2G7X - JenaLib

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Theoretical Model (Jmol Viewer)

Title :   HOMOLOGY MODEL OF THE CARBOXY TERMINAL REGION OF HUMAN WILM'S TUMOR PROTEIN, WT1 (SER415 TO ALA MUTANT)

Authors :   R. Khurshid, A. Salim, A. Abbasi

Date :   01 Mar 06 (Deposition) - 14 Mar 06 (Release) - 14 Mar 06 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,B,C,_^#
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Wilm'S Tumor Protein, Tumor Suppressor Protein, Wt1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Khurshid, A. Salim, A. Abbasi
Homology Model Of The Carboxy Terminal Region Of Human Wilm'S Tumor Protein, Wt1: Study Of Important Residues Implicated In Dna Binding
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - WILMS' TUMOR PROTEIN
	Chains	:	A
	Fragment	:	WT1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	WT33

*Molecule 2 - 5'-D(APGPCPGPTPGPGPGPCPGPT)-3'**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 3 - 5'-D(TPAPCPGPCPCPCPAPCPGPC)-3'**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES


Theoretical Model	:

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Theoretical Model (2, 4)

No.	Name	Count	Type	Full Name
1	CO	1	Ligand/Ion	COBALT (II) ION
2	ZN	3	Ligand/Ion	ZINC ION

(no "Site" information available for 2G7X)

(no "SS Bond" information available for 2G7X)

(no "Cis Peptide Bond" information available for 2G7X)

Theoretical Model (34, 34)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_015053	R	312	Q	WT1_HUMAN	Disease (NPHS4)	---	A	R	312	Q
02	UniProt	VAR_007743	C	330	Y	WT1_HUMAN	Disease (DDS)	---	A	C	330	Y
03	UniProt	VAR_015054	M	342	R	WT1_HUMAN	Disease (DDS)	---	A	M	342	R
04	UniProt	VAR_043799	C	355	G	WT1_HUMAN	Disease (WT1)	---	A	C	355	G
05	UniProt	VAR_015055	C	355	Y	WT1_HUMAN	Disease (DDS)	---	A	C	355	Y
06	UniProt	VAR_007744	C	360	G	WT1_HUMAN	Disease (DDS)	---	A	C	360	G
07	UniProt	VAR_043800	C	360	Y	WT1_HUMAN	Disease (DDS)	---	A	C	360	Y
08	UniProt	VAR_043801	F	364	L	WT1_HUMAN	Disease (NPHS4)	---	A	F	364	L
09	UniProt	VAR_007745	R	366	C	WT1_HUMAN	Disease (WT1)	---	A	R	366	C
10	UniProt	VAR_007746	R	366	H	WT1_HUMAN	Disease (WT1)	---	A	R	366	H
11	UniProt	VAR_043802	R	366	L	WT1_HUMAN	Disease (DDS)	---	A	R	366	L
12	UniProt	VAR_043803	Q	369	P	WT1_HUMAN	Disease (DDS)	---	A	Q	369	P
13	UniProt	VAR_007747	H	373	Q	WT1_HUMAN	Disease (WT1)	---	A	H	373	Q
14	UniProt	VAR_015056	H	373	Y	WT1_HUMAN	Disease (DDS)	---	A	H	373	Y
15	UniProt	VAR_015057	H	377	R	WT1_HUMAN	Disease (DDS)	---	A	H	377	R
16	UniProt	VAR_007748	H	377	Y	WT1_HUMAN	Disease (NPHS4)	---	A	H	377	Y
17	UniProt	VAR_043804	G	379	C	WT1_HUMAN	Disease (NPHS4)	---	A	G	379	C
18	UniProt	VAR_007749	F	383	L	WT1_HUMAN	Disease (NPHS4)	---	A	F	383	L
19	UniProt	VAR_015058	C	385	R	WT1_HUMAN	Disease (DDS)	---	A	C	385	R
20	UniProt	VAR_015059	C	388	F	WT1_HUMAN	Disease (DDS)	---	A	C	388	F
21	UniProt	VAR_043805	C	388	R	WT1_HUMAN	Disease (NPHS4)	---	A	C	388	R
22	UniProt	VAR_043806	C	388	Y	WT1_HUMAN	Disease (DDS)	---	A	C	388	Y
23	UniProt	VAR_015060	F	392	L	WT1_HUMAN	Disease (FS)	---	A	F	392	L
24	UniProt	VAR_043807	R	394	L	WT1_HUMAN	Disease (WT1)	---	A	R	394	L
25	UniProt	VAR_043808	R	394	P	WT1_HUMAN	Disease (DDS)	---	A	R	394	P
26	UniProt	VAR_015061	R	394	Q	WT1_HUMAN	Disease (DDS)	---	A	R	394	Q
27	UniProt	VAR_007750	R	394	W	WT1_HUMAN	Disease (WT1)	---	A	R	394	W
28	UniProt	VAR_007752	D	396	G	WT1_HUMAN	Disease (DDS)	---	A	D	396	G
29	UniProt	VAR_007751	D	396	N	WT1_HUMAN	Disease (NPHS4)	---	A	D	396	N
30	UniProt	VAR_043809	D	396	Y	WT1_HUMAN	Disease (DDS)	---	A	D	396	Y
31	UniProt	VAR_043810	H	397	P	WT1_HUMAN	Disease (NPHS4)	---	A	H	397	P
32	UniProt	VAR_015062	L	398	P	WT1_HUMAN	Disease (DDS)	---	A	L	398	P
33	UniProt	VAR_043811	H	401	Y	WT1_HUMAN	Disease (DDS)	---	A	H	401	Y
34	UniProt	VAR_043812	H	405	R	WT1_HUMAN	Disease (DDS)	---	A	H	405	R

