2R0V - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF THE RSC4 TANDEM BROMODOMAIN ACETYLATED AT K25

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 :   2.35

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (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
	Chains	:	A, B, C
	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 TBD (1-340)
	Gene	:	RSC4
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	REMODEL THE STRUCTURE OF CHROMATIN COMPLEX SUBUNIT 4

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	ALY	3	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	ALY	1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:177 , ASN A:180 , ARG A:303 , HOH A:399 , HOH A:468 , HOH B:455	BINDING SITE FOR RESIDUE SO4 A 341
2	AC2	SOFTWARE	HIS A:177 , LYS A:181	BINDING SITE FOR RESIDUE SO4 A 342
3	AC3	SOFTWARE	GLU A:47 , TYR A:251 , ILE A:254 , ASN A:286 , ILE A:289 , GLN A:290 , HOH A:480	BINDING SITE FOR RESIDUE SO4 A 343
4	AC4	SOFTWARE	HIS C:89 , PRO C:90 , GLN C:91 , TYR C:92 , TYR C:133	BINDING SITE FOR RESIDUE SO4 C 341
5	AC5	SOFTWARE	ALY C:25 , HIS C:89	BINDING SITE FOR RESIDUE SO4 C 342

(no "SS Bond" information available for 2R0V)

(no "Cis Peptide Bond" information available for 2R0V)

(no "SAP(SNP)/Variant" information available for 2R0V)

Asymmetric Unit (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	RSC4_YEAST	72-141 205-275	6	A:72-141 B:72-141 C:72-141 A:205-275 B:205-275 C:205-275
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	RSC4_YEAST	77-133 210-267	6	A:77-133 B:77-133 C:77-133 A:210-267 B:210-267 C: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 -

Biological Unit 3 (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	- - C:72-141 - - C:205-275
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	RSC4_YEAST	77-133 210-267	2	- - C:77-133 - - C:210-267

Asymmetric Unit (1, 3)

	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	3	A:19-311 B:23-310 (gaps) C:23-313	293 288 291

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
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   
           RSC4_YEAST    19 PKYLPGKHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFD 311
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------2r0vA01 A:46-159 Histone Acetyltransferase; Chain A                                                               2r0vA02 A:160-304 Histone Acetyltransferase; Chain A                                                                                             ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........................hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhh......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:19-311 UniProt: 1-625 [INCOMPLETE]                                                                                                                                                                                                                                                   Transcript 1
                 2r0v A  19 PKYLPGkHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFD 311
                                  | 28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   
                                 25-ALY

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with RSC4_YEAST | Q02206 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:288
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
           RSC4_YEAST    23 PGKHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEF 310
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -----------------------2r0vB01 B:46-159 Histone Acetyltransferase; Chain A                                                               2r0vB02 B:160-304 Histone Acetyltransferase; Chain A                                                                                             ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........--.............hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh......hhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhh.............hhhhh.........hhhhhh....hhhhhhhhhhh....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:23-310 (gaps) UniProt: 1-625 [INCOMPLETE]                                                                                                                                                                                                                                       Transcript 1
                 2r0v B  23 PGkHPKNQ--TPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEF 310
                              |    | -|       42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302        
                             25-ALY0 33

Chain C from PDB  Type:PROTEIN  Length:291
 aligned with RSC4_YEAST | Q02206 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:291
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312 
           RSC4_YEAST    23 PGKHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKF 313
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------2r0vC01 C:46-159 Histone Acetyltransferase; Chain A                                                               2r0vC02 C:160-304 Histone Acetyltransferase; Chain A                                                                                             --------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0vC01 C:201-280                                                   --------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0vC02 C:201-280                                                   --------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0vC03 C:201-280                                                   --------------------------------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0vC04 C:201-280                                                   --------------------------------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0vC05 C:201-280                                                   --------------------------------- Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Bromodomain-2r0vC06 C:201-280                                                   --------------------------------- Pfam domains (6)
         Sec.struct. author .......................hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhh.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------BROMODOMAIN_2  PDB: C:72-141 UniProt: 72-141                          ---------------------------------------------------------------BROMODOMAIN_2  PDB: C:205-275 UniProt: 205-275                         -------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------BROMODOMAIN_1  PDB: C:77-133 UniProt: 77-133             ----------------------------------------------------------------------------BROMODOMAIN_1  PDB: C:210-267 UniProt: 210-267            ---------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1  PDB: C:23-313 UniProt: 1-625 [INCOMPLETE]                                                                                                                                                                                                                                                 Transcript 1
                 2r0v C  23 PGkHPKNQEKTPHVDYNAPLNPKSELFLDDWHIPKFNRFISFTLDVLIDKYKDIFKDFIKLPSRKFHPQYYYKIQQPMSINEIKSRDYEYEDGPSNFLLDVELLTKNCQAYNEYDSLIVKNSMQVVMLIEFEVLKAKNLKRNYLINSEVKAKLLHYLNKLVDATEKKINQALLGASSPKNLDDKVKLSEPFMELVDKDELPEYYEIVHSPMALSIVKQNLEIGQYSKIYDFIIDMLLVFQNAHIFNDPSALIYKDATTLTNYFNYLIQKEFFPELQDLNERGEINLEFDKF 313
                              |     32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312 
                             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 2R0V)

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	2r0vA01	A:46-159
1b	2r0vA02	A:160-304
1c	2r0vB02	B:160-304
1d	2r0vC02	C:160-304
1e	2r0vB01	B:46-159
1f	2r0vC01	C:46-159

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-2r0vC01	C:201-280
1b	Bromodomain-2r0vC02	C:201-280
1c	Bromodomain-2r0vC03	C:201-280
1d	Bromodomain-2r0vC04	C:201-280
1e	Bromodomain-2r0vC05	C:201-280
1f	Bromodomain-2r0vC06	C:201-280

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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 Unit
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	RSC4_YEAST \| Q02206	:	2r0s 2r0y 2r10

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (1, 3)

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