1AU7 | PDR034 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   PIT-1 MUTANT/DNA COMPLEX

Authors :   E. M. Jacobson, P. Li, A. Leon-Del-Rio, M. G. Rosenfeld, A. K. Aggarwal

Date :   12 Sep 97 (Deposition) - 28 Jan 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Complex (Dna-Binding Protein/Dna), Pituitary, Cphd, Pou Domain, Transcription Factor, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. M. Jacobson, P. Li, A. Leon-Del-Rio, M. G. Rosenfeld, A. K. Aggarwal
Structure Of Pit-1 Pou Domain Bound To Dna As A Dimer: Unexpected Arrangement And Flexibility.
Genes Dev. V. 11 198 1997
PubMed-ID: 9009203
(for further references see the PDB file header)

Molecule 1 - CONSENSUS DNA 25-MER
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(CPTPTPCPCPTPCPAPTPGPTPAPTPAPTPAPC PAPTPGPAPGP GPA)-3')*
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - PROTEIN PIT-1
	Cell	:	LACTOTROPES, SOMATOTROPES
	Cellular Location	:	NUCLEAR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Cellular Location	:	INCLUSION BODIES
	Expression System Gene	:	PIT-1
	Expression System Plasmid	:	14B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	PIT-1
	Mutation	:	YES
	Organ	:	PITUITARY GLAND
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Strain	:	SPRAGUE-DAWLEY
	Synonym	:	GHF-1
	Tissue	:	ENDOCRINE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1AU7)

(no "Site" information available for 1AU7)

(no "SS Bond" information available for 1AU7)

(no "Cis Peptide Bond" information available for 1AU7)

(no "SAP(SNP)/Variant" information available for 1AU7)

Asymmetric/Biological Unit (4, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POU_1	PS00035	POU-specific (POUs) domain signature 1.	PIT1_RAT	142-154	2	A:19-31 B:19-31
2	POU_2	PS00465	POU-specific (POUs) domain signature 2.	PIT1_RAT	166-179	2	A:43-56 B:43-56
3	HOMEOBOX_2	PS50071	'Homeobox' domain profile.	PIT1_RAT	212-272	2	A:103-159 B:103-159
4	HOMEOBOX_1	PS00027	'Homeobox' domain signature.	PIT1_RAT	247-270	2	A:134-157 B:134-157

Asymmetric/Biological Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000000905	1	ENSRNOE00000362865	chr11:2959383-2959640	258	PIT1_RAT	1-48	48	0	-	-
1.2	ENSRNOT00000000905	2	ENSRNOE00000288076	chr11:2962179-2962328	150	PIT1_RAT	48-98	51	0	-	-
1.3	ENSRNOT00000000905	3	ENSRNOE00000005955	chr11:2971347-2971571	225	PIT1_RAT	98-173	76	2	A:5-50 B:5-50	46 46
1.4	ENSRNOT00000000905	4	ENSRNOE00000005956	chr11:2977249-2977413	165	PIT1_RAT	173-228	56	2	A:50-115 (gaps) B:50-115 (gaps)	56 56
1.5	ENSRNOT00000000905	5	ENSRNOE00000005957	chr11:2978069-2978129	61	PIT1_RAT	228-248	21	2	A:115-135 B:115-135	21 21
1.6	ENSRNOT00000000905	6	ENSRNOE00000005958	chr11:2978969-2980543	1575	PIT1_RAT	248-317	70	2	A:135-160 B:135-160	26 26

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:130
 aligned with PIT1_RAT | P10037 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:146
                                   137       147       157       167       177       187       197       207       217       227       237       247       257       267      
             PIT1_RAT   128 EIRELEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 273
               SCOP domains d1au7a2 A:5-76 Pit-1                                                    ----------------d1au7a1 A:103-160 Pit-1 POU homeodomain                    SCOP domains
               CATH domains 1au7A01 A:5-76 lambda repressor-like DNA-binding domains                ----------------1au7A02 A:103-159 Homeodomain-like                       - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...hhhhhhhhhh.......hhhhhhhh.....hhhhhhhhhhhhhhhhh...----------------.......hhhhhhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------POU_1        -----------POU_2         --------------------------------HOMEOBOX_2  PDB: A:103-159 UniProt: 212-272                  - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------HOMEOBOX_1              --- PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: A:5-50 UniProt: 98-173         ------------------------------------------------------Exon 1.5             ------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.4  PDB: A:50-115 (gaps) UniProt: 173-228         -------------------Exon 1.6  PDB: A:135-160   Transcript 1 (2)
                 1au7 A   5 GMRALEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKWLEEAEQ----------------KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 160
                                    14        24        34        44        54        64        74 |       -       104       114       124       134       144       154      
                                                                                                  76              103

