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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE RSC4 TANDEM BROMODOMAIN

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 :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Bromodomain, Chromatin, Remodeler, Rsc, Transcription, Acetylation, 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)

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
	Gene	:	RSC4
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	REMODEL THE STRUCTURE OF CHROMATIN COMPLEX SUBUNIT 4

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2R0S)

(no "SS Bond" information available for 2R0S)

(no "Cis Peptide Bond" information available for 2R0S)

(no "SAP(SNP)/Variant" information available for 2R0S)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	RSC4_YEAST	72-141 205-275	2	A:72-141 A:205-275
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	RSC4_YEAST	77-133 210-267	2	A:77-133 A:210-267

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YKR008W	1	YKR008W.1	XI:451844-453721	1878	RSC4_YEAST	1-625	625	1	A:36-320	285

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
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Chain A from PDB  Type:PROTEIN  Length:285
 aligned with RSC4_YEAST | Q02206 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:285
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315     
           RSC4_YEAST    36 VDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKFEFENYLA 320
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------2r0sA01 A:46-159 Histone Acetyltransferase; Chain A                                                               2r0sA02 A:160-304 Histone Acetyltransferase; Chain A                                                                                             ---------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0sA01 A:201-280                                                   ---------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0sA02 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:36-320 UniProt: 1-625 [INCOMPLETE]                                                                                                                                                                                                                                           Transcript 1
                 2r0s A  36 VDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPmSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSmQVVmLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFmELVDKDELPEYYEIVHSPmALSIVKQNLEIGQYSKIYDFIIDmLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKFEFENYLA 320
                                    45        55        65        75        85        95    |  105       115       125       135       145   |   155       165       175       185       195       205       215       225       235       245       255 |     265       275       285       295       305       315     
                                                                                          100-MSE                                      145-MSE                                                              214-MSE            233-MSE                 257-MSE                                                           
                                                                                                                                           149-MSE

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 '\|'

(no "SCOP Domain" information available for 2R0S)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Histone Acetyltransferase; Chain A (22)

Homologous Superfamily: Histone Acetyltransferase; Chain A (22)

Baker's yeast (Saccharomyces cerevisiae) (4)

1a	2r0sA01	A:46-159
1b	2r0sA02	A:160-304

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Bromodomain] (56)

Family: Bromodomain (56)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (4)

1a	Bromodomain-2r0sA01	A:201-280
1b	Bromodomain-2r0sA02	A:201-280

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.

Asymmetric/Biological Unit
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Description

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