2DVQ - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF THE N-TERMINAL BROMODOMAIN OF HUMAN BRD2 COMPLEXED WITH ACETYLATED HISTONE H4 PEPTIDE

Authors :   Y. Nakamura, T. Umehara, M. Shirouzu, B. Padmanabhan, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   01 Aug 06 (Deposition) - 07 Aug 07 (Release) - 16 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

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

Keywords :   Alpha-Helical Domain, Bromodomain, Binds To Acetylated Histones, 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 :   T. Umehara, Y. Nakamura, M. K. Jang, K. Nakano, A. Tanaka, K. Ozato, B. Padmanabhan, S. Yokoyama
Structural Basis For Acetylated Histone H4 Recognition By The Human Brd2 Bromodomain.
J. Biol. Chem. V. 285 7610 2010
PubMed-ID: 20048151 | Reference-DOI: 10.1074/JBC.M109.062422

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 2
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCR2.1-TOPO VECTOR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL BROMODOMAIN, BD1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	EXPRESSED BY CELL-FREE SYSTEM
	Synonym	:	RING3 PROTEIN, O27.1.1

Molecule 2 - HISTONE H4
	Chains	:	P, Q
	Engineered	:	YES
	Fragment	:	N-TERM TAIL
	Other Details	:	SYNTHETIC PEPTIDE
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 23)

No.	Name	Count	Type	Full Name
1	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	MSE	21	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 16)

No.	Name	Count	Type	Full Name
1	ALY	2	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 14)

No.	Name	Count	Type	Full Name
1	ALY	-1	Mod. Amino Acid	N(6)-ACETYLLYSINE
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2DVQ)

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

Asymmetric Unit

No.	Residues
1	Gly P:14	-	Ala P:15
2	Ser Q:1	-	Gly Q:2

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

Asymmetric Unit (3, 8)

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

Biological Unit 1 (3, 6)

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

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HISTONE_H4	PS00047	Histone H4 signature.	H4_YEAST	15-19	0	- -
2	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD2_HUMAN	91-163 364-436	2	- - C:91-163 -
3	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD2_HUMAN	96-155 369-428	2	- - C:96-155 -

Asymmetric Unit (4, 11)

	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	3	A:73-111 B:73-111 C:76-111	39 39 36
1.17	ENST00000399529	17	ENSE00001742408	HSCHR6_MHC_QBL:32871904-32872041	138	BRD2_HUMAN	112-157	46	3	A:112-157 B:112-157 C:112-157	46 46 46
1.18a	ENST00000399529	18a	ENSE00001669691	HSCHR6_MHC_QBL:32872548-32872686	139	BRD2_HUMAN	158-204	47	3	A:158-186 B:158-184 C:158-182	29 27 25
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	0	-	-
1.20g	ENST00000399529	20g	ENSE00001741071	HSCHR6_MHC_QBL:32873960-32874088	129	BRD2_HUMAN	401-443	43	0	-	-
1.21b	ENST00000399529	21b	ENSE00001731564	HSCHR6_MHC_QBL:32874275-32874523	249	BRD2_HUMAN	444-526	83	0	-	-
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	P:8-15 Q:1-15	8 15

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:114
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:114
                                    82        92       102       112       122       132       142       152       162       172       182    
           BRD2_HUMAN    73 GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEEQE 186
               SCOP domains d2dvqa_ A: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------------------BROMODOMAIN_2  PDB: A:91-163 UniProt: 91-163                             ----------------------- PROSITE (1)
                PROSITE (2) -----------------------BROMODOMAIN_1  PDB: A:96-155 UniProt: 96-155                ------------------------------- PROSITE (2)
               Transcript 1 Exon 1.16e  PDB: A:73-111 [INCOMPLETE] Exon 1.17  PDB: A:112-157 UniProt: 112-157    Exon 1.18a  PDB: A:158-186    Transcript 1
                 2dvq A  73 GRVTNQLQYLHKVVmKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPmDmGTIKRRLENNYYWAASECmQDFNTmFTNCYIYNKPTDDIVLmAQTLEKIFLQKVASmPQEEQE 186
                                    82    |   92       102       112       122|      132       142     | 152       162  |    172       182    
                                         87-MSE                           121-MSE              142-MSE |              165-MSE        180-MSE  
                                                                            123-MSE                  148-MSE

