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Description

Title :   CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN OF HUMAN BRD3 IN COMPLEX WITH THE INHIBITOR JQ1

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

Date :   31 May 11 (Deposition) - 29 Jun 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.36

Chains :   Asym./Biol. Unit : A

Keywords :   Brd3, Bromodomain Containing Protein 3, Orfx, Ring3 Like Gene, Ring3L, Jq1, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Filippakopoulos, S. Picaud, J. Qi, T. Keates, I. Felletar, O. Fedorov, J. Muniz, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, J. E. Bradner, S. Knapp
Crystal Structure Of The Second Bromodomain Of Human Brd3 I Complex With The Inhibitor Jq1
To Be Published
PubMed: search

Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 3
	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
	Gene	:	BRD3, KIAA0043, RING3L
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RING3-LIKE PROTEIN

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 2)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	JQ1	1	Ligand/Ion	(6S)-6-(2-TERT-BUTOXY-2-OXOETHYL)-4-(4-CHLOROPHENYL)-2,3,9-TRIMETHYL-6,7-DIHYDROTHIENO[3,2-F][1,2,4]TRIAZOLO[4,3-A][1,4]DIAZEPIN-10-IUM

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:2 , HOH A:116 , PRO A:333 , VAL A:338 , ALA A:342 , LEU A:343 , GLU A:344 , LEU A:345 , ASN A:391 , HIS A:395 , GLU A:396 , VAL A:397 , MET A:400	BINDING SITE FOR RESIDUE JQ1 A 1
2	AC2	SOFTWARE	HOH A:154 , GLN A:405 , ASP A:406	BINDING SITE FOR RESIDUE EDO A 417

SS Bonds (0, 0)

(no "SS Bond" information available for 3S92)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3S92)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3S92)

PROSITE Motifs (2, 2)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BROMODOMAIN_2	PS50014	Bromodomain profile.	BRD3_HUMAN	51-123 326-398	1	- A:326-398
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD3_HUMAN	56-115 331-390	1	- A:331-390

Exons (3, 3)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000303407	2a	ENSE00001798041	chr9:136933139-136933067	73	BRD3_HUMAN	-	0	0	-	-
1.5b	ENST00000303407	5b	ENSE00001677558	chr9:136918712-136918387	326	BRD3_HUMAN	1-71	71	0	-	-
1.6b	ENST00000303407	6b	ENSE00001647906	chr9:136917565-136917428	138	BRD3_HUMAN	72-117	46	0	-	-
1.7	ENST00000303407	7	ENSE00001616318	chr9:136916831-136916684	148	BRD3_HUMAN	118-167	50	0	-	-
1.8a	ENST00000303407	8a	ENSE00001628171	chr9:136915710-136915496	215	BRD3_HUMAN	167-238	72	0	-	-
1.9a	ENST00000303407	9a	ENSE00001723584	chr9:136913576-136913205	372	BRD3_HUMAN	239-362	124	1	A:307-362	56
1.10	ENST00000303407	10	ENSE00001739092	chr9:136910543-136910415	129	BRD3_HUMAN	363-405	43	1	A:363-405	43
1.11a	ENST00000303407	11a	ENSE00001633127	chr9:136907073-136906882	192	BRD3_HUMAN	406-469	64	1	A:406-416	11
1.12	ENST00000303407	12	ENSE00001129684	chr9:136905391-136905156	236	BRD3_HUMAN	470-548	79	0	-	-
1.13c	ENST00000303407	13c	ENSE00001129681	chr9:136901446-136901154	293	BRD3_HUMAN	548-646	99	0	-	-
1.14	ENST00000303407	14	ENSE00001129674	chr9:136899951-136899823	129	BRD3_HUMAN	646-689	44	0	-	-
1.15b	ENST00000303407	15b	ENSE00001129727	chr9:136898827-136897963	865	BRD3_HUMAN	689-726	38	0	-	-

Sequences/Alignments

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
	(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:110
 aligned with BRD3_HUMAN | Q15059 from UniProtKB/Swiss-Prot  Length:726

    Alignment length:110
                                   316       326       336       346       356       366       376       386       396       406       416
           BRD3_HUMAN   307 KLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMP 416
               SCOP domains d3s92a_ A: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Bromodomain-3s92A01 A:315-403                                                            ------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------BROMODOMAIN_2  PDB: A:326-398 UniProt: 326-398                           ------------------ PROSITE (1)
                PROSITE (2) ------------------------BROMODOMAIN_1  PDB: A:331-390 UniProt: 331-390              -------------------------- PROSITE (2)
               Transcript 1 Exon 1.9a  PDB: A:307-362 UniProt: 239-362 [INCOMPLETE] Exon 1.10  PDB: A:363-405 UniProt: 363-405 Exon 1.11a  Transcript 1
                 3s92 A 307 KLSEHLRYCDSILREMLSKKHAAYAWPFYKPVDAEALELHDYHDIIKHPMDLSTVKRKMDGREYPDAQGFAADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMP 416
                                   316       326       336       346       356       366       376       386       396       406       416

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)

Asymmetric/Biological 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)

d3s92a_

CATH Domains (0, 0)

(no "CATH Domain" information available for 3S92)

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Bromodomain] (56)

Family: Bromodomain (56)

Homo sapiens (Human) (44)

Bromodomain-3s92A01

A:315-403

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (BRD3_HUMAN | Q15059)

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: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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	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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Related Entries

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UniProtKB/Swiss-Prot
	BRD3_HUMAN \| Q15059	:	2e7n 2nxb 2oo1 2yw5 3s91 5a7c 5hfr 5hjc

Related Entries Specified in the PDB File

3s91