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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION NMR STRUCTURE OF TRANSCRIPTION FACTOR GATA-4 FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET HR4783B

Authors :   X. Xu, A. Eletsky, D. Lee, E. Kohn, H. Janjua, R. Xiao, T. B. Acton, J. K. Ev G. T. Montelione, T. Szyperski, Northeast Structural Genomics Co (Nesg)

Date :   20 Jun 13 (Deposition) - 10 Jul 13 (Release) - 10 Jul 13 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Structural Genomics, Northeast Structural Genomics Consortium (Nesg), Psi-Biology, Protein Structure Initiative, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Xu, A. Eletsky, D. Lee, E. Kohn, H. Janjua, R. Xiao, T. Acton, J. K. Everett, G. T. Montelione, T. Szyperski
Solution Nmr Structure Of A Transcription Factor Gata-4 Fro Homo Sapiens, Northeast Structural Genomics Consortium (Nesg) Target Hr4783B
To Be Published
PubMed: search

Molecule 1 - TRANSCRIPTION FACTOR GATA-4
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)PMGK
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15NANO6HT_NESG
	Fragment	:	GATA-TYPE 2 ZINC FINGER RESIDUES 262-321
	Gene	:	GATA4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GATA-BINDING FACTOR 4

		1
NMR Structure (20x)	:	A
NMR Structure * (1x)	:	A

Summary Information (see also Sequences/Alignments below)

NMR Structure (1, 1)

No.	Name	Count	Type	Full Name
1	ZN	1	Ligand/Ion	ZINC ION

NMR Structure * (0, 0)

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

NMR Structure (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:13 , CYS A:16 , CYS A:34 , CYS A:37	BINDING SITE FOR RESIDUE ZN A 101

(no "SS Bond" information available for 2M9W)

(no "Cis Peptide Bond" information available for 2M9W)

NMR Structure (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_072113	C	271	S	GATA4_HUMAN	Unclassified	---	A	C	13	S
2	UniProt	VAR_072114	T	279	S	GATA4_HUMAN	Unclassified	---	A	T	21	S
3	UniProt	VAR_067611	T	280	M	GATA4_HUMAN	Disease (ASD2)	387906771	A	T	22	M
4	UniProt	VAR_071516	N	285	S	GATA4_HUMAN	Disease (TOF)	---	A	N	27	S
5	UniProt	VAR_067612	G	296	C	GATA4_HUMAN	Disease (ASD2)	104894073	A	G	38	C
6	UniProt	VAR_067613	G	296	R	GATA4_HUMAN	Disease (VSD1)	104894073	A	G	38	R
7	UniProt	VAR_016204	G	296	S	GATA4_HUMAN	Disease (ASD2)	104894073	A	G	38	S
8	UniProt	VAR_067614	M	310	V	GATA4_HUMAN	Disease (ASD2)	387906772	A	M	52	V
9	UniProt	VAR_067615	Q	316	E	GATA4_HUMAN	Unclassified (ASD2)	56298569	A	Q	58	E

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

NMR Structure * (9, 9)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_072113	C	271	S	GATA4_HUMAN	Unclassified	---	A	C	13	S
2	UniProt	VAR_072114	T	279	S	GATA4_HUMAN	Unclassified	---	A	T	21	S
3	UniProt	VAR_067611	T	280	M	GATA4_HUMAN	Disease (ASD2)	387906771	A	T	22	M
4	UniProt	VAR_071516	N	285	S	GATA4_HUMAN	Disease (TOF)	---	A	N	27	S
5	UniProt	VAR_067612	G	296	C	GATA4_HUMAN	Disease (ASD2)	104894073	A	G	38	C
6	UniProt	VAR_067613	G	296	R	GATA4_HUMAN	Disease (VSD1)	104894073	A	G	38	R
7	UniProt	VAR_016204	G	296	S	GATA4_HUMAN	Disease (ASD2)	104894073	A	G	38	S
8	UniProt	VAR_067614	M	310	V	GATA4_HUMAN	Disease (ASD2)	387906772	A	M	52	V
9	UniProt	VAR_067615	Q	316	E	GATA4_HUMAN	Unclassified (ASD2)	56298569	A	Q	58	E

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

NMR Structure (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GATA_ZN_FINGER_2	PS50114	GATA-type zinc finger domain profile.	GATA4_HUMAN	211-265 265-318	1	- A:7-60
2	GATA_ZN_FINGER_1	PS00344	GATA-type zinc finger domain.	GATA4_HUMAN	217-241 271-295	1	- A:13-37

NMR Structure * (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GATA_ZN_FINGER_2	PS50114	GATA-type zinc finger domain profile.	GATA4_HUMAN	211-265 265-318	1	- A:7-60
2	GATA_ZN_FINGER_1	PS00344	GATA-type zinc finger domain.	GATA4_HUMAN	217-241 271-295	1	- A:13-37

(no "Exon" information available for 2M9W)

