2EH9 - JenaLib

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Asym. Unit - sites

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Biol. Unit 1 - sites

Biological Unit 2

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Description

Title :   CRYSTAL STRUCTURE OF THE HBAF250B AT-RICH INTERACTION DOMAIN (ARID)

Authors :   H. Niwa, A. Shimada, S. Yokoyama, Riken Structural Genomics/Proteo Initiative (Rsgi)

Date :   05 Mar 07 (Deposition) - 11 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Dna-Binding Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Shimada, H. Niwa, S. Yokoyama
Crystal Structure Of The Hbaf250B At-Rich Interaction Domai (Arid)
To Be Published
PubMed: search

Compounds

Molecule 1 - AT-RICH INTERACTIVE DOMAIN-CONTAINING PROTEIN 1B
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	PX041105-20
	Expression System Vector Type	:	PLASMID
	Fragment	:	AT-RICH INTERACTION DOMAIN (ARID)
	Gene	:	HBAF250B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL-FREE PROTEIN SYNTHESIS
	Synonym	:	ARID DOMAIN- CONTAINING PROTEIN 1B, OSA HOMOLOG 2, HOSA2, P250R, BRG1-BINDING PROTEIN HELD/OSA1, BRG1-ASSOCIATED FACTOR 250B, BAF250B

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 8)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	1	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:53 , GLU A:56	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	CYS A:53 , GLU A:56	BINDING SITE FOR RESIDUE ZN A 202
3	AC3	SOFTWARE	GLU A:29 , LYS A:89 , GLU A:108	BINDING SITE FOR RESIDUE ZN A 203
4	AC4	SOFTWARE	ASP A:21 , CYS A:101 , ARG A:105 , HOH A:208	BINDING SITE FOR RESIDUE ZN A 204
5	AC5	SOFTWARE	CYS A:53 , GLU A:56	BINDING SITE FOR RESIDUE CL A 205
6	AC6	SOFTWARE	GLU A:56 , ASN A:75 , LEU A:76	BINDING SITE FOR RESIDUE CL A 206
7	AC7	SOFTWARE	GLU A:29 , ASN A:64 , LYS A:89 , HOH A:222	BINDING SITE FOR RESIDUE CL A 207

SS Bonds (0, 0)

(no "SS Bond" information available for 2EH9)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2EH9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_067678	V	1092	I	ARI1B_HUMAN	Polymorphism	775526039	A	V	52	I

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_067678	V	1092	I	ARI1B_HUMAN	Polymorphism	775526039	A	V	52	I

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_067678	V	1092	I	ARI1B_HUMAN	Polymorphism	775526039	A	V	52	I

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

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARID	PS51011	ARID domain profile.	ARI1B_HUMAN	1053-1144	1	A:13-104

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARID	PS51011	ARID domain profile.	ARI1B_HUMAN	1053-1144	1	A:13-104

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARID	PS51011	ARID domain profile.	ARI1B_HUMAN	1053-1144	2	A:13-104

Exons (2, 2)