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:112
                                    82        92       102       112       122       132       142       152       162       172       182  
           BRD2_HUMAN    73 GRVTNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQEE 184
               SCOP domains d2dvqb_ B: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------BROMODOMAIN_2  PDB: B:91-163 UniProt: 91-163                             --------------------- PROSITE (1)
                PROSITE (2) -----------------------BROMODOMAIN_1  PDB: B:96-155 UniProt: 96-155                ----------------------------- PROSITE (2)
               Transcript 1 Exon 1.16e  PDB: B:73-111 [INCOMPLETE] Exon 1.17  PDB: B:112-157 UniProt: 112-157    Exon 1.18a  PDB: B:158-184  Transcript 1
                 2dvq B  73 GRVTNQLQYLHKVVmKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPmDmGTIKRRLENNYYWAASECmQDFNTmFTNCYIYNKPTDDIVLmAQTLEKIFLQKVASmPQEE 184
                                    82    |   92       102       112       122|      132       142     | 152       162  |    172       182  
                                         87-MSE                           121-MSE              142-MSE |              165-MSE        180-MSE
                                                                            123-MSE                  148-MSE

Chain C from PDB  Type:PROTEIN  Length:107
 aligned with BRD2_HUMAN | P25440 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:107
                                    85        95       105       115       125       135       145       155       165       175       
           BRD2_HUMAN    76 TNQLQYLHKVVMKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPMDMGTIKRRLENNYYWAASECMQDFNTMFTNCYIYNKPTDDIVLMAQTLEKIFLQKVASMPQ 182
               SCOP domains d2dvqc_ C: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------BROMODOMAIN_2  PDB: C:91-163 UniProt: 91-163                             ------------------- PROSITE (1)
                PROSITE (2) --------------------BROMODOMAIN_1  PDB: C:96-155 UniProt: 96-155                --------------------------- PROSITE (2)
               Transcript 1 Exon 1.16e  PDB: C:76-111           Exon 1.17  PDB: C:112-157 UniProt: 112-157    Exon 1.18a  PDB: C:158-18 Transcript 1
                 2dvq C  76 TNQLQYLHKVVmKALWKHQFAWPFRQPVDAVKLGLPDYHKIIKQPmDmGTIKRRLENNYYWAASECmQDFNTmFTNCYIYNKPTDDIVLmAQTLEKIFLQKVASmPQ 182
                                    85 |      95       105       115     | 125       135      |145  |    155       165       175    |  
                                      87-MSE                           121-MSE              142-MSE |              165-MSE        180-MSE
                                                                         123-MSE                  148-MSE

Chain P from PDB  Type:PROTEIN  Length:8
 aligned with H4_YEAST | P02309 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:8
             H4_YEAST     9 KGLGKGGA  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
                 2dvq P   8 KGLGkGGA  15
                                |   
                               12-ALY

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
                 2dvq Q   1 SGRGKGGKGLGkGGA  15
                                    10 |   
                                      12-ALY

Legend:		→ Mismatch	(orange background)
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		→ 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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

1a	d2dvqa_	A:
1b	d2dvqb_	B:
1c	d2dvqc_	C:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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 P,Q (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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	Sites
(no "Sites" information available for 2dvq)

	Cis Peptide Bonds
		Gly P:14 - Ala P:15	[ RasMol ]
		Ser Q:1 - Gly Q:2	[ RasMol ]

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	2dvq
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1x0j	NATIVE
2dvr
2dvs	RELATED ID: AR_001000221.4 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 23)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 8)

Exons (4, 11)

Sequences/Alignments

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SCOP Domains (1, 3)

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Gene Ontology (20, 23)

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