3UVY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX WITH A DIACETYLATED HISTONE 4 PEPTIDE (H4K16ACK20AC)

Authors :   P. Filippakopoulos, I. Felletar, S. Picaud, T. Keates, J. Muniz, O. Gil F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, Structural Genomics Consortium (Sgc)

Date :   30 Nov 11 (Deposition) - 18 Jan 12 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.02

Chains :   Asym./Biol. Unit : A,B

Keywords :   Bromodomain, Bromodomain Containing Protein 4, Cap, Hunk1, Mcap, Mitotic Chromosome Associated Protein, Peptide Complex, Structural Genomics Consortium, Sgc, Transcription, Transcription-Protein Binding Complex (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

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)-R3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 44-168
	Gene	:	BRD4, HUNK1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN HUNK1

Molecule 2 - HISTONE H4
	Chains	:	B
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 16-26
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PEPTIDE (H4K16ACK20AC)
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE

(no "Site" information available for 3UVY)

(no "SS Bond" information available for 3UVY)

(no "Cis Peptide Bond" information available for 3UVY)

(no "SAP(SNP)/Variant" information available for 3UVY)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD4_HUMAN	75-147 368-440	1	A:75-147 -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD4_HUMAN	80-139	1	A:80-139

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000263377	1	ENSE00001113198	chr19:15391262-15391075	188	BRD4_HUMAN	-	0	0	-	-
1.2	ENST00000263377	2	ENSE00001113202	chr19:15383944-15383626	319	BRD4_HUMAN	1-95	95	1	A:59-95	37
1.3	ENST00000263377	3	ENSE00000689046	chr19:15379853-15379716	138	BRD4_HUMAN	96-141	46	1	A:96-141	46
1.4	ENST00000263377	4	ENSE00000689047	chr19:15378362-15378227	136	BRD4_HUMAN	142-187	46	1	A:142-167	26
1.5	ENST00000263377	5	ENSE00000689048	chr19:15376454-15376165	290	BRD4_HUMAN	187-283	97	0	-	-
1.6	ENST00000263377	6	ENSE00000348853	chr19:15375577-15375215	363	BRD4_HUMAN	284-404	121	0	-	-
1.7	ENST00000263377	7	ENSE00000689050	chr19:15374359-15374231	129	BRD4_HUMAN	405-447	43	0	-	-
1.8	ENST00000263377	8	ENSE00000689051	chr19:15367984-15367775	210	BRD4_HUMAN	448-517	70	0	-	-
1.9	ENST00000263377	9	ENSE00000689052	chr19:15367074-15366875	200	BRD4_HUMAN	518-584	67	0	-	-
1.10	ENST00000263377	10	ENSE00000689053	chr19:15366403-15366108	296	BRD4_HUMAN	584-683	100	0	-	-
1.11	ENST00000263377	11	ENSE00001187704	chr19:15365073-15364963	111	BRD4_HUMAN	683-720	38	0	-	-
1.15	ENST00000263377	15	ENSE00001113203	chr19:15355573-15355521	53	BRD4_HUMAN	720-737	18	0	-	-
1.16	ENST00000263377	16	ENSE00001055985	chr19:15355411-15355042	370	BRD4_HUMAN	738-861	124	0	-	-
1.17	ENST00000263377	17	ENSE00001055976	chr19:15354298-15353711	588	BRD4_HUMAN	861-1057	197	0	-	-
1.18	ENST00000263377	18	ENSE00001136676	chr19:15350833-15350721	113	BRD4_HUMAN	1057-1094	38	0	-	-
1.19	ENST00000263377	19	ENSE00001113200	chr19:15350632-15350470	163	BRD4_HUMAN	1095-1149	55	0	-	-
1.20	ENST00000263377	20	ENSE00001113199	chr19:15350333-15350203	131	BRD4_HUMAN	1149-1192	44	0	-	-
1.21	ENST00000263377	21	ENSE00000951121	chr19:15350075-15349870	206	BRD4_HUMAN	1193-1261	69	0	-	-
1.22	ENST00000263377	22	ENSE00000951122	chr19:15349791-15349554	238	BRD4_HUMAN	1261-1340	80	0	-	-
1.23	ENST00000263377	23	ENSE00001055981	chr19:15349256-15348301	956	BRD4_HUMAN	1341-1362	22	0	-	-

