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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN BRD2 SECOND BROMODOMAIN IN COMPLEXED WITH THE ACETYLATED HISTONE H4 PEPTIDE

Authors :   B. Padmanabhan, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   27 Nov 06 (Deposition) - 11 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,Q,R
Biol. Unit 1: A,C,Q  (1x)
Biol. Unit 2: B,D,R  (1x)

Keywords :   Bromodomain, Binds To Acetylated Histone Tails, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Padmanabhan, T. Umehara, K. Nakano, M. K. Jang, K. Ozato, S. Yokohama
Structural Basis For Diacetylated Histone H4 Tail Recognition By The Second Bromodomain Of Human Brd2
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 2
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	THE SECOND BROMODOMAIN, BD2, RESIDUES 348-455
	Gene	:	BRD2, KIAA9001, RING3
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROTEIN RING3, O27.1.1

Molecule 2 - 15-MER PEPTIDE FROM HISTONE H4
	Chains	:	Q, R
	Engineered	:	YES
	Fragment	:	N-TERMINAL H4 DI-ACETYLATED TAIL
	Other Details	:	SYNTHETIC PEPTIDE. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN OTHER SOURCE ORGANISM IN ADDITION TO BAKER'S YEAST REFERED IN DBREF RECORD.
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	Q	R
Biological Unit 1 (1x)	:	A		C		Q
Biological Unit 2 (1x)	:		B		D		R

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ALY	4	Mod. Amino Acid	N(6)-ACETYLLYSINE

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

(no "Site" information available for 2E3K)

(no "SS Bond" information available for 2E3K)

(no "Cis Peptide Bond" information available for 2E3K)

(no "SAP(SNP)/Variant" information available for 2E3K)

Asymmetric Unit (3, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H4	PS00047	Histone H4 signature.	H4_YEAST	15-19	2	Q:14-15 R:14-15
2	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD2_HUMAN	91-163 364-436	4	- A:364-436 B:364-436 C:364-436 D:364-436
3	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD2_HUMAN	96-155 369-428	4	- A:369-428 B:369-428 C:369-428 D:369-428

Biological Unit 1 (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H4	PS00047	Histone H4 signature.	H4_YEAST	15-19	1	Q:14-15 -
2	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD2_HUMAN	91-163 364-436	2	- A:364-436 - C:364-436 -
3	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD2_HUMAN	96-155 369-428	2	- A:369-428 - C:369-428 -

Biological Unit 2 (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H4	PS00047	Histone H4 signature.	H4_YEAST	15-19	1	- R:14-15
2	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD2_HUMAN	91-163 364-436	2	- - B:364-436 - D:364-436
3	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD2_HUMAN	96-155 369-428	2	- - B:369-428 - D:369-428

Asymmetric Unit (4, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.7b	ENST00000399529	7b	ENSE00001705137	HSCHR6_MHC_QBL:32865184-32865580	397	BRD2_HUMAN	-	0	0	-	-
1.13b	ENST00000399529	13b	ENSE00002152230	HSCHR6_MHC_QBL:32868119-32869451	1333	BRD2_HUMAN	1-10	10	0	-	-
1.16e	ENST00000399529	16e	ENSE00001730437	HSCHR6_MHC_QBL:32870986-32871289	304	BRD2_HUMAN	10-111	102	0	-	-
1.17	ENST00000399529	17	ENSE00001742408	HSCHR6_MHC_QBL:32871904-32872041	138	BRD2_HUMAN	112-157	46	0	-	-
1.18a	ENST00000399529	18a	ENSE00001669691	HSCHR6_MHC_QBL:32872548-32872686	139	BRD2_HUMAN	158-204	47	0	-	-
1.19	ENST00000399529	19	ENSE00001606367	HSCHR6_MHC_QBL:32872768-32872982	215	BRD2_HUMAN	204-275	72	0	-	-
1.20b	ENST00000399529	20b	ENSE00002150037	HSCHR6_MHC_QBL:32873080-32873454	375	BRD2_HUMAN	276-400	125	4	A:348-400 B:1-400 (gaps) C:348-400 D:2-400 (gaps)	53 63 53 55
1.20g	ENST00000399529	20g	ENSE00001741071	HSCHR6_MHC_QBL:32873960-32874088	129	BRD2_HUMAN	401-443	43	4	A:401-443 B:401-443 C:401-443 D:401-443	43 43 43 43
1.21b	ENST00000399529	21b	ENSE00001731564	HSCHR6_MHC_QBL:32874275-32874523	249	BRD2_HUMAN	444-526	83	4	A:444-455 B:444-455 C:444-455 D:444-455	12 12 12 12
1.22c	ENST00000399529	22c	ENSE00001594402	HSCHR6_MHC_QBL:32874644-32874906	263	BRD2_HUMAN	527-614	88	0	-	-
1.24c	ENST00000399529	24c	ENSE00001800691	HSCHR6_MHC_QBL:32876345-32876649	305	BRD2_HUMAN	614-716	103	0	-	-
1.24d	ENST00000399529	24d	ENSE00001781532	HSCHR6_MHC_QBL:32876859-32876981	123	BRD2_HUMAN	716-757	42	0	-	-
1.25d	ENST00000399529	25d	ENSE00001732199	HSCHR6_MHC_QBL:32877099-32878022	924	BRD2_HUMAN	757-801	45	0	-	-

