1O4X - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   TERNARY COMPLEX OF THE DNA BINDING DOMAINS OF THE OCT1 AND SOX2 TRANSCRIPTION FACTORS WITH A 19MER OLIGONUCLEOTIDE FROM THE HOXB1 REGULATORY ELEMENT

Authors :   G. M. Clore, D. C. Williams

Date :   17 Jul 03 (Deposition) - 27 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C,D

Keywords :   Oct1, Pou, Pous, Pouhd, Sox2, Hmg-Box, Transcription Factors, Dna, Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. C. Williams, M. Cai, G. M. Clore
Molecular Basis For Synergistic Transcriptional Activation By Oct1 And Sox2 Revealed From The Solution Structure Of The 42-Kda Oct1. Sox2. Hoxb1-Dna Ternary Transcription Factor Complex.
J. Biol. Chem. V. 279 1449 2004
PubMed-ID: 14559893 | Reference-DOI: 10.1074/JBC.M309790200
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTION FACTOR OCT-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - TRANSCRIPTION FACTOR SOX-2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SOX2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

*Molecule 4 - 5'- D(CPAPTPTPAPGPCPAPTPGPAPCPAPAPAPGPAPCPA) -3'**
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES


NMR Structure	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1O4X)

(no "Site" information available for 1O4X)

(no "SS Bond" information available for 1O4X)

(no "Cis Peptide Bond" information available for 1O4X)

NMR Structure (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_075627	W	51	R	SOX2_HUMAN	Unclassified (MCOPS3)	---	B	W	218	R
2	UniProt	VAR_075628	R	74	P	SOX2_HUMAN	Unclassified (MCOPS3)	104893805	B	R	241	P
3	UniProt	VAR_075629	W	79	S	SOX2_HUMAN	Unclassified (MCOPS3)	---	B	W	246	S

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

NMR Structure (6, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HMG_BOX_2	PS50118	HMG boxes A and B DNA-binding domains profile.	SOX2_HUMAN	41-109	1	B:208-276
2	POU_3	PS51179	POU-specific (POUs) domain profile.	PO2F1_HUMAN	280-354	1	A:5-79
3	POU_1	PS00035	POU-specific (POUs) domain signature 1.	PO2F1_HUMAN	298-310	1	A:23-35
4	POU_2	PS00465	POU-specific (POUs) domain signature 2.	PO2F1_HUMAN	322-335	1	A:47-60
5	HOMEOBOX_2	PS50071	'Homeobox' domain profile.	PO2F1_HUMAN	377-437	1	A:110-162
6	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	PO2F1_HUMAN	412-435	1	A:137-160

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000325404	1	ENSE00001228743	chr3:181429722-181432221	2500	SOX2_HUMAN	1-460	460	1	B:206-282	77

NMR Structure

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:129
 aligned with PO2F1_HUMAN | P14859 from UniProtKB/Swiss-Prot  Length:743

    Alignment length:159
                                   289       299       309       319       329       339       349       359       369       379       389       399       409       419       429         
          PO2F1_HUMAN   280 EEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLEKWLNDAENLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 438
               SCOP domains d1o4xa2 A:5-79 Oct-1                                                       ------------------------------d1o4xa1 A:110-163 Oct-1 POU Homeodomain                SCOP domains
               CATH domains ----1o4xA01 A:9-78 lambda repressor-like DNA-binding domains              1                              o4xA02 A:79-162 Homeodomain-like                     - CATH domains
               Pfam domains Pou-1o4xA02 A:5-79                                                         ------------------------------Homeobox-1o4xA01 A:110-161                          -- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh------------------------------..hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) POU_3  PDB: A:5-79 UniProt: 280-354                                        ----------------------HOMEOBOX_2  PDB: A:110-162 UniProt: 377-437                  - PROSITE (1)
                PROSITE (2) ------------------POU_1        -----------POU_2         ----------------------------------------------------------------------------HOMEOBOX_1              --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o4x A   5 EEPSDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMAKLKPLLEKWLNDAE------------------------------SIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 163
                                    14        24        34        44        54        64        74    |    -         -         -     | 114       124       134       144       154         
                                                                                                     79                            110

