2NXB - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN BROMODOMAIN CONTAINING PROTEIN 3 (BRD3)

Authors :   P. Filippakopoulos, A. Bullock, C. Cooper, K. Keates, G. Berridge, A. P G. Bunkoczi, A. Edwards, C. Arrowsmith, M. Sundstrom, F. Von Delft, S Structural Genomics Consortium (Sgc)

Date :   17 Nov 06 (Deposition) - 12 Dec 06 (Release) - 11 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Brd3, Bromodomain Containing Protein 3, Orfx, Ring3 Like Gene, Ring3L, Structural Genomics, Structural Genomics Consortium, Sgc, Signaling Protein (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 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	ROSETTA-R3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BROMO 1 DOMAIN
	Gene	:	BRD3, KIAA0043, RING3L
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	RING3-LIKE PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
2	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:36 , GLN A:38 , SER A:97 , ALA A:98 , GLU B:91	BINDING SITE FOR RESIDUE NA A 301
2	AC2	SOFTWARE	TRP A:57 , MET A:125 , HOH A:429 , TRP B:51 , TYR B:60	BINDING SITE FOR RESIDUE EDO A 302
3	AC3	SOFTWARE	VAL B:63 , LEU B:70 , TYR B:73 , ASN B:116 , HOH B:342 , HOH B:384 , HOH B:425	BINDING SITE FOR RESIDUE EDO B 303
4	AC4	SOFTWARE	LEU A:134 , ILE B:76 , ILE B:77 , LYS B:78 , ASN B:79 , ASN B:111	BINDING SITE FOR RESIDUE EDO B 304
5	AC5	SOFTWARE	GLN A:54 , TRP A:96 , HOH A:354 , HOH A:429 , LYS B:87	BINDING SITE FOR RESIDUE EDO B 305
6	AC6	SOFTWARE	GLN A:38 , MET A:140 , GLN A:142 , LYS B:75 , LYS B:78 , ASN B:92	BINDING SITE FOR RESIDUE EDO B 306
7	AC7	SOFTWARE	GLN A:139 , HOH A:342 , HOH A:347 , ILE B:114 , HOH B:312	BINDING SITE FOR RESIDUE EDO A 307
8	AC8	SOFTWARE	ARG B:34 , LYS B:35 , HIS B:74 , ILE B:77 , PRO B:80 , ASN B:93 , HOH B:405	BINDING SITE FOR RESIDUE EDO B 308

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

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041913	T	36	N	BRD3_HUMAN	Unclassified	---	A/B	T	36	N

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041913	T	36	N	BRD3_HUMAN	Unclassified	---	A	T	36	N

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041913	T	36	N	BRD3_HUMAN	Unclassified	---	B	T	36	N

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

Asymmetric Unit (2, 4)

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

Biological Unit 1 (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:51-123 - -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD3_HUMAN	56-115 331-390	1	A:56-115 - -

Biological Unit 2 (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	- B:51-123 -
2	BROMODOMAIN_1	PS00633	Bromodomain signature.	BRD3_HUMAN	56-115 331-390	1	- B:56-115 -

Asymmetric Unit (3, 6)

	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	2	A:34-71 B:23-71	38 49
1.6b	ENST00000303407	6b	ENSE00001647906	chr9:136917565-136917428	138	BRD3_HUMAN	72-117	46	2	A:72-117 B:72-117	46 46
1.7	ENST00000303407	7	ENSE00001616318	chr9:136916831-136916684	148	BRD3_HUMAN	118-167	50	2	A:118-144 B:118-143	27 26
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	0	-	-
1.10	ENST00000303407	10	ENSE00001739092	chr9:136910543-136910415	129	BRD3_HUMAN	363-405	43	0	-	-
1.11a	ENST00000303407	11a	ENSE00001633127	chr9:136907073-136906882	192	BRD3_HUMAN	406-469	64	0	-	-
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	-	-

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:111
 aligned with BRD3_HUMAN | Q15059 from UniProtKB/Swiss-Prot  Length:726

    Alignment length:111
                                    43        53        63        73        83        93       103       113       123       133       143 
           BRD3_HUMAN    34 RKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEE 144
               SCOP domains d2nxba_ A: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --N------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------BROMODOMAIN_2  PDB: A:51-123 UniProt: 51-123                             --------------------- PROSITE (1)
                PROSITE (2) ----------------------BROMODOMAIN_1  PDB: A:56-115 UniProt: 56-115                ----------------------------- PROSITE (2)
               Transcript 1 Exon 1.5b  PDB: A:34-71 UniProt: 1-71 Exon 1.6b  PDB: A:72-117 UniProt: 72-117      Exon 1.7  PDB: A:118-144    Transcript 1
                 2nxb A  34 RKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQEE 144
                                    43        53        63        73        83        93       103       113       123       133       143

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with BRD3_HUMAN | Q15059 from UniProtKB/Swiss-Prot  Length:726

    Alignment length:121
                                    32        42        52        62        72        82        92       102       112       122       132       142 
           BRD3_HUMAN    23 PPEVSNPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQE 143
               SCOP domains d2nxbb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------Bromodomain-2nxbB01 B:42-128                                                           --------------- Pfam domains (1)
           Pfam domains (2) -------------------Bromodomain-2nxbB02 B:42-128                                                           --------------- Pfam domains (2)
         Sec.struct. author .............hhhhhhhhhhhhhhhhh...hhhhh...........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------N----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------BROMODOMAIN_2  PDB: B:51-123 UniProt: 51-123                             -------------------- PROSITE (1)
                PROSITE (2) ---------------------------------BROMODOMAIN_1  PDB: B:56-115 UniProt: 56-115                ---------------------------- PROSITE (2)
               Transcript 1 Exon 1.5b  PDB: B:23-71 UniProt: 1-71            Exon 1.6b  PDB: B:72-117 UniProt: 72-117      Exon 1.7  PDB: B:118-143   Transcript 1
                 2nxb B  23 MPEVSNPSKPGRKTNQLQYMQNVVVKTLWKHQFAWPFYQPVDAIKLNLPDYHKIIKNPMDMGTIKKRLENNYYWSASECMQDFNTMFTNCYIYNKPTDDIVLMAQALEKIFLQKVAQMPQE 143
                                    32        42        52        62        72        82        92       102       112       122       132       142

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	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	d2nxba_	A:
1b	d2nxbb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Bromodomain (56)

Homo sapiens (Human) (44)

1a	Bromodomain-2nxbB01	B:42-128
1b	Bromodomain-2nxbB02	B:42-128

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	BRD3_HUMAN \| Q15059	:	2e7n 2oo1 2yw5 3s91 3s92 5a7c 5hfr 5hjc

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Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

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