2CCN - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   PLI E20C IS ANTIPARALLEL

Authors :   M. K. Yadav, L. J. Leman, D. J. Price, C. L. Brooks Iii, C. D. Stout, M. R. Ghadiri

Date :   16 Jan 06 (Deposition) - 06 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Four Helix Bundle, Antiparallel, Parallel, Pli, Dna-Binding, Nuclear Protein, Transcription, Transcription Regulation, Activator, Amino-Acid Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. K. Yadav, L. J. Leman, D. J. Price, C. L. Brooks Iii, C. D. Stout, M. R. Ghadiri
Coiled Coils At The Edge Of Configurational Heterogeneity. Structural Analyses Of Parallel And Antiparallel Homotetrameric Coiled Coils Reveal Configurational Sensitivity To A Single Solvent- Exposed Amino Acid Substitution.
Biochemistry V. 45 4463 2006
PubMed-ID: 16584182 | Reference-DOI: 10.1021/BI060092Q

Molecule 1 - GENERAL CONTROL PROTEIN GCN4
	Chains	:	A, B
	Fragment	:	RESIDUES 249-281
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN

		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 2CCN)

(no "Site" information available for 2CCN)

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

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

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

(no "PROSITE Motif" information available for 2CCN)

Asymmetric Unit (1, 2)

	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	2	A:1-33 B:1-33	33 33

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
	(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:33
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:33
                                   258       268       278   
           GCN4_YEAST   249 RMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains d2ccna1 A:1-33 GCN4               SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-33             Transcript 1
                 2ccn A   1 RMKQIEDKLEEILSKLYHICNELARIKKLLGER  33
                                    10        20        30

Chain B from PDB  Type:PROTEIN  Length:33
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:33
                                   258       268       278   
           GCN4_YEAST   249 RMKQLEDKVEELLSKNYHLENEVARLKKLVGER 281
               SCOP domains d2ccnb_ B: GCN4                   SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-33             Transcript 1
                 2ccn B   1 RMKQIEDKLEEILSKLYHICNELARIKKLLGER  33
                                    10        20        30

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 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: GCN4 (64)

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

1a	d2ccna1	A:1-33
1b	d2ccnb_	B:

(no "CATH Domain" information available for 2CCN)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric 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
(no "Ligands, Modified Residues, Ions" information available for 2ccn)

	Sites
(no "Sites" information available for 2ccn)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ccn)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 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)

