2K7S - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   HUMAN ARNT C-TERMINAL PAS DOMAIN, 3 RESIDUE IB SLIP

Authors :   M. R. Evans, P. B. Card, K. H. Gardner

Date :   20 Aug 08 (Deposition) - 20 Jan 09 (Release) - 10 Mar 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Arnt Pas-B, Beta-Strand Slip, Pas Domain, Activator, Alternative Splicing, Dna-Binding, Nucleus, Polymorphism, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. Evans, P. B. Card, K. H. Gardner
Arnt Pas-B Has A Fragile Native State Structure With An Alternative Beta-Sheet Register Nearby In Sequence Space
Proc. Natl. Acad. Sci. Usa V. 106 2617 2009
PubMed-ID: 19196990 | Reference-DOI: 10.1073/PNAS.0808270106
(for further references see the PDB file header)

Molecule 1 - ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHIS-PARALLEL
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ARNT PAS-B
	Gene	:	ARNT
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ARNT PROTEIN, DIOXIN RECEPTOR, NUCLEAR TRANSLOCATOR, HYPOXIA-INDUCIBLE FACTOR 1 BETA, HIF-1 BETA


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2K7S)

(no "Site" information available for 2K7S)

(no "SS Bond" information available for 2K7S)

NMR Structure

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20	Asn A:97	-	Pro A:98

NMR Structure (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024280	R	430	Q	ARNT_HUMAN	Polymorphism	2229175	A	R	79	Q
2	UniProt	VAR_049537	E	435	K	ARNT_HUMAN	Polymorphism	2229176	A	E	84	K

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

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAS	PS50112	PAS repeat profile.	ARNT_HUMAN	161-235 368-419	1	- A:17-68

NMR Structure (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000358595	1a	ENSE00002062254	chr1:150849244-150849019	226	ARNT_HUMAN	1-9	9	0	-	-
1.3	ENST00000358595	3	ENSE00001717520	chr1:150830936-150830825	112	ARNT_HUMAN	9-46	38	0	-	-
1.5b	ENST00000358595	5b	ENSE00001071957	chr1:150825282-150825238	45	ARNT_HUMAN	46-61	16	0	-	-
1.6	ENST00000358595	6	ENSE00000960027	chr1:150818783-150818739	45	ARNT_HUMAN	61-76	16	0	-	-
1.7	ENST00000358595	7	ENSE00001263986	chr1:150814944-150814900	45	ARNT_HUMAN	76-91	16	0	-	-
1.8b	ENST00000358595	8b	ENSE00000960029	chr1:150812130-150811917	214	ARNT_HUMAN	91-162	72	0	-	-
1.9c	ENST00000358595	9c	ENSE00000960030	chr1:150808969-150808756	214	ARNT_HUMAN	163-234	72	0	-	-
1.10b	ENST00000358595	10b	ENSE00000960031	chr1:150807116-150807014	103	ARNT_HUMAN	234-268	35	0	-	-
1.11	ENST00000358595	11	ENSE00000960032	chr1:150804875-150804810	66	ARNT_HUMAN	268-290	23	0	-	-
1.12a	ENST00000358595	12a	ENSE00000960033	chr1:150804379-150804294	86	ARNT_HUMAN	290-319	30	0	-	-
1.13d	ENST00000358595	13d	ENSE00001417988	chr1:150802456-150802380	77	ARNT_HUMAN	319-344	26	0	-	-
1.15b	ENST00000358595	15b	ENSE00001414390	chr1:150801703-150801569	135	ARNT_HUMAN	345-389	45	1	A:2-38	37
1.16	ENST00000358595	16	ENSE00001186051	chr1:150799093-150799019	75	ARNT_HUMAN	390-414	25	1	A:39-63	25
1.17	ENST00000358595	17	ENSE00001804030	chr1:150795821-150795670	152	ARNT_HUMAN	415-465	51	1	A:64-114	51
1.18b	ENST00000358595	18b	ENSE00001044530	chr1:150790506-150790396	111	ARNT_HUMAN	465-502	38	1	A:114-119	6
1.19c	ENST00000358595	19c	ENSE00001044549	chr1:150789909-150789837	73	ARNT_HUMAN	502-526	25	0	-	-
1.20	ENST00000358595	20	ENSE00001044525	chr1:150789678-150789558	121	ARNT_HUMAN	527-567	41	0	-	-
1.21	ENST00000358595	21	ENSE00001044520	chr1:150789366-150789264	103	ARNT_HUMAN	567-601	35	0	-	-
1.22a	ENST00000358595	22a	ENSE00001044548	chr1:150788882-150788735	148	ARNT_HUMAN	601-650	50	0	-	-
1.23a	ENST00000358595	23a	ENSE00001151505	chr1:150786715-150786553	163	ARNT_HUMAN	651-705	55	0	-	-
1.24a	ENST00000358595	24a	ENSE00001371736	chr1:150785814-150785648	167	ARNT_HUMAN	705-760	56	0	-	-
1.25f	ENST00000358595	25f	ENSE00001855735	chr1:150784586-150782181	2406	ARNT_HUMAN	761-789	29	0	-	-