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

Theoretical Model (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_FINGER_C2H2_1	PS00028	Zinc finger C2H2 type domain signature.	WT1_HUMAN	325-347 355-377 385-405 416-438	4	A:325-347 A:355-377 A:385-405 A:416-438

(no "Exon" information available for 2G7X)

Theoretical Model

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:140
 aligned with WT1_HUMAN | P19544 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:140
                                   319       329       339       349       359       369       379       389       399       409       419       429       439       449
            WT1_HUMAN   310 LVRSASETSEKRPFMCAYPGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGKTSEKPFSCRWPSCQKKFARSDELVRHHNMHQRNMTKLQLAL 449
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..................hhhhhhhhhhhhhhh..ee........ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh......ee........ee.hhhhhhhhhhhhhh......... Sec.struct. author
             SAPs(SNPs) (1) --Q-----------------Y-----------R------------G----G---L-C--P---Q---R-C---L-R--F---L-L-GPP--Y---R-------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------Y----Y-----H------Y---Y----------R-----P-N----------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------L---------------------Y-----Q-Y----------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) ------------------------------------------------------------------------------------W------------------------------------------------------- SAPs(SNPs) (4)
                    PROSITE ---------------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1   ----------ZINC_FINGER_C2H2_1     ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g7x A 310 LVRSASETSEKRPFMCAYPGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGKTSEKPFACRWPSCQKKFARSDELVRHHNMHQRNMTKLQLAL 449
                                   319       329       339       349       359       369       379       389       399       409       419       429       439       449

Chain B from PDB  Type:DNA  Length:11
                                           
                 2g7x B   1 AGCGTGGGCGT  11
                                    10

Chain C from PDB  Type:DNA  Length:11
                                           
                 2g7x C  51 TACGCCCACGC  61
                                    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 '\|'

(no "SCOP Domain" information available for 2G7X)

(no "CATH Domain" information available for 2G7X)

(no "Pfam Domain" information available for 2G7X)

Theoretical Model(hide GO term definitions)

