2DGC | PDT029 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DNA

Authors :   W. Keller, P. Koenig, T. J. Richmond

Date :   28 Sep 95 (Deposition) - 08 Mar 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Basic Domain, Leucine Zipper, Dna Binding, Eukaryotic Regulatory Protein, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Keller, P. Konig, T. J. Richmond
Crystal Structure Of A Bzip/Dna Complex At 2. 2 A: Determinants Of Dna Specific Recognition.
J. Mol. Biol. V. 254 657 1995
PubMed-ID: 7500340 | Reference-DOI: 10.1006/JMBI.1995.0645
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(TPGPGPAPGPAPTPGPAPCPGPTPCPAPTPCPT PCPC)-3')**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - PROTEIN (GCN4)
	Chains	:	A
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2DGC)

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

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

(no "SAP(SNP)/Variant" information available for 2DGC)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BZIP	PS50217	Basic-leucine zipper (bZIP) domain profile.	GCN4_YEAST	231-276	1	A:231-276
2	BZIP_BASIC	PS00036	Basic-leucine zipper (bZIP) domain signature.	GCN4_YEAST	231-245	1	A:231-245

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BZIP	PS50217	Basic-leucine zipper (bZIP) domain profile.	GCN4_YEAST	231-276	2	A:231-276
2	BZIP_BASIC	PS00036	Basic-leucine zipper (bZIP) domain signature.	GCN4_YEAST	231-245	2	A:231-245

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YEL009C	1	YEL009C.1	V:139763-138918	846	GCN4_YEAST	1-281	281	1	A:229-277	49

Asymmetric 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:49
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:49
                                   238       248       258       268         
           GCN4_YEAST   229 ALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKL 277
               SCOP domains d2dgca_ A: GCN4                                   SCOP domains
               CATH domains 2dgcA00 A:229-277 Classic Zinc Finger             CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --BZIP_BASIC     -------------------------------- PROSITE (1)
                PROSITE (2) --BZIP  PDB: A:231-276 UniProt: 231-276         - PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:229-277 UniProt: 1-281           Transcript 1
                 2dgc A 229 ALKRARNTEAARRSRARKLQRMKQLEDKVEELLSKNYHLENEVARLKKL 277
                                   238       248       258       268

Chain B from PDB  Type:DNA  Length:19
                                                   
                 2dgc B -10 TGGAGATGACGTCATCTCC   9
                                    -1|        
                                    -1|        
                                      1

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Coiled coil proteins (689)

Fold: Parallel coiled-coil (407)

Superfamily: Leucine zipper domain (105)

Family: Leucine zipper domain (105)

Protein domain: GCN4 (64)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (63)

d2dgca_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: Classic Zinc Finger (45)

[unclassified] (29)

2dgcA00

A:229-277

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

Asymmetric Unit(hide GO term definitions)

Chain A (GCN4_YEAST | P03069)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003700	DNA-binding transcription factor activity	A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
	GO:0000978	RNA polymerase II proximal promoter sequence-specific DNA binding	Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter of a gene transcribed by RNA polymerase II. The proximal promoter is in cis with and relatively close to the core promoter.
	GO:0001135	RNA polymerase II transcription regulator recruiting activity	The function of binding to an RNA polymerase II (RNAP II) transcription regulator and recruiting it to the general transcription machinery complex in order to modulate transcription initiation.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0001084	obsolete transcription factor activity, TFIID-class binding	OBSOLETE. Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
	GO:0001190	obsolete transcriptional activator activity, RNA polymerase II transcription factor binding	OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
	GO:0001191	obsolete transcriptional repressor activity, RNA polymerase II transcription factor binding	OBSOLETE. Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
	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.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0010691	negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels	Any process that decreases the frequency, rate or extent of the synthesis of RNA from ribosomal protein genes by RNA polymerase II, originating at an RNA polymerase II promoter, as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
	GO:0000122	negative regulation of transcription by RNA polymerase II	Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
	GO:0001080	nitrogen catabolite activation of transcription from RNA polymerase II promoter	A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
	GO:0045899	positive regulation of RNA polymerase II transcriptional preinitiation complex assembly	Any process that activates or increases the frequency, rate or extent of RNA polymerase II transcriptional preinitiation complex assembly.
	GO:1903833	positive regulation of cellular response to amino acid starvation	Any process that activates or increases the frequency, rate or extent of cellular response to amino acid starvation.
	GO:0060261	positive regulation of transcription initiation from RNA polymerase II promoter	Any process that increases the rate, frequency or extent of a process involved in starting 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:0006366	transcription by RNA polymerase II	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:0000790	nuclear chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
	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.

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1dgc	2DGC IS A HIGH RESOLUTION, FULLY REFINED VERSION OF 1DGC THAT INCLUDES 46 WATER MOLECULES.

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