Asymmetric Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000350026	1a	ENSE00002076297	chr6:157099063-157100605	1543	ARI1B_HUMAN	1-514	514	0	-	-
1.2	ENST00000350026	2	ENSE00002193707	chr6:157150361-157150555	195	ARI1B_HUMAN	515-579	65	0	-	-
1.5b	ENST00000350026	5b	ENSE00002196548	chr6:157222510-157222659	150	ARI1B_HUMAN	580-629	50	0	-	-
1.6a	ENST00000350026	6a	ENSE00001744727	chr6:157256600-157256710	111	ARI1B_HUMAN	630-666	37	0	-	-
1.7a	ENST00000350026	7a	ENSE00002178237	chr6:157405796-157406039	244	ARI1B_HUMAN	667-748	82	0	-	-
1.8a	ENST00000350026	8a	ENSE00002147736	chr6:157431606-157431695	90	ARI1B_HUMAN	748-778	31	0	-	-
1.9a	ENST00000350026	9a	ENSE00000765473	chr6:157454162-157454341	180	ARI1B_HUMAN	778-838	61	0	-	-
1.10a	ENST00000350026	10a	ENSE00001332230	chr6:157469758-157470085	328	ARI1B_HUMAN	838-947	110	0	-	-
1.11	ENST00000350026	11	ENSE00002140579	chr6:157488174-157488319	146	ARI1B_HUMAN	947-996	50	0	-	-
1.12	ENST00000350026	12	ENSE00002197298	chr6:157495142-157495251	110	ARI1B_HUMAN	996-1032	37	0	-	-
1.14a	ENST00000350026	14a	ENSE00001696442	chr6:157502103-157502312	210	ARI1B_HUMAN	1033-1102	70	1	A:2-62	61
1.15a	ENST00000350026	15a	ENSE00000975824	chr6:157505365-157505569	205	ARI1B_HUMAN	1103-1171	69	1	A:63-111	49
1.16	ENST00000350026	16	ENSE00001142078	chr6:157510776-157510914	139	ARI1B_HUMAN	1171-1217	47	0	-	-
1.17	ENST00000350026	17	ENSE00001142072	chr6:157511172-157511344	173	ARI1B_HUMAN	1217-1275	59	0	-	-
1.18	ENST00000350026	18	ENSE00001142064	chr6:157517299-157517449	151	ARI1B_HUMAN	1275-1325	51	0	-	-
1.19	ENST00000350026	19	ENSE00001142057	chr6:157519945-157520041	97	ARI1B_HUMAN	1325-1357	33	0	-	-
1.20a	ENST00000350026	20a	ENSE00000975829	chr6:157521839-157522622	784	ARI1B_HUMAN	1358-1619	262	0	-	-
1.21	ENST00000350026	21	ENSE00001142049	chr6:157525000-157525130	131	ARI1B_HUMAN	1619-1662	44	0	-	-
1.22c	ENST00000350026	22c	ENSE00002020018	chr6:157527301-157530284	2984	ARI1B_HUMAN	1663-2236	574	0	-	-

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:110
 aligned with ARI1B_HUMAN | Q8NFD5 from UniProtKB/Swiss-Prot  Length:2236

    Alignment length:110
                                  1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151
         ARI1B_HUMAN   1042 EKITKVYELGNEPERKLWVDRYLTFMEERGSPVSSLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQYLFAFECKIERGEEPPP 1151
               SCOP domains d2eh9a_ A: automated matches                                                                                   SCOP domains
               CATH domains 2eh9A00 A:2-111  [code=1.10.150.60, no name defined]                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.....hhhhhhhhhhhhhhhh........ee..ee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------I----------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------ARID  PDB: A:13-104 UniProt: 1053-1144                                                      ------- PROSITE
               Transcript 1 Exon 1.14a  PDB: A:2-62 UniProt: 1033-1102 [INCOMPLETE]      Exon 1.15a  PDB: A:63-111 UniProt: 1103-1171      Transcript 1
                2eh9 A    2 EKITKVYELGNEPERKLWVDRYLTFmEERGSPVSSLPAVGKKPLDLFRLYVCVKEIGGLAQVNKNKKWRELATNLNVGTSSSAASSLKKQYIQYLFAFECKIERGEEPPP  111
                                    11        21     |  31        41        51        61        71        81        91       101       111
                                                    27-MSE

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: ARID-like (14)

Family: ARID domain (12)

Protein domain: automated matches (5)

Human (Homo sapiens) [TaxId: 9606] (4)

d2eh9a_

CATH Domains (1, 1)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: DNA polymerase; domain 1 (617)

Homologous Superfamily: [code=1.10.150.60, no name defined] (11)

Human (Homo sapiens) (7)

2eh9A00

A:2-111

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2EH9)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A (ARI1B_HUMAN | Q8NFD5)

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:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
biological process
	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:0048096	chromatin-mediated maintenance of transcription	Maintenance of transcription by remodelling of chromatin into an 'open configuration'. Once established, this regulation is mitotically stable and is maintained over many cell divisions. It is also heritable.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	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:0090544	BAF-type complex	A SWI/SNF-type complex that contains a subunit from the BAF (Brahma-Associated Factor) family.
	GO:0016514	SWI/SNF complex	A SWI/SNF-type complex that contains nine or more proteins, including both conserved (core) and nonconserved components; the Swi2/Snf2 ATPase is one of the core components.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0071565	nBAF complex	A SWI/SNF-type complex that is found in post-mitotic neurons, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B genes. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.
	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.

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	ARI1B_HUMAN \| Q8NFD5	:	2cxy

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