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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST AF-9 HOMOLOG PROTEIN YAF9
 
Authors :  S. D. Chen, L. J. Wu, Y. F. Liu
Date :  20 Apr 11  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Yeats Domain, Histone, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. F. Liu
Crystal Structure Of Yeast Af-9 Homolog Protein Yaf9
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN AF-9 HOMOLOG
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentYEATS DOMAIN, RESIDUES IN UNP 9-176
    GeneYAF9
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymYAF9

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3RLS)

(-) Sites  (0, 0)

(no "Site" information available for 3RLS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RLS)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:80 -Pro A:81
2His A:118 -Pro A:119
3Pro B:80 -Pro B:81
4Pro B:119 -Tyr B:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RLS)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YEATSPS51037 YEATS domain profile.AF9_YEAST15-123
 
  2A:15-119
B:15-120
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YEATSPS51037 YEATS domain profile.AF9_YEAST15-123
 
  1A:15-119
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1YEATSPS51037 YEATS domain profile.AF9_YEAST15-123
 
  1-
B:15-120

(-) Exons   (0, 0)

(no "Exon" information available for 3RLS)

(-) Sequences/Alignments

Asymmetric 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:152
 aligned with AF9_YEAST | P53930 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:186
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
            AF9_YEAST     9 IKTLSVSRPIIYGNTAKKMGSVKPPNAPAEHTHLWTIFVRGPQNEDISYFIKKVVFKLHDTYPNPVRSIEAPPFELTETGWGEFDINIKVYFVEEANEKVLNFYHRLRLHPYANPVPNSDNGNEQNTTDHNSKDAEVSSVYFDEIVFNEPNEEFFKILMSRPGNLLPSNKTDDCVYSKQLEQEEID 194
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeeeee..............eeeeeeeehhhhh.....eeeeeee........eeee....eeeeeee....eeeeeeee.hhhh...eeeeee.....-----------------------..eeeeeeeeeee...hhhhhhhhhhh.......-----------....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------YEATS  PDB: A:15-119 UniProt: 15-123                                                                         ----------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rls A   9 IKTLSVSRPIIYGNTAKKMGSVKPPNAPAEHTHLWTIFVRGPQNEDISYFIKKVVFKLHDTYPNPVRSIEAPPFELTETGWGEFDINIKVYFVEEANEKVLNFYHRLRLHP-----------------------AEVSSVYFDEIVFNEPNEEFFKILMSRPGNLLPS-----------LERPHRD 183
                                    18        28        38        48        58        68        78        88        98       108       118|        -         -    |  148       158       168       | -       177      
                                                                                                                                        119                     143                              176         177      

Chain B from PDB  Type:PROTEIN  Length:144
 aligned with AF9_YEAST | P53930 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:177
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
            AF9_YEAST    12 LSVSRPIIYGNTAKKMGSVKPPNAPAEHTHLWTIFVRGPQNEDISYFIKKVVFKLHDTYPNPVRSIEAPPFELTETGWGEFDINIKVYFVEEANEKVLNFYHRLRLHPYANPVPNSDNGNEQNTTDHNSKDAEVSSVYFDEIVFNEPNEEFFKILMSRPGNLLPSNKTDDCVYSKQL 188
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------YEATS-3rlsB01 B:40-120                                                           -------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------YEATS-3rlsB02 B:40-120                                                           -------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeeee..............eeeeeeee..........eeeeeee........eeee.....eeeeee....eeeeeeee.hhhh...eeeeee......----------------------..eeeeeeeeeeee..hhhhhhhhhhh.......-----------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---YEATS  PDB: B:15-120 UniProt: 15-123                                                                         ----------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rls B  12 LSVSRPIIYGNTAKKMGSVKPPNAPAEHTHLWTIFVRGPQNEDISYFIKKVVFKLHDTYPNPVRSIEAPPFELTETGWGEFDINIKVYFVEEANEKVLNFYHRLRLHPY----------------------AEVSSVYFDEIVFNEPNEEFFKILMSRPGNLLPS-----------L 177
                                    21        31        41        51        61        71        81        91       101       111        |-         -         - |     151       161       171    |    -      |
                                                                                                                                      120                    143                              176         177

   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 3RLS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RLS)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AF9_YEAST | P53930)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0006348    chromatin silencing at telomere    Repression of transcription of telomeric DNA by altering the structure of chromatin.
    GO:0043486    histone exchange    The replacement, within chromatin, of resident histones or histone subunits with alternative, sometimes variant, histones or subunits.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0035267    NuA4 histone acetyltransferase complex    A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
    GO:0000812    Swr1 complex    A multisubunit protein complex that is involved in chromatin remodeling. It is required for the incorporation of the histone variant H2AZ into chromatin. In S. cerevisiae, the complex contains Swr1p, a Swi2/Snf2-related ATPase, and 12 additional subunits.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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    His A:118 - Pro A:119   [ RasMol ]  
    Pro A:80 - Pro A:81   [ RasMol ]  
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 Related Entries

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        AF9_YEAST | P539303fk3

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