1BC8 | PD0020 - JenaLib

Title :   STRUCTURES OF SAP-1 BOUND TO DNA SEQUENCES FROM THE E74 AND C-FOS PROMOTERS PROVIDE INSIGHTS INTO HOW ETS PROTEINS DISCRIMINATE BETWEEN RELATED DNA TARGETS

Authors :   Y. Mo, B. Vaessen, K. Johnston, R. Marmorstein

Date :   05 May 98 (Deposition) - 01 Dec 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.93

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

Keywords :   Ets Domain, Dna-Binding Domain, Winged Helix-Turn-Helix, Crystal Structure, Dna-Binding Specificity, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Mo, B. Vaessen, K. Johnston, R. Marmorstein
Structures Of Sap-1 Bound To Dna Targets From The E74 And C-Fos Promoters: Insights Into Dna Sequence Discrimination By Ets Proteins.
Mol. Cell V. 2 201 1998
PubMed-ID: 9734357 | Reference-DOI: 10.1016/S1097-2765(00)80130-6
(for further references see the PDB file header)

Compounds

*Molecule 1 - DNA (5'-D(TPAPCPCPGPGPAPAPGPT)-3')*
	Chains	:	A
	Engineered	:	YES
	Synonym	:	E74 DNA FRAGMENT
	Synthetic	:	YES

*Molecule 2 - DNA (5'-D(APAPCPTPTPCPCPGPGPT)-3')*
	Chains	:	B
	Engineered	:	YES
	Synonym	:	E74 DNA FRAGMENT
	Synthetic	:	YES

Molecule 3 - PROTEIN (SAP-1 ETS DOMAIN)
	Cellular Location	:	NUCLEUS
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Variant	:	LYSS
	Expression System Vector	:	PRSETA
	Expression System Vector Type	:	BACTERIA
	Fragment	:	ETS DOMAIN, RESIDUES 1-93
	Gene	:	SAP-1 RESIDUES 1-93
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SAP-1

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (2, 2)

Sequences/Alignments

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:DNA  Length:10
                                         
                  1bc8 A  1 TACCGGAAGT 10
                                    10

Chain B from PDB  Type:DNA  Length:10
                                         
                  1bc8 B 11 AACTTCCGGT 20
                                    20

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with ELK4_HUMAN | P28324 from UniProtKB/Swiss-Prot  Length:431

    Alignment length:93
                                    10        20        30        40        50        60        70        80        90   
            ELK4_HUMAN    1 MDSAITLWQFLLQLLQKPQNKHMICWTSNDGQFKLLQAEEVARLWGIRKNKPNMNYDKLSRALRYYYVKNIIKKVNGQKFVYKFVSYPEILNM 93
               SCOP domains d1bc8c_ C: Serum response factor accessory protein 1a, SAP-1                                  SCOP domains
               CATH domains 1bc8C00 C:1-93 'winged helix' repressor DNA binding domain                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh...ee.....eee..hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eee......eeee...hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ETS_DOMAIN_3  PDB: C:5-85 UniProt: 5-85                                          -------- PROSITE (1)
                PROSITE (2) ------ETS_DOMAI-----------------------------------ETS_DOMAIN_2    --------------------------- PROSITE (2)
               Transcript 1 Exon 1.3  PDB: C:1-69 UniProt: 1-69                                  Exon 1.4b  PDB: C:70-93  Transcript 1
                  1bc8 C  1 MDSAITLWQFLLQLLQKPQNKHMICWTSNDGQFKLLQAEEVARLWGIRKNKPNMNYDKLSRALRYYYVKNIIKKVNGQKFVYKFVSYPEILNM 93
                                    10        20        30        40        50        60        70        80        90

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

Chain C (ELK4_HUMAN | P28324)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0001047	core promoter binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. 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: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:0003712	transcription cofactor activity	Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory 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.
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:0070932	histone H3 deacetylation	The modification of histone H3 by the removal of one or more acetyl groups.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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.

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