3M52 - JenaLib

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Description

Title :   CRYSTAL STRUCTURE OF THE BTB DOMAIN FROM THE MIZ-1/ZBTB17 TRANSCRIPTION REGULATOR

Authors :   P. J. Stogios, J. A. Cuesta-Seijo, L. Chen, G. G. Prive

Date :   12 Mar 10 (Deposition) - 09 Jun 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.59

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

Keywords :   Btb Domain, Poz Domain, Btb/Poz Domain, Miz-1, Zinc Finger Protein 151, Myc-Interacting Zinc Finger Protein, Miz-1 Protein, Zfp151, Zfp-151, Znf151, Miz1, Zinc Finger And Btb Domain-Containing Protein 17, Zinc Finger Protein 60, Protein-Protein Interaction Domain, Transcription Regulator, Transcription Activator, Zinc-Finger Protein, Alpha/Beta Protein, Developmental Protein, Dna-Binding, Metal-Binding, Nucleus, Transcription, Transcription Regulation, Zinc-Finger, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. Stogios, J. A. Cuesta-Seijo, L. Chen, N. C. Pomroy, G. G. Prive
Insights Into Strand Exchange In Btb Domain Dimers From The Crystal Structures Of Fazf And Miz1.
J. Mol. Biol. V. 400 983 2010
PubMed-ID: 20493880 | Reference-DOI: 10.1016/J.JMB.2010.05.028

Compounds

Molecule 1 - ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 17
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-32(A)
	Expression System Strain	:	BL21(DE3) CODON PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BTB DOMAIN FROM MIZ-1/ZBTB17
	Gene	:	MIZ1, ZBTB17, ZNF151, ZNF60
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ZINC FINGER PROTEIN 60, ZINC FINGER PROTEIN 151, MYC- INTERACTING ZINC FINGER PROTEIN 1, MIZ-1

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 8)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	ZN	6	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:6 , HIS A:9 , HOH A:122 , ASP B:103	BINDING SITE FOR RESIDUE ZN A 116
2	AC2	SOFTWARE	HIS A:34 , HOH A:134 , HOH A:138	BINDING SITE FOR RESIDUE ZN A 117
3	AC3	SOFTWARE	ASP A:103 , ACT A:120 , HIS B:6 , HIS B:9	BINDING SITE FOR RESIDUE ZN B 116
4	AC4	SOFTWARE	HIS B:34	BINDING SITE FOR RESIDUE ZN B 117
5	AC5	SOFTWARE	GLU A:87 , LYS B:57 , HIS B:61	BINDING SITE FOR RESIDUE ZN A 118
6	AC6	SOFTWARE	ASP A:55 , ASP A:58 , VAL B:54	BINDING SITE FOR RESIDUE ZN A 119
7	AC7	SOFTWARE	CYS A:45 , PHE A:76 , MET A:101 , GLN A:102 , ASP A:103 , ILE A:104 , HIS B:6 , HIS B:9 , ZN B:116	BINDING SITE FOR RESIDUE ACT A 120
8	AC8	SOFTWARE	GLY A:69 , LEU A:70 , GLY A:71 , GLN A:72	BINDING SITE FOR RESIDUE ACT A 121

SS Bonds (0, 0)

(no "SS Bond" information available for 3M52)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 3M52)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 3M52)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BTB	PS50097	BTB domain profile.	ZBT17_HUMAN	24-86	2	A:24-86 B:24-86

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BTB	PS50097	BTB domain profile.	ZBT17_HUMAN	24-86	2	A:24-86 B:24-86

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BTB	PS50097	BTB domain profile.	ZBT17_HUMAN	24-86	2	A:24-86 B:24-86

Exons (2, 4)

Asymmetric Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000375743	1b	ENSE00001839520	chr1:16302621-16302478	144	ZBT17_HUMAN	-	0	0	-	-
1.2	ENST00000375743	2	ENSE00001348924	chr1:16299620-16299534	87	ZBT17_HUMAN	-	0	0	-	-
1.4	ENST00000375743	4	ENSE00002171255	chr1:16274992-16274786	207	ZBT17_HUMAN	1-69	69	2	A:1-69 B:1-69	69 69
1.6b	ENST00000375743	6b	ENSE00001695578	chr1:16273618-16273430	189	ZBT17_HUMAN	69-132	64	2	A:69-115 B:69-115	47 47
1.7b	ENST00000375743	7b	ENSE00001722255	chr1:16272789-16272649	141	ZBT17_HUMAN	132-179	48	0	-	-
1.7h	ENST00000375743	7h	ENSE00001738306	chr1:16272335-16272210	126	ZBT17_HUMAN	179-221	43	0	-	-
1.8b	ENST00000375743	8b	ENSE00001755221	chr1:16271697-16271432	266	ZBT17_HUMAN	221-309	89	0	-	-
1.9	ENST00000375743	9	ENSE00001602262	chr1:16271334-16271192	143	ZBT17_HUMAN	310-357	48	0	-	-
1.10b	ENST00000375743	10b	ENSE00001684066	chr1:16271095-16270795	301	ZBT17_HUMAN	357-457	101	0	-	-
1.10i	ENST00000375743	10i	ENSE00000751342	chr1:16270390-16270303	88	ZBT17_HUMAN	458-487	30	0	-	-
1.10k	ENST00000375743	10k	ENSE00000751341	chr1:16270210-16270094	117	ZBT17_HUMAN	487-526	40	0	-	-
1.11b	ENST00000375743	11b	ENSE00000751340	chr1:16270014-16269894	121	ZBT17_HUMAN	526-566	41	0	-	-
1.11f	ENST00000375743	11f	ENSE00000751339	chr1:16269689-16269559	131	ZBT17_HUMAN	566-610	45	0	-	-
1.13a	ENST00000375743	13a	ENSE00000751338	chr1:16269233-16269024	210	ZBT17_HUMAN	610-680	71	0	-	-
1.13e	ENST00000375743	13e	ENSE00002146007	chr1:16268915-16268826	90	ZBT17_HUMAN	680-710	31	0	-	-
1.14b	ENST00000375743	14b	ENSE00001653173	chr1:16268747-16268364	384	ZBT17_HUMAN	710-803	94	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
	(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:117
 aligned with ZBT17_HUMAN | Q13105 from UniProtKB/Swiss-Prot  Length:803