2.1	YNL030W	1	YNL030W.1	XIV:576729-577040	312	H4_YEAST	1-103	103	2	Q:1-15 R:3-15	15 13

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:108
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:108
                                   357       367       377       387       397       407       417       427       437       447        
           BRD2_HUMAN   348 EQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------BROMODOMAIN_2  PDB: A:364-436 UniProt: 364-436                           ------------------- PROSITE (1)
                PROSITE (2) ---------------------BROMODOMAIN_1  PDB: A:369-428 UniProt: 369-428              --------------------------- PROSITE (2)
               Transcript 1 Exon 1.20b  PDB: A:348-400 UniProt: 276-400          Exon 1.20g  PDB: A:401-443 UniProt: 401-443Exon 1.21b   Transcript 1
                 2e3k A 348 EQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
                                   357       367       377       387       397       407       417       427       437       447

Chain B from PDB  Type:PROTEIN  Length:110
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:118
                                   347       357       367       377       387       397       407       417       427       437       447        
           BRD2_HUMAN   338 HQSSKKGKLSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h--------hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------BROMODOMAIN_2  PDB: B:364-436 UniProt: 364-436                           ------------------- PROSITE (1)
                PROSITE (2) -------------------------------BROMODOMAIN_1  PDB: B:369-428 UniProt: 369-428              --------------------------- PROSITE (2)
               Transcript 1 Exon 1.20b  PDB: B:1-400 (gaps) UniProt: 276-400 [INCOMPLETE]  Exon 1.20g  PDB: B:401-443 UniProt: 401-443Exon 1.21b   Transcript 1
                 2e3k B   1 HM--------EQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
                             |       -|      357       367       377       387       397       407       417       427       437       447        
                             2      348

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:108
                                   357       367       377       387       397       407       417       427       437       447        
           BRD2_HUMAN   348 EQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------BROMODOMAIN_2  PDB: C:364-436 UniProt: 364-436                           ------------------- PROSITE (1)
                PROSITE (2) ---------------------BROMODOMAIN_1  PDB: C:369-428 UniProt: 369-428              --------------------------- PROSITE (2)
               Transcript 1 Exon 1.20b  PDB: C:348-400 UniProt: 276-400          Exon 1.20g  PDB: C:401-443 UniProt: 401-443Exon 1.21b   Transcript 1
                 2e3k C 348 EQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
                                   357       367       377       387       397       407       417       427       437       447

Chain D from PDB  Type:PROTEIN  Length:109
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:110
                                   355       365       375       385       395       405       415       425       435       445       455
           BRD2_HUMAN   346 LSEQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author h-hhhhhhhhhhhhhhh..hhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------BROMODOMAIN_2  PDB: D:364-436 UniProt: 364-436                           ------------------- PROSITE (1)
                PROSITE (2) -----------------------BROMODOMAIN_1  PDB: D:369-428 UniProt: 369-428              --------------------------- PROSITE (2)
               Transcript 1 Exon 1.20b  PDB: D:2-400 (gaps) UniProt: 276-400       Exon 1.20g  PDB: D:401-443 UniProt: 401-443Exon 1.21b   Transcript 1
                 2e3k D   2 M-EQLKHCNGILKELLSKKHAAYAWPFYKPVDASALGLHDYHDIIKHPMDLSTVKRKMENRDYRDAQEFAADVRLMFSNCYKYNPPDHDVVAMARKLQDVFEFRYAKMPD 455
                            | |    355       365       375       385       395       405       415       425       435       445       455
                            2 |                                                                                                           
                            348

Chain Q from PDB  Type:PROTEIN  Length:15
 aligned with H4_YEAST | P02309 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:15
                                    11     
             H4_YEAST     2 SGRGKGGKGLGKGGA  16
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE -------------HI PROSITE
               Transcript 2 Exon 2.1        Transcript 2
                 2e3k Q   1 SGRGkGGKGLGkGGA  15
                                |   10 |   
                                5-ALY 12-ALY

Chain R from PDB  Type:PROTEIN  Length:13
 aligned with H4_YEAST | P02309 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:13
                                    13   
             H4_YEAST     4 RGKGGKGLGKGGA  16
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE -----------HI PROSITE
               Transcript 2 Exon 2.1      Transcript 2
                 2e3k R   3 RGkGGKGLGkGGA  15
                              |     12   
                              5-ALY 12-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 '\|'

(no "SCOP Domain" information available for 2E3K)

(no "CATH Domain" information available for 2E3K)

(no "Pfam Domain" information available for 2E3K)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (BRD2_HUMAN | P25440)

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: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: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:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007283	spermatogenesis	The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular 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.

Chain Q,R (H4_YEAST | P02309)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006333	chromatin assembly or disassembly	The formation or destruction of chromatin structures.
	GO:0034729	histone H3-K79 methylation	The modification of histone H3 by addition of a methyl group to lysine at position 79 of the histone.
	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:0043935	sexual sporulation resulting in formation of a cellular spore	The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
	GO:0061587	transfer RNA gene-mediated silencing	The chromatin silencing that results in the inhibition of RNA polymerase II-transcribed genes located in the vicinity of tRNA genes.
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:0000788	nuclear nucleosome	A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
	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:0031298	replication fork protection complex	A protein complex conserved in eukaryotes and associated with the replication fork; the complex stabilizes stalled replication forks and is thought to be involved in coordinating leading- and lagging-strand synthesis and in replication checkpoint signaling.

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2dvv	NATIVE STRUCTURE RELATED ID: HSO003006073.1 RELATED DB: TARGETDB

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