4AVP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF HUMAN ETV1.

Authors :   C. K. Allerston, C. D. O. Cooper, T. Krojer, A. Chaikuad, P. Filippakopo P. Canning, C. H. Arrowsmith, A. Edwards, C. Bountra, F. Von Delft, O.

Date :   28 May 12 (Deposition) - 20 Jun 12 (Release) - 10 Jun 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

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

Keywords :   Transcription, Transcriptional Activation And Repression, Dna Binding Protein, E Twenty-Six, Erwing Sarcoma, Prostate Cancer, Melanoma, Gastrointestinal Stromal Tumour (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 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3-PRARE2
	Expression System Vector Type	:	PLASMID
	Fragment	:	DNA-BINDING DOMAIN, RESIDUES 326-429
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ETS-RELATED PROTEIN 81

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:381 , ALA B:383 , LYS B:388 , HOH B:2037 , LYS D:364 , ILE D:366	BINDING SITE FOR RESIDUE EDO B1427
2	AC2	SOFTWARE	PRO B:348 , SER D:334 , LYS D:379	BINDING SITE FOR RESIDUE EDO D1427

Asymmetric Unit

No.	Residues
1	A:416	-	B:416
2	C:416	-	D:416

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

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

Asymmetric Unit (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETS_DOMAIN_3	PS50061	Ets-domain profile.	ETV1_HUMAN	335-415	4	A:335-415 B:335-415 C:335-415 D:335-415
2	ETS_DOMAIN_1	PS00345	Ets-domain signature 1.	ETV1_HUMAN	337-345	4	A:337-345 B:337-345 C:337-345 D:337-345
3	ETS_DOMAIN_2	PS00346	Ets-domain signature 2.	ETV1_HUMAN	381-396	4	A:381-396 B:381-396 C:381-396 D:381-396

Biological Unit 1 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETS_DOMAIN_3	PS50061	Ets-domain profile.	ETV1_HUMAN	335-415	2	A:335-415 B:335-415 - -
2	ETS_DOMAIN_1	PS00345	Ets-domain signature 1.	ETV1_HUMAN	337-345	2	A:337-345 B:337-345 - -
3	ETS_DOMAIN_2	PS00346	Ets-domain signature 2.	ETV1_HUMAN	381-396	2	A:381-396 B:381-396 - -

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETS_DOMAIN_3	PS50061	Ets-domain profile.	ETV1_HUMAN	335-415	2	- - C:335-415 D:335-415
2	ETS_DOMAIN_1	PS00345	Ets-domain signature 1.	ETV1_HUMAN	337-345	2	- - C:337-345 D:337-345
3	ETS_DOMAIN_2	PS00346	Ets-domain signature 2.	ETV1_HUMAN	381-396	2	- - C:381-396 D:381-396

(no "Exon" information available for 4AVP)

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:93
 aligned with ETV1_HUMAN | P50549 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:93
                                   343       353       363       373       383       393       403       413       423   
           ETV1_HUMAN   334 SLQLWQFLVALLDDPSNSHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAF 426
               SCOP domains d4avpa_ A: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..eee.....eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.eee......eeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ETS_DOMAIN_3  PDB: A:335-415 UniProt: 335-415                                    ----------- PROSITE (1)
                PROSITE (2) ---ETS_DOMAI-----------------------------------ETS_DOMAIN_2    ------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4avp A 334 SLQLWQFLVALLDDPSNSHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAF 426
                                   343       353       363       373       383       393       403       413       423

Chain B from PDB  Type:PROTEIN  Length:93
 aligned with ETV1_HUMAN | P50549 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:93
                                   343       353       363       373       383       393       403       413       423   
           ETV1_HUMAN   334 SLQLWQFLVALLDDPSNSHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAF 426
               SCOP domains d4avpb_ B: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..eee.....eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eee......eeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ETS_DOMAIN_3  PDB: B:335-415 UniProt: 335-415                                    ----------- PROSITE (1)
                PROSITE (2) ---ETS_DOMAI-----------------------------------ETS_DOMAIN_2    ------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4avp B 334 SLQLWQFLVALLDDPSNSHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAF 426
                                   343       353       363       373       383       393       403       413       423

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with ETV1_HUMAN | P50549 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:93
                                   343       353       363       373       383       393       403       413       423   
           ETV1_HUMAN   334 SLQLWQFLVALLDDPSNSHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAF 426
               SCOP domains d4avpc_ C: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..eee.....eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eee......eeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ETS_DOMAIN_3  PDB: C:335-415 UniProt: 335-415                                    ----------- PROSITE (1)
                PROSITE (2) ---ETS_DOMAI-----------------------------------ETS_DOMAIN_2    ------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4avp C 334 SLQLWQFLVALLDDPSNSHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAF 426
                                   343       353       363       373       383       393       403       413       423

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with ETV1_HUMAN | P50549 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:93
                                   343       353       363       373       383       393       403       413       423   
           ETV1_HUMAN   334 SLQLWQFLVALLDDPSNSHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAF 426
               SCOP domains d4avpd_ D: automated matches                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..eee.....eeee.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eee......eeee..hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ETS_DOMAIN_3  PDB: D:335-415 UniProt: 335-415                                    ----------- PROSITE (1)
                PROSITE (2) ---ETS_DOMAI-----------------------------------ETS_DOMAIN_2    ------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4avp D 334 SLQLWQFLVALLDDPSNSHFIAWTGRGMEFKLIEPEEVARRWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKFVCDPEALFSMAF 426
                                   343       353       363       373       383       393       403       413       423

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

1a	d4avpa_	A:
1b	d4avpb_	B:
1c	d4avpc_	C:
1d	d4avpd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ETV1_HUMAN | P50549)

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: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:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0007638	mechanosensory behavior	Behavior that is dependent upon the sensation of a mechanical stimulus.
	GO:0007517	muscle organ development	The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
	GO:0048935	peripheral nervous system neuron development	The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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: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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Description

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