    Alignment length:117
                              1                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       
          ZBT17_HUMAN     - --MDFPQHSQHVLEQLNQQRQLGLLCDCTFVVDGVHFKAHKAVLAACSEYFKMLFVDQKDVVHLDISNAAGLGQVLEFMYTAKLSLSPENVDDVLAVATFLQMQDIITACHALKSLA 115
               SCOP domains d3m52a_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------BTB  PDB: A:24-86 UniProt: 24-86                               ----------------------------- PROSITE
           Transcript 1 (1) --Exon 1.4  PDB: A:1-69 UniProt: 1-69                                  ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.6b  PDB: A:69-115 UniProt: 69-132        Transcript 1 (2)
                 3m52 A  -1 GSMDFPQHSQHVLEQLNQQRQLGLLCDCTFVVDGVHFKAHKAVLAACSEYFKMLFVDQKDVVHLDISNAAGLGQVLEFMYTAKLSLSPENVDDVLAVATFLQMQDIITACHALKSLA 115
                                     8        18        28        38        48        58        68        78        88        98       108

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with ZBT17_HUMAN | Q13105 from UniProtKB/Swiss-Prot  Length:803

    Alignment length:117
                              1                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       
          ZBT17_HUMAN     - --MDFPQHSQHVLEQLNQQRQLGLLCDCTFVVDGVHFKAHKAVLAACSEYFKMLFVDQKDVVHLDISNAAGLGQVLEFMYTAKLSLSPENVDDVLAVATFLQMQDIITACHALKSLA 115
               SCOP domains d3m52b_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------BTB-3m52B01 B:14-113                                                                                -- Pfam domains (1)
           Pfam domains (2) ---------------BTB-3m52B02 B:14-113                                                                                -- Pfam domains (2)
         Sec.struct. author ..ee.hhhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------BTB  PDB: B:24-86 UniProt: 24-86                               ----------------------------- PROSITE
           Transcript 1 (1) --Exon 1.4  PDB: B:1-69 UniProt: 1-69                                  ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.6b  PDB: B:69-115 UniProt: 69-132        Transcript 1 (2)
                 3m52 B  -1 GSMDFPQHSQHVLEQLNQQRQLGLLCDCTFVVDGVHFKAHKAVLAACSEYFKMLFVDQKDVVHLDISNAAGLGQVLEFMYTAKLSLSPENVDDVLAVATFLQMQDIITACHALKSLA 115
                                     8        18        28        38        48        58        68        78        88        98       108

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, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: POZ domain (79)

Superfamily: POZ domain (79)

Family: automated matches (23)

Protein domain: automated matches (23)

Human (Homo sapiens) [TaxId: 9606] (18)

1a	d3m52a_	A:
1b	d3m52b_	B:

CATH Domains (0, 0)

(no "CATH Domain" information available for 3M52)

Pfam Domains (1, 2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: POZ (36)

Family: BTB (12)

Homo sapiens (Human) (12)

1a	BTB-3m52B01	B:14-113
1b	BTB-3m52B02	B:14-113

Gene Ontology (17, 17)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ZBT17_HUMAN | Q13105)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic 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:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0036498	IRE1-mediated unfolded protein response	A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
	GO:0007398	ectoderm development	The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.
	GO:0001702	gastrulation with mouth forming second	A gastrulation process in which the initial invagination becomes the anus and the mouth forms second.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0045786	negative regulation of cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
	GO:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:1903146	regulation of mitophagy	Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
	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: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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	3m52
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	ZBT17_HUMAN \| Q13105	:	2lvr 2lvt 2lvu 2m0d 2m0e 2m0f 2n25 2n26 2q81 4u2m 4u2n 5ion

Related Entries Specified in the PDB File

3m4t	CRYSTAL STRUCTURE OF THE BTB DOMAIN FROM KAISO/ZBTB33
3m5b	CRYSTAL STRUCTURE OF THE BTB DOMAIN FROM FAZF/ZBTB32