTEIN 10,SWI/SNF CHROMATIN-REMODELING COMPLEX SUBUNIT TAF14,SWI/SNF COMPLEX 29 KDA SUBUNIT,SWI/SNF COMPLEX SUBUNIT TAF14,TBP-ASSOCIATED FACTOR 14,TBP-ASSOCIATED FACTOR 30 KDA,TRANSCRIPTION FACTOR G 30 KDA SUBUNIT,TRANSCRIPTION INITIATION FACTOR TFIIF 30 KDA SUBUNIT
 
Molecule 2 - (ACE)QTAR(KCR)ST
    Chains: C
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: THIS PEPTIDE IS N-TERMINALLY ACETYLATED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2KCR1Mod. Amino AcidN-6-CROTONYL-L-LYSINE
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:0 , GLU A:20 , LYS A:53 , THR A:68 , PHE A:91 , GLU A:129 , HOH A:302binding site for residue PEG A 201
2AC2SOFTWAREMET A:1 , LYS A:95 , ARG A:99 , GLN A:119 , HOH A:361binding site for residue PEG A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IOK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:72 -Pro A:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IOK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IOK)

(-) Exons   (0, 0)

(no "Exon" information available for 5IOK)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeeeeeeeeeeee............eeeeeeeeee.....eee...eeeeeee........eeee......eeeee...eeeeeeeee.hhh.eeeeeeee.....eeeeeeeeeee..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iok A  -4 GPLGSMVATVKRTIRIKTQQHILPEVPPVENFPVRQWSIEIVLLDDEGKEIPATIFDKVIYHLHPTFANPNRTFTDPPFRIEEQGWGGFPLDISVFLLEKAGERKIPHDLNFLQESYEVEHVIQIPLNKPLLTEELAKSGST 137
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135  


Chain C from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 5iok C   3 xQTARxST  10
                            |    |  
                            3-ACE|  
                                 8-KCR
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5IOK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IOK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IOK)

(-) Gene Ontology  (37, 39)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    KCR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:72 - Pro A:73   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5iok
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  H3_YEAST | P61830
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  TAF14_YEAST | P35189
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  H3_YEAST | P61830
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TAF14_YEAST | P35189
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        H3_YEAST | P61830: 1id3 1m1d 1peg 1pu9 1pua 1qsn 2cnx 2h2g 2idc 2jmj 2rnw 2rnx 2rsn 3mp1 3mp6 3q33 4jjn 4kud 4psx 5d7e
        TAF14_YEAST | P35189: 2l7e 3qrl 5d7e 5sva

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5IOK)