3HMF - JenaLib

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

Authors :   P. Filippakopoulos, S. Picaud, T. Keates, J. Muniz, F. Von Delft, C. H. Arrowsmith, A. Edwards, J. Weigelt, C. Bountra, S. Knapp

Date :   29 May 09 (Deposition) - 23 Jun 09 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.63

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

Keywords :   Pb1, Polybromo 1 Isoform 1, Baf180, Polybromo-1D, Pbrm1, Brg1- Associated Factor 180, Bromodomain, Chromatin Regulator, Dna- Binding, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Structural Genomics, Structural Genomics Consortium, Sgc (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
	Fragment	:	BROMODOMAIN, UNP RESIDUES 178-291
	Gene	:	PB1, PBRM1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PB1, HPB1, POLYBROMO-1D, BRG1-ASSOCIATED FACTOR 180, BAF180

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:246 , HIS A:289 , CL A:293 , CL A:294	BINDING SITE FOR RESIDUE ZN A 1
2	AC2	SOFTWARE	GLU A:184 , GLU A:187 , HIS A:290 , GLU A:291	BINDING SITE FOR RESIDUE ZN A 2
3	AC3	SOFTWARE	HOH A:10 , TYR A:281 , LYS A:284 , ALA A:285 , GLU A:288 , CL A:293 , HOH A:321	BINDING SITE FOR RESIDUE EDO A 292
4	AC4	SOFTWARE	ZN A:1 , HIS A:246 , LYS A:284 , HIS A:289 , EDO A:292	BINDING SITE FOR RESIDUE CL A 293
5	AC5	SOFTWARE	ZN A:1 , HIS A:246 , HIS A:289	BINDING SITE FOR RESIDUE CL A 294

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 7)

Asymmetric Unit (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	A	R	202	C
2	UniProt	VAR_064661	E	206	K	PB1_HUMAN	Unclassified	---	A	E	206	K
3	UniProt	VAR_064662	E	226	G	PB1_HUMAN	Unclassified	---	A	E	226	G
4	UniProt	VAR_064663	I	228	V	PB1_HUMAN	Polymorphism	201022657	A	I	228	V
5	UniProt	VAR_064664	T	232	P	PB1_HUMAN	Unclassified	---	A	T	232	P
6	UniProt	VAR_064665	I	233	T	PB1_HUMAN	Unclassified	---	A	I	233	T
7	UniProt	VAR_064666	A	256	T	PB1_HUMAN	Polymorphism	776146971	A	A	256	T

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

Biological Unit 1 (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	A	R	202	C
2	UniProt	VAR_064661	E	206	K	PB1_HUMAN	Unclassified	---	A	E	206	K
3	UniProt	VAR_064662	E	226	G	PB1_HUMAN	Unclassified	---	A	E	226	G
4	UniProt	VAR_064663	I	228	V	PB1_HUMAN	Polymorphism	201022657	A	I	228	V
5	UniProt	VAR_064664	T	232	P	PB1_HUMAN	Unclassified	---	A	T	232	P
6	UniProt	VAR_064665	I	233	T	PB1_HUMAN	Unclassified	---	A	I	233	T
7	UniProt	VAR_064666	A	256	T	PB1_HUMAN	Polymorphism	776146971	A	A	256	T

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

Biological Unit 2 (7, 14)

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

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

PROSITE Motifs (2, 2)

Asymmetric Unit (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:200-270 - - - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	PB1_HUMAN	72-126 205-262 405-462 548-600 681-738	1	- A:205-262 - - -

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:200-270 - - - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	PB1_HUMAN	72-126 205-262 405-462 548-600 681-738	1	- A:205-262 - - -

Biological Unit 2 (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:200-270 - - - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	PB1_HUMAN	72-126 205-262 405-462 548-600 681-738	2	- A:205-262 - - -

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
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Chain A from PDB  Type:PROTEIN  Length:116
 aligned with PB1_HUMAN | Q86U86 from UniProtKB/Swiss-Prot  Length:1689

    Alignment length:116
                                   185       195       205       215       225       235       245       255       265       275       285      
            PB1_HUMAN   176 GSSPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEHHE 291
               SCOP domains d3hmfa_ A: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh........hhhhh.......hhhhhhhh....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------C---K-------------------G-V---PT----------------------T----------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------BROMODOMAIN_2  PDB: A:200-270 UniProt: 200-270                         --------------------- PROSITE (1)
                PROSITE (2) -----------------------------BROMODOMAIN_1  PDB: A:205-262 UniProt: 205-262            ----------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3hmf A 176 SMSPAYLKEILEQLLEAIVVATNPSGRLISELFQKLPSKVQYPDYYAIIKEPIDLKTIAQRIQNGSYKSIHAMAKDIDLLAKNAKTYNEPGSQVFKDANSIKKIFYMKKAEIEHHE 291
                                   185       195       205       215       225       235       245       255       265       275       285

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 (0, 0)

Gene Ontology (11, 11)

Asymmetric 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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