3K2J - JenaLib

Title :   CRYSTAL STRUCTURE OF THE 3RD BROMODOMAIN OF HUMAN POLY-BROMODOMAIN CONTAINING PROTEIN 1 (PB1)

Authors :   P. Filippakopoulos, S. Picaud, T. Keates, A. Chaikuad, A. C. W. Pike, T. R. Sethi, F. Von Delft, C. H. Arrowsmith, A. Edwards, J. Weigelt, C. Bo S. Knapp, Structural Genomics Consortium (Sgc)

Date :   30 Sep 09 (Deposition) - 13 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Pb1, Polybromo 1 Isoform 1, Baf180, Polybromo01D, Pbrm1, Brg1- Associated Factor 180, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Filippakopoulos, S. Picaud, T. Keates, A. Chaikuad, A. C. W. Pike, T. Krojer, R. Sethi, F. Von Delft, C. H. Arrowsmith, A. Edwards, J. Weigelt, C. Bountra, S. Knapp
Crystal Structure Of The 3Rd Bromodomain Of Human Poly-Bromodomain Containing Protein 1 (Pb1)
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	PB1_HUMAN	64-134 200-270 400-470 538-608 676-746 817-862	2	- - A:368-438 B:368-438 - - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	PB1_HUMAN	72-126 205-262 405-462 548-600 681-738	2	- - A:373-430 B:373-430 - -

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	PB1_HUMAN	64-134 200-270 400-470 538-608 676-746 817-862	1	- - A:368-438 - - - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	PB1_HUMAN	72-126 205-262 405-462 548-600 681-738	1	- - A:373-430 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	PB1_HUMAN	64-134 200-270 400-470 538-608 676-746 817-862	1	- - - B:368-438 - - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	PB1_HUMAN	72-126 205-262 405-462 548-600 681-738	1	- - - B:373-430 - -

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	PB1_HUMAN	64-134 200-270 400-470 538-608 676-746 817-862	2	- - A:368-438 B:368-438 - - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	PB1_HUMAN	72-126 205-262 405-462 548-600 681-738	2	- - A:373-430 B:373-430 - -

Exons (0, 0)

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:121
 aligned with PB1_HUMAN | Q86U86 from UniProtKB/Swiss-Prot  Length:1689

    Alignment length:183
                                   321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491   
            PB1_HUMAN   312 GPSHSKGSLGEERNPTSKYYRNKRAVQGGRLSAITMALQYGSESEEDAALAAARYEEGESEAESITSFMDVSNPFYQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARRDDIE 494
               SCOP domains d     3k2ja_     A: au                                                     tomated matches                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----..hhhhh----hhhhh-----------------------------------------------------hhhhhhhhh.........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------BROMODOMAIN_2  PDB: A:368-438 UniProt: 400-470                         ------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------BROMODOMAIN_1  PDB: A:373-430 UniProt: 405-462            -------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2j A 342 G-----VDLGTEN----LYFQS-----------------------------------------------------MQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARRDDIE 462
                            |     |346  |    352 |       -         -         -         -         -     | 359       369       379       389       399       409       419       429       439       449       459   
                            |   343   349  350 354                                                   355                                                                                                           
                          342

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PB1_HUMAN | Q86U86 from UniProtKB/Swiss-Prot  Length:1689

    Alignment length:183
                                   321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491   
            PB1_HUMAN   312 GPSHSKGSLGEERNPTSKYYRNKRAVQGGRLSAITMALQYGSESEEDAALAAARYEEGESEAESITSFMDVSNPFYQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARRDDIE 494
               SCOP domains d     3k2jb_     B: au                                                     tomated matches                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .-----..hhhhh----hhhhh-----------------------------------------------------hhhhhhhhh.........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------BROMODOMAIN_2  PDB: B:368-438 UniProt: 400-470                         ------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------BROMODOMAIN_1  PDB: B:373-430 UniProt: 405-462            -------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2j B 342 G-----VDLGTEN----LYFQS-----------------------------------------------------MQLYDTVRSCRNNQGQLIAEPFYHLPSKKKYPDYYQQIKMPISLQQIRTKLKNQEYETLDHLECDLNLMFENAKRYNVPNSAIYKRVLKLQQVMQAKKKELARRDDIE 462
                            |     |346  |    352 |       -         -         -         -         -     | 359       369       379       389       399       409       419       429       439       449       459   
                          342   343   349  350 354                                                   355

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 (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PB1_HUMAN | Q86U86)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	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: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:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	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:0090544	BAF-type complex	A SWI/SNF-type complex that contains a subunit from the BAF (Brahma-Associated Factor) family.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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