2.1	ENST00000377803	1	ENSE00001475159	chr6:26104104-26104518	415	H4_HUMAN	1-127	127	1	B:15-24	10

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)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:109
 aligned with BRD4_HUMAN | O60885 from UniProtKB/Swiss-Prot  Length:1362

    Alignment length:109
                                    68        78        88        98       108       118       128       138       148       158         
           BRD4_HUMAN    59 QTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTE 167
               SCOP domains d3uvya_ A: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------BROMODOMAIN_2  PDB: A:75-147 UniProt: 75-147                             -------------------- PROSITE (1)
                PROSITE (2) ---------------------BROMODOMAIN_1  PDB: A:80-139 UniProt: 80-139                ---------------------------- PROSITE (2)
               Transcript 1 Exon 1.2  PDB: A:59-95 UniProt: 1-95 Exon 1.3  PDB: A:96-141 UniProt: 96-141       Exon 1.4  PDB: A:142-167   Transcript 1
                 3uvy A  59 QTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTE 167
                                    68        78        88        98       108       118       128       138       148       158

Chain B from PDB  Type:PROTEIN  Length:10
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:10
                                    25
             H4_HUMAN    16 AKRHRKVLRD  25
               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 2 Exon 2.1   Transcript 2
                 3uvy B  15 AkRHRkVLRD  24
                             |   |  24
                            16-ALY    
                                20-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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: Bromodomain-like (339)

Superfamily: Bromodomain (203)

Family: automated matches (169)

Protein domain: automated matches (169)

Human (Homo sapiens) [TaxId: 9606] (162)

d3uvya_

(no "CATH Domain" information available for 3UVY)

(no "Pfam Domain" information available for 3UVY)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (BRD4_HUMAN | O60885)

molecular function
	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:0070577	lysine-acetylated histone binding	Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
	GO:0002039	p53 binding	Interacting selectively and non-covalently with one of the p53 family of proteins.
	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:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	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:2000002	negative regulation of DNA damage checkpoint	Any process that stops, prevents, or reduces the frequency, rate or extent of a DNA damage checkpoint.
	GO:0010971	positive regulation of G2/M transition of mitotic cell cycle	Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
	GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
	GO:1901407	regulation of phosphorylation of RNA polymerase II C-terminal domain	Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain.
	GO:0000083	regulation of transcription involved in G1/S transition of mitotic cell cycle	Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
	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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000794	condensed nuclear chromosome	A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Chain B (H4_HUMAN | P62805)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042393	histone binding	Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
	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).
	GO:0019904	protein domain specific binding	Interacting selectively and non-covalently with a specific domain of a protein.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0034080	CENP-A containing nucleosome assembly	The formation of nucleosomes containing the histone H3 variant CENP-A to form centromeric chromatin. This specialised chromatin occurs at centromeric region in point centromeres, and the central core in modular centromeres.
	GO:0006335	DNA replication-dependent nucleosome assembly	The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
	GO:0006336	DNA replication-independent nucleosome assembly	The formation of nucleosomes outside the context of DNA replication.
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:1904837	beta-catenin-TCF complex assembly	The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
	GO:0044267	cellular protein metabolic process	The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
	GO:0000183	chromatin silencing at rDNA	Repression of transcription of ribosomal DNA by altering the structure of chromatin.
	GO:0006303	double-strand break repair via nonhomologous end joining	The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0045814	negative regulation of gene expression, epigenetic	Any epigenetic process that stops, prevents or reduces the rate of gene expression.
	GO:0045653	negative regulation of megakaryocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
	GO:0006334	nucleosome assembly	The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
	GO:0045815	positive regulation of gene expression, epigenetic	Any epigenetic process that activates or increases the rate of gene expression.
	GO:0051290	protein heterotetramerization	The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
	GO:0016233	telomere capping	A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
	GO:0032200	telomere organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
cellular component
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0000784	nuclear chromosome, telomeric region	The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0000786	nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
	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.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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