Chain B from PDB  Type:PROTEIN  Length:77
 aligned with SOX2_HUMAN | P48431 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:77
                                    48        58        68        78        88        98       108       
           SOX2_HUMAN    39 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRK 115
               SCOP domains d1o4xb_ B: Sox-2                                                              SCOP domains
               CATH domains 1o4xB00 B:206-282 DNA Binding (I), subunit A                                  CATH domains
               Pfam domains --HMG_box-1o4xB01 B:208-276                                            ------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------R----------------------P----S------------------------------------ SAPs(SNPs)
                    PROSITE --HMG_BOX_2  PDB: B:208-276 UniProt: 41-109                            ------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:206-282 UniProt: 1-460 [INCOMPLETE]                          Transcript 1
                 1o4x B 206 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRK 282
                                   215       225       235       245       255       265       275

Chain C from PDB  Type:DNA  Length:19
                                                   
                 1o4x C 301 TGTCTTTGTCATGCTAATG 319
                                   310

Chain D from PDB  Type:DNA  Length:19
                                                   
                 1o4x D 320 CATTAGCATGACAAAGACA 338
                                   329

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HMG-box (15)

Family: HMG_box (14)

Homo sapiens (Human) (5)

HMG_box-1o4xB01

B:208-276

Clan: HTH (544)

Family: Homeobox (36)

Homo sapiens (Human) (9)

Homeobox-1o4xA01

A:110-161

Family: Pou (5)

Homo sapiens (Human) (3)

Pou-1o4xA02

A:5-79

NMR Structure(hide GO term definitions)

Chain A (PO2F1_HUMAN | P14859)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	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:0000976	transcription 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 transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
biological process
	GO:0097421	liver regeneration	The regrowth of lost or destroyed liver.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042795	snRNA transcription from RNA polymerase II promoter	The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	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.

Chain B (SOX2_HUMAN | P48431)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0035198	miRNA binding	Interacting selectively and non-covalently with a microRNA, a 21-23 nucleotide RNA that is processed from a stem-loop RNA precursor (pre-miRNA) that is encoded within plant and animal genomes.
	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:0000976	transcription 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 transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
	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:0021984	adenohypophysis development	The progression of the adenohypophysis over time from its initial formation until its mature state. The adenohypophysis is the anterior part of the pituitary. It secretes a variety of hormones and its function is regulated by the hypothalamus.
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0006325	chromatin organization	Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
	GO:0001714	endodermal cell fate specification	The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an endoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.
	GO:0001654	eye development	The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
	GO:0030900	forebrain development	The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
	GO:0021781	glial cell fate commitment	The process in which the developmental fate of a cell becomes restricted such that it will develop into a glial cell.
	GO:0048839	inner ear development	The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0090090	negative regulation of canonical Wnt signaling pathway	Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
	GO:0050680	negative regulation of epithelial cell proliferation	Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
	GO:0045665	negative regulation of neuron differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation.
	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:0097150	neuronal stem cell population maintenance	Any process in by an organism or tissue maintains a population of neuronal stem cells.
	GO:0001649	osteoblast differentiation	The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
	GO:0021983	pituitary gland development	The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands.
	GO:0043410	positive regulation of MAPK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
	GO:0045597	positive regulation of cell differentiation	Any process that activates or increases the frequency, rate or extent of cell differentiation.
	GO:0022409	positive regulation of cell-cell adhesion	Any process that activates or increases the rate or extent of cell adhesion to another cell.
	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:0043281	regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that modulates the activity of a cysteine-type endopeptidase involved in apoptosis.
	GO:0010468	regulation of gene expression	Any process that modulates 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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0070848	response to growth factor	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 growth factor stimulus.
	GO:0009611	response to wounding	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 damage to the organism.
	GO:0035019	somatic stem cell population maintenance	Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
	GO:0042246	tissue regeneration	The regrowth of lost or destroyed tissues.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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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	PO2F1_HUMAN \| P14859	:	1cqt 1e3o 1gt0 1hf0 1oct 1pog 1pou
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