1D66 | PDT003 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX

Authors :   R. Marmorstein, M. Carey, M. Ptashne, S. C. Harrison

Date :   06 Mar 92 (Deposition) - 06 Mar 92 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Protein-Dna Complex, Double Helix, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Marmorstein, M. Carey, M. Ptashne, S. C. Harrison
Dna Recognition By Gal4: Structure Of A Protein-Dna Complex.
Nature V. 356 408 1992
PubMed-ID: 1557122 | Reference-DOI: 10.1038/356408A0
(for further references see the PDB file header)

*Molecule 1 - DNA (5'- D(CPCPGPGPAPGPGPAPCPAPGPTPCPCPTPCPC PGPG)-3')**
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - DNA (5'- D(CPCPGPGPAPGPGPAPCPTPGPTPCPCPTPCPC PGPG)-3')**
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - PROTEIN (GAL4)
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CD	4	Ligand/Ion	CADMIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS B:11 , CYS B:28 , CYS B:31 , CYS B:38 , CD B:68	BINDING SITE FOR RESIDUE CD B 67
2	AC2	SOFTWARE	CYS B:11 , CYS B:14 , CYS B:21 , CYS B:28 , CD B:67	BINDING SITE FOR RESIDUE CD B 68
3	AC3	SOFTWARE	CYS A:11 , CYS A:28 , CYS A:31 , CYS A:38 , CD A:68	BINDING SITE FOR RESIDUE CD A 67
4	AC4	SOFTWARE	CYS A:11 , CYS A:14 , CYS A:21 , CYS A:28 , CD A:67	BINDING SITE FOR RESIDUE CD A 68

(no "SS Bond" information available for 1D66)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:25	-	Pro A:26
2	Lys B:25	-	Pro B:26

(no "SAP(SNP)/Variant" information available for 1D66)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZN2_CY6_FUNGAL_1	PS00463	Zn(2)-C6 fungal-type DNA-binding domain signature.	GAL4_YEAST	10-38	2	A:10-38 B:10-38
2	ZN2_CY6_FUNGAL_2	PS50048	Zn(2)-C6 fungal-type DNA-binding domain profile.	GAL4_YEAST	10-40	2	A:10-40 B:10-40

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YPL248C	1	YPL248C.1	XVI:82356-79711	2646	GAL4_YEAST	1-881	881	2	A:8-64 B:8-64	57 57

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:PROTEIN  Length:57
 aligned with GAL4_YEAST | P04386 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:57
                                    17        27        37        47        57       
            GAL4_YEAST    8 EQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERL 64
               SCOP domains d1d66a1 A:8-48 Gal4                      d1d66a2 A:49-64  SCOP domains
               CATH domains 1d66A00 A:8-64 CD2-Gal4                                   CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.........hhhhhhhh..............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --ZN2_CY6_FUNGAL_1  PDB: A:10-3-------------------------- PROSITE (1)
                PROSITE (2) --ZN2_CY6_FUNGAL_2  PDB: A:10-40 ------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: A:8-64 UniProt: 1-881 [INCOMPLETE]         Transcript 1
                  1d66 A  8 EQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERL 64
                                    17        27        37        47        57

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with GAL4_YEAST | P04386 from UniProtKB/Swiss-Prot  Length:881

    Alignment length:57
                                    17        27        37        47        57       
            GAL4_YEAST    8 EQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERL 64
               SCOP domains d1d66b1 B:8-48 Gal4                      d1d66b2 B:49-64  SCOP domains
               CATH domains 1d66B01 B:8-40 CD2-Gal4          ---------1d66B02 B:50-64 CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.........hhhhhhhh..............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --ZN2_CY6_FUNGAL_1  PDB: B:10-3-------------------------- PROSITE (1)
                PROSITE (2) --ZN2_CY6_FUNGAL_2  PDB: B:10-40 ------------------------ PROSITE (2)
               Transcript 1 Exon 1.1  PDB: B:8-64 UniProt: 1-881 [INCOMPLETE]         Transcript 1
                  1d66 B  8 EQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTRAHLTEVESRLERL 64
                                    17        27        37        47        57