NMR Structure

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:63
 aligned with GATA4_HUMAN | P43694 from UniProtKB/Swiss-Prot  Length:442

    Alignment length:63
                                   268       278       288       298       308       318   
          GATA4_HUMAN   259 RRLSASRRVGLSCANCQTTTTTLWRRNAEGEPVCNACGLYMKLHGVPRPLAMRKEGIQTRKRK 321
               SCOP domains d2m9wa_ A: automated matches                                    SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eee.....eeehhhhhhhhhh................... Sec.struct. author
             SAPs(SNPs) (1) ------------S-------SM----S----------C-------------V-----E----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------R------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------S------------------------- SAPs(SNPs) (3)
                PROSITE (1) GATA_ZN-----GATA_ZN_FINGER_1         -------------------------- PROSITE (1)
                PROSITE (2) ------GATA_ZN_FINGER_2  PDB: A:7-60 UniProt: 265-318        --- PROSITE (2)
                 Transcript --------------------------------------------------------------- Transcript
                 2m9w A   1 SHMSASRRVGLSCANCQTTTTTLWRRNAEGEPVCNACGLYMKLHGVPRPLAMRKEGIQTRKRK  63
                                    10        20        30        40        50        60

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 '\|'

NMR Structure

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Glucocorticoid receptor-like (DNA-binding domain) (292)

Superfamily: Glucocorticoid receptor-like (DNA-binding domain) (292)

Family: Erythroid transcription factor GATA-1 (13)

Protein domain: automated matches (3)

Human (Homo sapiens) [TaxId: 9606] (1)

d2m9wa_

(no "CATH Domain" information available for 2M9W)

(no "Pfam Domain" information available for 2M9W)

NMR Structure(hide GO term definitions)

Chain A (GATA4_HUMAN | P43694)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0051525	NFAT protein binding	Interacting selectively and non-covalently with NFAT (nuclear factor of activated T cells) proteins, a family of transcription factors. NFAT proteins have crucial roles in the development and function of the immune system.
	GO:0000977	RNA polymerase II regulatory region sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by 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:0001085	RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
	GO:0033613	activating transcription factor binding	Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription.
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0070410	co-SMAD binding	Interacting selectively and non-covalently with a common mediator SMAD signaling protein.
	GO:0001158	enhancer sequence-specific DNA binding	Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	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: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.
	GO:0001076	transcription factor activity, RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
	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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0001228	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0048646	anatomical structure formation involved in morphogenesis	The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
	GO:0060413	atrial septum morphogenesis	The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another.
	GO:0003289	atrial septum primum morphogenesis	The process in which anatomical structure of an atrial septum primum is generated and organized.
	GO:0003290	atrial septum secundum morphogenesis	The process in which anatomical structure of an atrial septum secundum is generated and organized.
	GO:0007596	blood coagulation	The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
	GO:0055007	cardiac muscle cell differentiation	The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
	GO:0003215	cardiac right ventricle morphogenesis	The process in which the right cardiac ventricle is generated and organized.
	GO:0003208	cardiac ventricle morphogenesis	The process in which the cardiac ventricle is generated and organized. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart.
	GO:0048468	cell development	The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
	GO:0045165	cell fate commitment	The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
	GO:0061049	cell growth involved in cardiac muscle cell development	The growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0071333	cellular response to glucose stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
	GO:0048617	embryonic foregut morphogenesis	The process in which the anatomical structures of the foregut are generated and organized, during the embryonic phase.
	GO:0035054	embryonic heart tube anterior/posterior pattern specification	The establishment, maintenance and elaboration of cell differentiation that results in the anterior/posterior subdivision of the embryonic heart tube. In Drosophila this results in subdivision of the dorsal vessel into to the posterior heart proper and the anterior aorta.
	GO:0003197	endocardial cushion development	The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves.
	GO:0007492	endoderm development	The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
	GO:0001947	heart looping	The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation.
	GO:0060575	intestinal epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell of the intestine.
	GO:0008584	male gonad development	The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
	GO:0010507	negative regulation of autophagy	Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:0030513	positive regulation of BMP signaling pathway	Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0051891	positive regulation of cardioblast differentiation	Any process that activates or increases the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating.
	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:0010575	positive regulation of vascular endothelial growth factor production	Any process that increases or activates the frequency, rate, or extent of production of vascular endothelial growth factor.
	GO:0086004	regulation of cardiac muscle cell contraction	Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0009612	response to mechanical stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0033189	response to vitamin A	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin A stimulus.
	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.
	GO:0060290	transdifferentiation	The conversion of a differentiated cell of one fate into a differentiated cell of another fate without first undergoing cell division or reversion to a more primitive or stem cell-like fate.
	GO:0003281	ventricular septum development	The progression of the ventricular septum over time from its formation to the mature structure.
cellular component
	GO:0090575	RNA polymerase II transcription factor complex	A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase II.
	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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