2KTB - JenaLib

Title :   SOLUTION STRUCTURE OF THE SECOND BROMODOMAIN OF HUMAN POLYBROMO IN COMPLEX WITH AN ACETYLATED PEPTIDE FROM HISTONE 3

Authors :   Z. Charlop-Powers, Q. Zhang, L. Zeng

Date :   26 Jan 10 (Deposition) - 12 May 10 (Release) - 19 May 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Bromodomain, Alternative Splicing, Chromatin Regulator, Dna-Binding, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Charlop-Powers, L. Zeng, Q. Zhang, M. M. Zhou
Structural Insights Into Selective Histone H3 Recognition By The Human Polybromo Bromodomain 2.
Cell Res. V. 20 529 2010
PubMed-ID: 20368734 | Reference-DOI: 10.1038/CR.2010.43

Compounds

Molecule 1 - H3_PEPTIDE
	Chains	:	A
	Engineered	:	YES
	Fragment	:	H3(1-20)K14AC
	Mutation	:	YES
	Synthetic	:	YES

Molecule 2 - PROTEIN POLYBROMO-1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Fragment	:	POLYBROMO BROMDOMAIN 2
	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 (1, 1)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 7)

NMR Structure (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_064660	R	202	C	PB1_HUMAN	Polymorphism	765525545	B	R	202	C
2	UniProt	VAR_064661	E	206	K	PB1_HUMAN	Unclassified	---	B	E	206	K
3	UniProt	VAR_064662	E	226	G	PB1_HUMAN	Unclassified	---	B	E	226	G
4	UniProt	VAR_064663	I	228	V	PB1_HUMAN	Polymorphism	201022657	B	I	228	V
5	UniProt	VAR_064664	T	232	P	PB1_HUMAN	Unclassified	---	B	T	232	P
6	UniProt	VAR_064665	I	233	T	PB1_HUMAN	Unclassified	---	B	I	233	T
7	UniProt	VAR_064666	A	256	T	PB1_HUMAN	Polymorphism	776146971	B	A	256	T

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

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

NMR Structure

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:20
                                                    
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .................... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 2ktb A   1 ARTKQTARKSTGGkAPRKQL  20
                                    10   |    20
                                        14-ALY

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

    Alignment length:121
                                   182       192       202       212       222       232       242       252       262       272       282       292 
            PB1_HUMAN   173 VTEGSSPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEHHEMA 293
               SCOP domains d2ktbb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Bromodomain-2ktbB01 B:186-275                                                             ------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh.......hhhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------C---K-------------------G-V---PT----------------------T------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------BROMODOMAIN_2  PDB: B:200-270 UniProt: 200-270                         ----------------------- PROSITE (1)
                PROSITE (2) --------------------------------BROMODOMAIN_1  PDB: B:205-262 UniProt: 205-262            ------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ktb B 173 STEGSSPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEHHEMA 293
                                   182       192       202       212       222       232       242       252       262       272       282       292

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, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

NMR Structure(hide GO term definitions)

Chain 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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