Access by PDB/NDB ID
	2ccn
		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
	GCN4_YEAST \| P03069
		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
	GCN4_YEAST \| P03069
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1ce9	HELIX CAPPING IN THE GCN4 LEUCINE ZIPPER
1dgc	GCN4 LEUCINE ZIPPER COMPLEXED WITH SPECIFIC ATF/CREB SITE DEOXYRIBONUCLEIC ACID
1env	ATOMIC STRUCTURE OF THE ECTODOMAIN FROM HIV -1 GP41
1fav	THE STRUCTURE OF AN HIV-1 SPECIFIC CELL ENTRY INHIBITOR INCOMPLEX WITH THE HIV-1 GP41 TRIMERIC CORE
1gcl	GCN4 LEUCINE ZIPPER CORE MUTANT P-LI
1gcm	GCN4 LEUCINE ZIPPER CORE MUTANT P-LI
1gk6	HUMAN VIMENTIN COIL 2B FRAGMENT LINKED TO GCN4 LEUCINE ZIPPER (Z2B)
1gzl	CRYSTAL STRUCTURE OF C14LINKMID/IQN17: A CROSS-LINKED INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 HYDROPHOBIC POCKET
1ihq	GLYTM1BZIP: A CHIMERIC PEPTIDE MODEL OF THE N-TERMINUS OF ARAT SHORT ALPHA TROPOMYOSIN WITH THE N-TERMINUS ENCODED BYEXON 1B
1ij0	COILED COIL TRIMER GCN4-PVLS SER AT BURIED D POSITION
1ij1	GCN4-PVLT COILED-COIL TRIMER WITH THREONINE AT THE D(12)POSITION
1ij2	GCN4-PVTL COILED-COIL TRIMER WITH THREONINE AT THE A(16)POSITION
1ij3	GCN4-PVSL COILED-COIL TRIMER WITH SERINE AT THE A(16)POSITION
1kql	CRYSTAL STRUCTURE OF THE C-TERMINAL REGION OF STRIATEDMUSCLE ALPHA- TROPOMYOSIN AT 2.7 ANGSTROM RESOLUTION
1ld4	PLACEMENT OF THE STRUCTURAL PROTEINS IN SINDBIS VIRUS
1llm	CRYSTAL STRUCTURE OF A ZIF23-GCN4 CHIMERA BOUND TO DNA
1nkn	VISUALIZING AN UNSTABLE COILED COIL: THE CRYSTAL STRUCTUREOF AN N- TERMINAL SEGMENT OF THE SCALLOP MYOSIN ROD
1piq	CRYSTAL STRUCTURE OF GCN4-PIQ, A TRIMERIC COILED COIL WITH BURIED POLAR RESIDUES
1rb1	GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A TRIGONAL AUTOMATICSOLUTION
1rb4	ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT ASN16A TETRAGONAL AUTOMATIC SOLUTION
1rb5	ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT ASN16A TRIGONAL FORM
1rb6	ANTIPARALLEL TRIMER OF GCN4-LEUCINE ZIPPER CORE MUTANT ASN16A TETRAGONAL FORM
1swi	GCN4-LEUCINE ZIPPER CORE MUTANT AS N16A COMPLEXED WITH BENZENE
1tmz	TMZIP: A CHIMERIC PEPTIDE MODEL OF THE N- TERMINUS OF ALPHA TROPOMYOSIN, NMR, 15 STRUCTURES
1unt	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unu	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unv	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unw	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unx	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uny	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1unz	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo0	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo1	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo2	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo3	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo4	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1uo5	STRUCTURE BASED ENGINEERING OF INTERNAL MOLECULAR SURFACES OF FOUR HELIX BUNDLES
1vzl	AN ANTI-PARALLEL FOUR HELIX BUNDLE MUTANT PLI-E20C
1w5g	AN ANTI-PARALLEL FOUR HELIX BUNDLE ( ACETIMIDE MODIFICATION).
1w5h	AN ANTI-PARALLEL FOUR HELIX BUNDLE.
1w5i	ABA DOES NOT AFFECT TOPOLOGY OF PLI.
1w5j	AN ANTI-PARALLEL FOUR HELIX BUNDLE
1w5k	AN ANTI-PARALLEL FOUR HELIX BUNDLE
1w5l	AN ANTI-PARALLEL TO PARALLEL SWITCH.
1ysa	GCN4 (BASIC REGION, LEUCINE ZIPPER) COMPLEX WITH AP-1 DEOXYRIBONUCLEIC ACID
1zii	GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE DIMERIC STATE
1zij	GCN4-LEUCINE ZIPPER CORE MUTANT ASN16ABA IN THE TRIMERIC STATE
1zik	GCN4-LEUCINE ZIPPER CORE MUTANT ASN16LYS IN THE DIMERIC STATE
1zil	GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE DIMERIC STATE
1zim	GCN4-LEUCINE ZIPPER CORE MUTANT ASN16GLN IN THE TRIMERIC STATE
1zta	LEUCINE ZIPPER MONOMER (NMR, 20 STRUCTURES)
2bni	PLI MUTANT E20C L16G Y17H, ANTIPARALLEL
2cce	PARALLEL CONFIGURATION OF PLI E20S
2ccf	ANTIPARALLEL CONFIGURATION OF PLI E20S
2dgc	GCN4 BASIC DOMAIN, LEUCINE ZIPPER COMPLEXED WITH ATF/CREB SITE DEOXYRIBONUCLEIC ACID
2zta	GCN4 LEUCINE ZIPPER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (25, 25)

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