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with PIT1_RAT | P10037 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:146
                                   137       147       157       167       177       187       197       207       217       227       237       247       257       267      
             PIT1_RAT   128 EIRELEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 273
               SCOP domains d1au7b2 B:5-74 Pit-1                                                  ------------------d1au7b1 B:103-160 Pit-1 POU homeodomain                    SCOP domains
               CATH domains 1au7B01 B:5-74 lambda repressor-like DNA-binding domains              -------------------1au7B02 B:104-159 Homeodomain-like                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhhhhhh....hhhhhhhhhhhhhhhhh.------------------..........hhhhhhhh.......hhhhhhhhhhh...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------POU_1        -----------POU_2         --------------------------------HOMEOBOX_2  PDB: B:103-159 UniProt: 212-272                  - PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------HOMEOBOX_1              --- PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: B:5-50 UniProt: 98-173         ------------------------------------------------------Exon 1.5             ------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.4  PDB: B:50-115 (gaps) UniProt: 173-228         -------------------Exon 1.6  PDB: B:135-160   Transcript 1 (2)
                 1au7 B   5 GMRALEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKWLEEA------------------KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 160
                                    14        24        34        44        54        64        74         -       104       114       124       134       144       154      
                                                                                                74                103

Chain C from PDB  Type:DNA  Length:25
                                                         
                 1au7 C 449 TCCTCATGTATATACATGAGGAAGG 473
                                   458       468

Chain D from PDB  Type:DNA  Length:24
                                                        
                 1au7 D 475 CTTCCTCATGTATATACATGAGGA 498
                                   484       494

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Homeodomain-like (373)

Family: Homeodomain (93)

Protein domain: Pit-1 POU homeodomain (1)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

1a	d1au7a1	A:103-160
1b	d1au7b1	B:103-160

Fold: lambda repressor-like DNA-binding domains (180)

Superfamily: lambda repressor-like DNA-binding domains (180)

Family: POU-specific domain (9)

Protein domain: Pit-1 (1)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

2a	d1au7a2	A:5-76
2b	d1au7b2	B:5-74

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: 434 Repressor (Amino-terminal Domain) (116)

Homologous Superfamily: lambda repressor-like DNA-binding domains (100)

[unclassified] (45)

1a	1au7A01	A:5-76
1b	1au7B01	B:5-74

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

[unclassified] (65)

2a	1au7A02	A:103-159
2b	1au7B02	B:104-159

(no "Pfam Domain" information available for 1AU7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PIT1_RAT | P10037)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0001102	RNA polymerase II activating transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
	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:0001105	RNA polymerase II transcription coactivator activity	Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
	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: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: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:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
	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: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:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	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:0001708	cell fate specification	The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment.
	GO:0008340	determination of adult lifespan	The control of viability and duration in the adult phase of the life-cycle.
	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:0051169	nuclear transport	The directed movement of substances into, out of, or within the nucleus.
	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:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0032962	positive regulation of inositol trisphosphate biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of inositol trisphosphate.
	GO:0040018	positive regulation of multicellular organism growth	Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size.
	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:0043567	regulation of insulin-like growth factor receptor signaling pathway	Any process that modulates the frequency, rate or extent of insulin-like growth factor receptor signaling.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0060133	somatotropin secreting cell development	The process whose specific outcome is the progression of a somatotropin secreting cell over time, from its formation to the mature structure. A somatotropin secreting cell is an acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin.
	GO:0060126	somatotropin secreting cell differentiation	The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a somatotropin secreting cell. A somatotropin secreting cell is an acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin.
	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: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.

Asymmetric/Biological Unit
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	1au7
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Description

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Ligands, Modified Residues, Ions (0, 0)

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PROSITE Motifs (4, 8)

Exons (4, 8)

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SCOP Domains (2, 4)

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