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Title :   CRYSTAL STRUCTURE OF ZHX2 HD2 (ZINC-FINGERS AND HOMEOBOXES PROTEIN 2, HOMEODOMAIN 2)

Authors :   J. Ren, L. E. Bird, R. J. Owens, D. K. Stammers, Oxford Protein Product Facility (Oppf)

Date :   02 Jun 10 (Deposition) - 07 Jul 10 (Release) - 07 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Zhx2, Corepressor, Homeodomain, Domain Swapping, Structural Genomics, Oxford Protein Production Facility, Oppf, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. E. Bird, J. Ren, J. E. Nettleship, G. E. Folkers, R. J. Owens, D. K. Stammers
Novel Structural Features In Two Zhx Homeodomains Derived From A Systematic Study Of Single And Multiple Domains
Bmc Struct. Biol. V. 10 13 2010
PubMed-ID: 20509910 | Reference-DOI: 10.1186/1472-6807-10-13

Molecule 1 - ZINC FINGERS AND HOMEOBOXES PROTEIN 2
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	OPPF2273
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HD2 DOMAIN, HOMEOBOX 2, RESIDUES 444-501
	Gene	:	ZHX2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ZHX2, ZINC FINGER AND HOMEODOMAIN PROTEIN 2, ALPHA- FETOPROTEIN REGULATOR 1, AFP REGULATOR 1, REGULATOR OF AFP

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:486 , HIS A:490 , ARG A:493 , ILE B:451	BINDING SITE FOR RESIDUE SO4 A 302

Asymmetric/Biological Unit

No.	Residues
1	A:494	-	B:494

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HOMEOBOX_2	PS50071	'Homeobox' domain profile.	ZHX2_HUMAN	447-497 537-587 636-686	2	A:447-497 B:447-497 - -

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000314393	1	ENSE00001310974	chr8:123793633-123794185	553	ZHX2_HUMAN	-	0	0	-	-
1.2b	ENST00000314393	2b	ENSE00001292641	chr8:123875716-123875778	63	ZHX2_HUMAN	-	0	0	-	-
1.3b	ENST00000314393	3b	ENSE00001252625	chr8:123963532-123966268	2737	ZHX2_HUMAN	1-910	910	2	A:446-501 B:446-501	56 56
1.4b	ENST00000314393	4b	ENSE00001326276	chr8:123985482-123986750	1269	ZHX2_HUMAN	-	0	0	-	-

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:56
 aligned with ZHX2_HUMAN | Q9Y6X8 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:56
                                   455       465       475       485       495      
           ZHX2_HUMAN   446 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIVHI 501
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HOMEOBOX_2  PDB: A:447-497 UniProt: 447-497        ---- PROSITE
               Transcript 1 Exon 1.3b  PDB: A:446-501 UniProt: 1-910 [INCOMPLETE]    Transcript 1
                 3nau A 446 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIVHI 501
                                   455       465       475       485       495

Chain B from PDB  Type:PROTEIN  Length:56
 aligned with ZHX2_HUMAN | Q9Y6X8 from UniProtKB/Swiss-Prot  Length:837

    Alignment length:56
                                   455       465       475       485       495      
           ZHX2_HUMAN   446 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIVHI 501
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
           Pfam domains (1) Homeobox-3nauB01 B:446-496                         ----- Pfam domains (1)
           Pfam domains (2) Homeobox-3nauB02 B:446-496                         ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HOMEOBOX_2  PDB: B:447-497 UniProt: 447-497        ---- PROSITE
               Transcript 1 Exon 1.3b  PDB: B:446-501 UniProt: 1-910 [INCOMPLETE]    Transcript 1
                 3nau B 446 KTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGIVHI 501
                                   455       465       475       485       495

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 '\|'

(no "SCOP Domain" information available for 3NAU)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: Homeobox (36)

Homo sapiens (Human) (9)

1a	Homeobox-3nauB01	B:446-496
1b	Homeobox-3nauB02	B:446-496

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ZHX2_HUMAN | Q9Y6X8)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	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:0006402	mRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
	GO:0045665	negative regulation of neuron differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
	GO:0000122	negative regulation of transcription from RNA polymerase II promoter	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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:0035019	somatic stem cell population maintenance	Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
	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: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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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3nar	CRYSTAL STRUCTURE OF ZHX1 HD4 (ZINC-FINGERS AND HOMEOBOXES PROTEIN 1, HOMEODOMAIN 4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (1, 2)

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Gene Ontology (20, 20)

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