2R10 - JenaLib

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Title :   STRUCTURE OF AN ACETYLATED RSC4 TANDEM BROMODOMAIN HISTONE CHIMERA

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 :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

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)

Molecule 1 - CHROMATIN STRUCTURE-REMODELING COMPLEX PROTEIN RSC4, LINKER, HISTONE H3
	Chains	:	A, B
	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	:	FUSION PROTEIN COMPRISES HISTONE H3 (6-18) AND RSC4 TBD (22-361)
	Gene	:	RSC4
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	REMODEL THE STRUCTURE OF CHROMATIN COMPLEX SUBUNIT 4

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:174 , HIS A:177 , GLU A:296 , HOH A:989	BINDING SITE FOR RESIDUE EDO A 788
2	AC2	SOFTWARE	PRO A:56 , LYS A:57 , PHE A:61 , PHE A:64	BINDING SITE FOR RESIDUE EDO A 789

(no "SS Bond" information available for 2R10)

(no "Cis Peptide Bond" information available for 2R10)

(no "SAP(SNP)/Variant" information available for 2R10)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	RSC4_YEAST	72-141 205-275	4	A:72-141 B:72-141 A:205-275 B:205-275
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	RSC4_YEAST	77-133 210-267	4	A:77-133 B:77-133 A:210-267 B:210-267

Biological Unit 1 (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 -

Biological Unit 2 (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	- B:72-141 - B:205-275
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	RSC4_YEAST	77-133 210-267	2	- B:77-133 - B:210-267

Asymmetric Unit (1, 2)

	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	2	A:18-310 B:18-315	293 298

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:293
 aligned with RSC4_YEAST | Q02206 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:293
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307   
           RSC4_YEAST    18 RPKYLPGKHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEF 310
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------2r10A01 A:46-159 Histone Acetyltransferase; Chain A                                                               2r10A02 A:160-304 Histone Acetyltransferase; Chain A                                                                                             ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh........hhhhhhh....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:18-310 UniProt: 1-625 [INCOMPLETE]                                                                                                                                                                                                                                                   Transcript 1
                 2r10 A  18 RPKYLPGkHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEF 310
                                   |27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307   
                                  25-ALY

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with RSC4_YEAST | Q02206 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:298
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307        
           RSC4_YEAST    18 RPKYLPGKHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKFEF 315
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------2r10B01 B:46-159 Histone Acetyltransferase; Chain A                                                               2r10B02 B:160-304 Histone Acetyltransferase; Chain A                                                                                             ----------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r10B01 B:201-280                                                   ----------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r10B02 B:201-280                                                   ----------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r10B03 B:201-280                                                   ----------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r10B04 B:201-280                                                   ----------------------------------- Pfam domains (4)
         Sec.struct. author ............................hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhh.........hhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------BROMODOMAIN_2  PDB: B:72-141 UniProt: 72-141                          ---------------------------------------------------------------BROMODOMAIN_2  PDB: B:205-275 UniProt: 205-275                         ---------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------BROMODOMAIN_1  PDB: B:77-133 UniProt: 77-133             ----------------------------------------------------------------------------BROMODOMAIN_1  PDB: B:210-267 UniProt: 210-267            ------------------------------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:18-315 UniProt: 1-625 [INCOMPLETE]                                                                                                                                                                                                                                                        Transcript 1
                 2r10 B  18 RPKYLPGkHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKFEF 315
                                   |27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307        
                                  25-ALY

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 2R10)

Asymmetric 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	2r10A01	A:46-159
1b	2r10B02	B:160-304
1c	2r10B01	B:46-159
1d	2r10A02	A:160-304

Asymmetric 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-2r10B01	B:201-280
1b	Bromodomain-2r10B02	B:201-280
1c	Bromodomain-2r10B03	B:201-280
1d	Bromodomain-2r10B04	B:201-280

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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