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:119
 aligned with ARNT_HUMAN | P27540 from UniProtKB/Swiss-Prot  Length:789

    Alignment length:139
                                   341       351       361       371       381       391       401       411       421       431       441       451       461         
           ARNT_HUMAN   332 GSKFCLVAIGRLQVTSSPNCTDMSNVCQPTEFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSFTFQNPYSDEIEYIICTNTNVKNSSQE 470
               SCOP domains d                    2k7sa_ A: automated matches                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------------.........eeeeee.....eeee..hhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeeeee....hhhhheeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------Q----K----------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------PAS  PDB: A:17-68 UniProt: 368-419                  --------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.13d   Exon 1.15b  PDB: A:2-38 UniProt: 345-389     Exon 1.16  PDB: A:39-63  Exon 1.17  PDB: A:64-114 UniProt: 415-465          ----- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------1.18b  Transcript 1 (2)
                 2k7s A   1 G--------------------AMDNVCQPTEFISRHNIEGIFTFVDHRCVATVGYQPQELLGKNIVEFCHPEDQQLLRDSFQQVVKLKGQVLSVMFRFRSKNQEWLWMRTSSQTAQNPYSDEIETIICTNTNVKNSSQE 119
                            |        -         - |      10        20        30        40        50        60        70        80        90       100       110         
                            |                    2                                                                                                                     
                            1

Legend:		→ Mismatch	(orange background)
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		→ 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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Profilin-like (304)

Superfamily: PYP-like sensor domain (PAS domain) (163)

Family: automated matches (33)

Protein domain: automated matches (33)

Human (Homo sapiens) [TaxId: 9606] (15)

d2k7sa_

(no "CATH Domain" information available for 2K7S)

(no "Pfam Domain" information available for 2K7S)

NMR Structure(hide GO term definitions)

Chain A (ARNT_HUMAN | P27540)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004874	aryl hydrocarbon receptor activity	Combining with an aryl hydrocarbon and transmitting the signal to initiate a change in cell activity. The aryl hydrocarbon receptor is a ligand-activated transcription factor which translocates to the nucleus to activate transcription upon ligand-binding.
	GO:0017162	aryl hydrocarbon receptor binding	Interacting selectively and non-covalently with an aryl hydrocarbon receptor.
	GO:0035326	enhancer binding	Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
	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:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	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:0003705	transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
	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:0000989	transcription factor activity, transcription factor binding	Interacting selectively and non-covalently with a specific 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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	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:0001892	embryonic placenta development	The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
	GO:0030522	intracellular receptor signaling pathway	Any series of molecular signals initiated by a ligand binding to an receptor located within a cell.
	GO:0042789	mRNA transcription from RNA polymerase II promoter	The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
	GO:0001938	positive regulation of endothelial cell proliferation	Any process that activates or increases the rate or extent of endothelial cell proliferation.
	GO:0045648	positive regulation of erythrocyte differentiation	Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation.
	GO:0045821	positive regulation of glycolytic process	Any process that activates or increases the frequency, rate or extent of glycolysis.
	GO:0046886	positive regulation of hormone biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones.
	GO:0033235	positive regulation of protein sumoylation	Any process that activates or increases the frequency, rate or extent of the addition of SUMO groups to a protein.
	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:0030949	positive regulation of vascular endothelial growth factor receptor signaling pathway	Any process that activates or increases the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
	GO:0061418	regulation of transcription from RNA polymerase II promoter in response to hypoxia	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a hypoxia stimulus.
	GO:0043619	regulation of transcription from RNA polymerase II promoter in response to oxidative stress	Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0001666	response to hypoxia	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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
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: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:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

NMR Structure
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(no "Sites" information available for 2k7s)

	Cis Peptide Bonds
		Asn A:97 - Pro A:98	[ RasMol ]

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1x0o	ARNT PAS-B WILDTYPE RELATED ID: 15928 RELATED DB: BMRB

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 20)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (1, 1)

Exons (4, 4)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (0, 0)

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Gene Ontology (36, 36)

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