4CO8 - JenaLib

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Title :   STRUCTURE OF THE DNA BINDING ETS DOMAIN OF HUMAN ETV4

Authors :   J. A. Newman, C. D. O. Cooper, L. Shrestha, N. Burgess-Brown, J. Kopec, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, O. Gileadi

Date :   27 Jan 14 (Deposition) - 05 Feb 14 (Release) - 10 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.05

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

Keywords :   Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. D. O. Cooper, J. A. Newman, H. Aitkenhead, C. K. Allerston, O. Gileadi
Structures Of The Ets Domains Of Transcription Factors Etv1 Etv4, Etv5 And Fev: Determinants Of Dna Binding And Redox Regulation By Disulfide Bond Formation.
J. Biol. Chem. V. 290 13692 2015
PubMed-ID: 25866208 | Reference-DOI: 10.1074/JBC.M115.646737

Molecule 1 - ETS TRANSLOCATION VARIANT 4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	ETS DOMAIN, RESIDUES 338-470
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ADENOVIRUS E1A ENHANCER-BINDING PROTEIN, E1A-F, POLYOMAVIRUS ENHANCER ACTIVATOR 3 HOMOLOG, PROTEIN PEA3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:340 , LEU A:341 , TRP A:362 , EDO A:1437 , HOH A:2025 , HOH A:2039 , HOH A:2067	BINDING SITE FOR RESIDUE EDO A1435
2	AC2	SOFTWARE	GLN A:342 , TRP A:344 , SER A:429 , PRO A:433 , HOH A:2033 , HOH A:2034	BINDING SITE FOR RESIDUE EDO A1436
3	AC3	SOFTWARE	LEU A:351 , ASP A:352 , ARG A:387 , GLU A:425 , EDO A:1435 , HOH A:2028 , HOH A:2067 , HOH A:2085	BINDING SITE FOR RESIDUE EDO A1437

Asymmetric Unit

No.	Residues
1	A:422	-	A:422

(no "Cis Peptide Bond" information available for 4CO8)

(no "SAP(SNP)/Variant" information available for 4CO8)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETS_DOMAIN_3	PS50061	Ets-domain profile.	ETV4_HUMAN	341-421	1	A:341-421
2	ETS_DOMAIN_1	PS00345	Ets-domain signature 1.	ETV4_HUMAN	343-351	1	A:343-351
3	ETS_DOMAIN_2	PS00346	Ets-domain signature 2.	ETV4_HUMAN	387-402	1	A:387-402

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETS_DOMAIN_3	PS50061	Ets-domain profile.	ETV4_HUMAN	341-421	2	A:341-421
2	ETS_DOMAIN_1	PS00345	Ets-domain signature 1.	ETV4_HUMAN	343-351	2	A:343-351
3	ETS_DOMAIN_2	PS00346	Ets-domain signature 2.	ETV4_HUMAN	387-402	2	A:387-402

(no "Exon" information available for 4CO8)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:98
 aligned with ETV4_HUMAN | P43268 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:98
                                   346       356       366       376       386       396       406       416       426        
           ETV4_HUMAN   337 RRGALQLWQFLVALLDDPTNAHFIAWTGRGMEFKLIEPEEVARLWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCEPEALFSLAFPD 434
               SCOP domains d4co8a_ A: automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh..eee.....eeee.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..eee......eeee..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ETS_DOMAIN_3  PDB: A:341-421 UniProt: 341-421                                    ------------- PROSITE (1)
                PROSITE (2) ------ETS_DOMAI-----------------------------------ETS_DOMAIN_2    -------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4co8 A 337 MRGALQLWQFLVALLDDPTNAHFIAWTGRGMEFKLIEPEEVARLWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCEPEALFSLAFPD 434
                                   346       356       366       376       386       396       406       416       426

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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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

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

Superfamily: Winged helix DNA-binding domain (576)

Family: automated matches (118)

Protein domain: automated matches (118)

Human (Homo sapiens) [TaxId: 9606] (10)

d4co8a_

(no "CATH Domain" information available for 4CO8)

(no "Pfam Domain" information available for 4CO8)

Asymmetric Unit(hide GO term definitions)

Chain A (ETV4_HUMAN | P43268)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000978	RNA polymerase II core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	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:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	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.
	GO:0001077	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0060444	branching involved in mammary gland duct morphogenesis	The process in which the branching structure of the mammary gland duct is generated and organized. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0008045	motor neuron axon guidance	The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0033600	negative regulation of mammary gland epithelial cell proliferation	Any process that stops, prevents or reduces the rate or extent of mammary gland epithelial cell proliferation.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	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:0060762	regulation of branching involved in mammary gland duct morphogenesis	Any process that modulates the rate, frequency, or extent of branching involved in mammary gland duct morphogenesis.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0048863	stem cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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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