Chain A (WT1_HUMAN | P19544)

molecular function
	GO:0070742	C2H2 zinc finger domain binding	Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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: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: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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	GO:0035802	adrenal cortex formation	The process that gives rise to the adrenal cortex. This process pertains to the initial formation of a structure from unspecified parts. The adrenogonadal primordium from which the adrenal cortex is formed derives from a condensation of coelomic epithelial cells (the urogenital ridge; the same structure from which gonads and kidney also originate).
	GO:0030325	adrenal gland development	The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells.
	GO:0001658	branching involved in ureteric bud morphogenesis	The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.
	GO:0043010	camera-type eye development	The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
	GO:0060923	cardiac muscle cell fate commitment	The commitment of cells to specific cardiac muscle cell fates and their capacity to differentiate into cardiac muscle cells. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction.
	GO:0071320	cellular response to cAMP	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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0071371	cellular response to gonadotropin 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 gonadotropin stimulus.
	GO:0060539	diaphragm development	The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs.
	GO:0030855	epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
	GO:0007281	germ cell development	The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism.
	GO:0032836	glomerular basement membrane development	The process whose specific outcome is the progression of the glomerular basement membrane over time, from its formation to the mature structure. The glomerular basement membrane is the basal laminal portion of the glomerulus which performs the actual filtration.
	GO:0072112	glomerular visceral epithelial cell differentiation	The process in which a relatively unspecialized cell acquires specialized features of a glomerular visceral epithelial cell. A glomerular visceral epithelial cell is a specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells.
	GO:0032835	glomerulus development	The progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney. The glomerulus is part of the nephron and is restricted to one body segment.
	GO:0008406	gonad development	The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones.
	GO:0007507	heart development	The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
	GO:0001822	kidney development	The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
	GO:0030539	male genitalia development	The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure.
	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:0060231	mesenchymal to epithelial transition	A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell.
	GO:0072284	metanephric S-shaped body morphogenesis	The process in which the metanephric S-shaped body is generated and organized. The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros.
	GO:0072207	metanephric epithelium development	The process whose specific outcome is the progression of an epithelium in the metanephros over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
	GO:0072075	metanephric mesenchyme development	The biological process whose specific outcome is the progression of a metanephric mesenchyme from an initial condition to its mature state. This process begins with the formation of metanephric mesenchyme and ends with the mature structure. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0030308	negative regulation of cell growth	Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:2000195	negative regulation of female gonad development	Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development.
	GO:0072302	negative regulation of metanephric glomerular mesangial cell proliferation	Any process that decreases the frequency, rate or extent of metanephric glomerular mesangial cell proliferation.
	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:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0060421	positive regulation of heart growth	Any process that increases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
	GO:2000020	positive regulation of male gonad development	Any process that activates or increases the frequency, rate or extent of male gonad development.
	GO:2001076	positive regulation of metanephric ureteric bud development	Any process that activates or increases the frequency, rate or extent of metanephric ureteric bud development.
	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:0072166	posterior mesonephric tubule development	The progression of the posterior mesonephric tubule over time, from its initial formation to the mature structure. The posterior mesonephric tubule is an epithelial tube that is part of the mesonephros.
	GO:0003156	regulation of animal organ formation	Any process that modulates the rate, frequency or extent of animal organ formation. Organ formation is the process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment.
	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:0007530	sex determination	Any process that establishes and transmits the specification of sexual status of an individual organism.
	GO:0007356	thorax and anterior abdomen determination	Specification of the central (trunk) regions of the embryo by the gap genes; exemplified in insects by the actions of the Kruppel gene product.
	GO:0009888	tissue development	The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
	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:0001657	ureteric bud development	The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure.
	GO:0001570	vasculogenesis	The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
	GO:0061032	visceral serous pericardium development	The progression of the visceral serous pericardium from its formation to the mature structure. The visceral serous pericardium is the inner layer of the pericardium.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	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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1lu6	THEORETICAL MODEL OF THE CARBOXY TERMINAL REGION OF HUMAN WILM'S TUMOR PROTEIN, WT1
2g7t
2g7u
2g7v

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (34, 34)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (65, 65)

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