3IU5 - JenaLib

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

Authors :   P. Filippakopoulos, S. Picaud, T. Keates, E. Ugochukwu, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. Knapp, Stru Genomics Consortium (Sgc)

Date :   30 Aug 09 (Deposition) - 22 Sep 09 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

Chains :   Asym./Biol. Unit : A

Keywords :   Pb1, Polybromo 1 Isoform 1, Baf180, Polybromo0Id, Pbrm1, Brg1- Associated Factor 180, Structural Genomics, Sgc, Structural Genomics Consortium, Bromodomain, Chromatin Regulator, Dna-Binding, Nucleus, Phosphoprotein, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Filippakopoulos, S. Picaud, M. Mangos, T. Keates, J. P. Lambert, D. Barsyte-Lovejoy, I. Felletar, R. Volkmer, S. Muller, T. Pawson, A. C. Gingras, C. H. Arrowsmith, S. Knapp
Histone Recognition And Large-Scale Structural Analysis Of The Human Bromodomain Family.
Cell(Cambridge, Mass. ) V. 149 214 2012
PubMed-ID: 22464331 | Reference-DOI: 10.1016/J.CELL.2012.02.013

Compounds

Molecule 1 - PROTEIN POLYBROMO-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)-R3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PB1, PBRM1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HPB1, POLYBROMO-1D, BRG1-ASSOCIATED FACTOR 180, BAF180

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_064653	V	49	L	PB1_HUMAN	Unclassified	---	A	V	49	L
2	UniProt	VAR_064654	T	56	A	PB1_HUMAN	Unclassified	---	A	T	56	A
3	UniProt	VAR_064656	R	66	G	PB1_HUMAN	Polymorphism	368888772	A	R	66	G
4	UniProt	VAR_064657	Q	90	E	PB1_HUMAN	Unclassified	---	A	Q	90	E
5	UniProt	VAR_064658	Y	144	F	PB1_HUMAN	Unclassified	---	A	Y	144	F

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (2, 2)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:114
 aligned with PB1_HUMAN | Q86U86 from UniProtKB/Swiss-Prot  Length:1689

    Alignment length:116
                                    48        58        68        78        88        98       108       118       128       138       148      
            PB1_HUMAN    39 SNLPTVDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQK 154
               SCOP domains d  3iu5a_ A: automated matches                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--...hhhhhhhhhhhhhhhh......hhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------L------A---------G-----------------------E-----------------------------------------------------F---------- SAPs(SNPs)
                PROSITE (1) -------------------------BROMODOMAIN_2  PDB: A:64-134 UniProt: 64-134                           -------------------- PROSITE (1)
                PROSITE (2) ---------------------------------BROMODOMAIN_1  PDB: A:72-126 UniProt: 72-126           ---------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3iu5 A  41 S--MTVDPIAVCHELYNTIRDYKDEQGRLLCELFIRAPKRRNQPDYYEVVSQPIDLMKIQQKLKMEEYDDVNLLTADFQLLFNNAKSYYKPDSPEYKAACKLWDLYLRTRNEFVQK 154
                            |  |    48        58        68        78        88        98       108       118       128       138       148      
                            | 42                                                                                                                
                           41

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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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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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