Chain D from PDB  Type:DNA  Length:19
                                                  
                  1d66 D  1 CCGGAGGACAGTCCTCCGG 19
                                    10

Chain E from PDB  Type:DNA  Length:19
                                                  
                  1d66 E 20 CCGGAGGACTGTCCTCCGG 38
                                    29

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Coiled coil proteins (689)

Fold: Parallel coiled-coil (407)

Superfamily: Leucine zipper domain (105)

Family: Leucine zipper domain (105)

Protein domain: CD2-Gal4 (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d1d66a2	A:49-64
1b	d1d66b2	B:49-64

Class: Small proteins (3458)

Fold: Zn2/Cys6 DNA-binding domain (15)

Superfamily: Zn2/Cys6 DNA-binding domain (15)

Family: Zn2/Cys6 DNA-binding domain (15)

Protein domain: Gal4 (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

2a	d1d66a1	A:8-48
2b	d1d66b1	B:8-48

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: CD2-Gal4 (10)

Homologous Superfamily: CD2-Gal4 (10)

[unclassified] (3)

1a	1d66A00	A:8-64
1b	1d66B01	B:8-40

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces (552)

Homologous Superfamily: Single helix bin (2)

[unclassified] (1)

1d66B02

B:50-64

(no "Pfam Domain" information available for 1D66)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GAL4_YEAST | P04386)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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: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:0001133	RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region 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 by RNA polymerase II and recruiting another transcription factor to the DNA in order to modulate transcription by RNAP II.
	GO:0001085	RNA polymerase II transcription factor binding	Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006012	galactose metabolic process	The chemical reactions and pathways involving galactose, the aldohexose galacto-hexose. D-galactose is widely distributed in combined form in plants, animals and microorganisms as a constituent of oligo- and polysaccharides; it also occurs in galactolipids and as its glucoside in lactose and melibiose.
	GO:0000435	positive regulation of transcription from RNA polymerase II promoter by galactose	Any process involving galactose that activates or increases the rate 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: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: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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:25 - Pro A:26	[ RasMol ]
		Lys B:25 - Pro B:26	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)
Insightii
	DNA: ribbon, sticks; protein: ribbon, secondary structure; Cd [ mono GIF format \| stereo GIF format ]
	DNA: spacefill; protein: ribbon, secondadry structure; Cd [ mono GIF format \| stereo GIF format ]
	spacefill; Cd; water [ mono GIF format \| stereo GIF format ]
	DNA: ribbon, sticks; protein: spacefill; Cd; water [ mono GIF format \| stereo GIF format ]
Midas
	sticks; water; Cd [ mono GIF format \| stereo GIF format ]
	spacefill; water [ mono GIF format \| stereo GIF format ]
	DNA: ribbon, plates; protein: ribbon, secondary structutre, sticks; water; Cd [ mono GIF format \| stereo GIF format ]
Setor
	ribbon; chain specific coloring; DNA: labeling [ mono GIF format \| stereo GIF format ]
	DNA: ribbon, sticks; protein: spacefill; chain specific coloring [ mono GIF format \| stereo GIF format ]
	DNA: sticks; protein: spacefill; chain specific coloring [ mono GIF format \| stereo GIF format ]
	DNA: ribbon, sticks; protein: ribbon, secondary structure; chain specific coloring; water; Cd [ mono GIF format \| stereo GIF format ]
	DNA: spacefill; protein: sticks; detailed view [ mono GIF format \| stereo GIF format ]
	DNA: sticks; protein: spacefill; detailed view [ mono GIF format \| stereo GIF format ]
Distance Plot
	representative atoms: CA, O3* [ mono GIF format \| mono PDF format ]

Access by PDB/NDB ID
	1d66
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GAL4_YEAST \| P04386
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GAL4_YEAST \| P04386
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GAL4_YEAST \| P04386	:	1aw6 1hbw 3bts 3coq

(no "Related Entries Specified in the PDB File" available for 1D66)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File