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(-) Description

Title :  STRUCTURE OF THE RSC4 TANDEM BROMODOMAIN IN COMPLEX WITH AN ACETYLATED H3 PEPTIDE
 
Authors :  A. P. Vandemark, M. M. Kasten, E. Ferris, A. Heroux, C. P. Hill, B. R. Cairns
Date :  21 Aug 07  (Deposition) - 30 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bromodomain, Chromatin, Remodeler, Rsc, Histone, Acetylation, Transcription, Chromatin Regulator, Nucleus, Phosphorylation, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Vandemark, M. M. Kasten, E. Ferris, A. Heroux, C. P. Hill, B. R. Cairns
Autoregulation Of The Rsc4 Tandem Bromodomain By Gcn5 Acetylation.
Mol. Cell V. 27 817 2007
PubMed-ID: 17803945  |  Reference-DOI: 10.1016/J.MOLCEL.2007.08.018
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHROMATIN STRUCTURE-REMODELING COMPLEX PROTEIN RSC4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151-D/TOPO
    Expression System Strain: BL21(DE3)CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RSC4 TANDEM BROMODOMAIN (36-340)
    Gene: RSC4
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: REMODEL THE STRUCTURE OF CHROMATIN COMPLEX SUBUNIT 4
 
Molecule 2 - HISTONE H3 PEPTIDE
    Chains: B
    Engineered: YES
    Fragment: RESIDUES 6-18
    Mutation: YES
    Other Details: SYNTHESIZED PEPTIDE HISTONE H3 (6-18) K14AC
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1ALY1Mod. Amino AcidN(6)-ACETYLLYSINE
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2R0Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R0Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R0Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R0Y)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.RSC4_YEAST72-141
205-275		  2A:72-141
A:205-275
2BROMODOMAIN_1PS00633 Bromodomain signature.RSC4_YEAST77-133
210-267		  2A:77-133
A:210-267

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKR008W1YKR008W.1XI:451844-4537211878RSC4_YEAST1-6256251A:37-319283

(-) 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:283
 aligned with RSC4_YEAST | Q02206 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:283
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316   
           RSC4_YEAST    37 DYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKFEFENYL 319
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------2r0yA01 A:46-159 Histone Acetyltransferase; Chain A                                                               2r0yA02 A:160-304 Histone Acetyltransferase; Chain A                                                                                             --------------- CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0yA01 A:201-280                                                   --------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0yA02 A:201-280                                                   --------------------------------------- Pfam domains (2)
         Sec.struct. author .........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh.......hhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------BROMODOMAIN_2  PDB: A:72-141 UniProt: 72-141                          ---------------------------------------------------------------BROMODOMAIN_2  PDB: A:205-275 UniProt: 205-275                         -------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------BROMODOMAIN_1  PDB: A:77-133 UniProt: 77-133             ----------------------------------------------------------------------------BROMODOMAIN_1  PDB: A:210-267 UniProt: 210-267            ---------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:37-319 UniProt: 1-625 [INCOMPLETE]                                                                                                                                                                                                                                         Transcript 1
                 2r0y A  37 DYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPmSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSmQVVmLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFmELVDKDELPEYYEIVHSPmALSIVKQNLEIGQYSKIYDFIIDmLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKFEFENYL 319
                                    46        56        66        76        86        96   |   106       116       126       136       146  |    156       166       176       186       196       206       216       226      |236       246       256|      266       276       286       296       306       316   
                                                                                         100-MSE                                      145-MSE                                                              214-MSE            233-MSE                 257-MSE                                                          
                                                                                                                                          149-MSE                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:1
                         37      
               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
                 2r0y B  37 k  14
                                                                                                                                                                                                                                                                                                                       |
                                                                                                                                                                                                                                                                                                                      14-ALY
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2R0Y)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Bromodomain] (56)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RSC4_YEAST | Q02206)
molecular function
    GO:0015616    DNA translocase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive movement along a single- or double-stranded DNA molecule.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    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:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:0006337    nucleosome disassembly    The controlled breakdown of nucleosomes, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006368    transcription elongation from RNA polymerase II promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016586    RSC complex    A protein complex similar to, but more abundant than, the Swi/Snf complex. The RSC complex is generally recruited to RNA polymerase III promoters and is specifically recruited to RNA polymerase II promoters by transcriptional activators and repressors; it is also involved in non-homologous end joining.
    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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 Related Entries

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UniProtKB/Swiss-Prot
        RSC4_YEAST | Q02206: 2r0s 2r0v 2r10

(-) Related Entries Specified in the PDB File

2r0s 2r0v 2r10