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NMR Structure - model 1 (Jmol Viewer)

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Title :   STRUCTURE OF THE COMPLEX OF THE CENTRAL ACTIVATION DOMAIN OF GCN4 BOUND TO THE MEDIATOR CO-ACTIVATOR DOMAIN 1 OF GAL11/MED15

Authors :   P. S. Brzovic, C. C. Heikaus, L. Kisselev, R. Vernon, E. Herbig, D. Pache L. Warfield, P. Littlefield, D. Baker, R. E. Klevit, S. Hahn

Date :   07 Feb 12 (Deposition) - 22 Feb 12 (Release) - 22 Feb 12 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (13x)
NMR Structure *: A,B  (1x)

Keywords :   Mediator, Activator, Co-Activator, Transcription, Nucleus, Phosphoprotein, Transcription Regulation, Amino Acid Biosynthesis, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. S. Brzovic, C. C. Heikaus, L. Kisselev, R. Vernon, E. Herbig, D. Pacheco, L. Warfield, P. Littlefield, D. Baker, R. E. Klevit, S. Hah
The Acidic Transcription Activator Gcn4 Binds The Mediator Subunit Gal11/Med15 Using A Simple Protein Interface Formin A Fuzzy Complex.
Mol. Cell V. 44 942 2011
PubMed-ID: 22195967 | Reference-DOI: 10.1016/J.MOLCEL.2011.11.008

Molecule 1 - MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 15
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET21A
	Fragment	:	UNP RESIDUES 158-238
	Gene	:	ABE1, GAL11, MED15, RAR3, SDS4, SPT13, YOL051W
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	AUTONOMOUS REPLICATION REGULATORY PROTEIN 3, BASAL EXPRESSION ACTIVATOR PROTEIN 1, DEFECTIVE SILENCING SUPPRESSOR PROTEIN 4, MEDIATOR COMPLEX SUBUNIT 15, TRANSCRIPTION REGULATORY PROTEIN GAL11, TY INSERTION SUPPRESSOR PROTEIN 13

Molecule 2 - GENERAL CONTROL PROTEIN GCN4
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PETSUMO
	Fragment	:	TRANSCRIPTIONAL ACTIVATION REGION, RESIDUES 101-134
	Gene	:	AAS3, ARG9, GCN4, YEL009C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Strain	:	ATCC 204508 / S288C
	Synonym	:	AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN

		1	2
NMR Structure (13x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2LPB)

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

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

NMR Structure (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GCN4_YEAST_005 *	D	125	A	GCN4_YEAST	---	---	B	D	125	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure * (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GCN4_YEAST_005 *	D	125	A	GCN4_YEAST	---	---	B	D	125	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

NMR Structure (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	B:101-134	34

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:81
 aligned with MED15_YEAST | P19659 from UniProtKB/Swiss-Prot  Length:1081

    Alignment length:81
                                   167       177       187       197       207       217       227       237 
          MED15_YEAST   158 QRRQLTPQQQQLVNQMKVAPIPKQLLQRIPNIPPNINTWQQVTALAQQKLLTPQDMEAAKEVYKIHQQLLFKARLQQQQAQ 238
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2lpb A 158 QRRQLTPQQQQLVNQMKVAPIPKQLLQRIPNIPPNINTWQQVTALAQQKLLTPQDMEAAKEVYKIHQQLLFKARLQQQQAQ 238
                                   167       177       187       197       207       217       227       237

Chain B from PDB  Type:PROTEIN  Length:34
 aligned with GCN4_YEAST | P03069 from UniProtKB/Swiss-Prot  Length:281

    Alignment length:34
                                   110       120       130    
           GCN4_YEAST   101 STDSTPMFEYENLEDNSKEWTSLFDNDIPVTTDD 134
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------A--------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:101-134           Transcript 1
                 2lpb B 101 STDSTPMFEYENLEDNSKEWTSLFDNDIPVTTDD 134
                                   110       120       130

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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 '\|'

(no "SCOP Domain" information available for 2LPB)

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

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

NMR Structure(hide GO term definitions)

Chain A (MED15_YEAST | P19659)

molecular function
	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:0001128	RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly	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 stability of the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC). Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
	GO:0001104	RNA polymerase II transcription cofactor 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 modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery.
	GO:0001095	TFIIE-class transcription factor binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIE class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
	GO:0001097	TFIIH-class transcription factor binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIH class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
	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:0001135	transcription factor activity, RNA polymerase II transcription factor recruiting	The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
	GO:0001088	transcription factor activity, TFIIE-class binding	Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIE class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
biological process
	GO:0051123	RNA polymerase II transcriptional preinitiation complex assembly	The aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase.
	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:2000219	positive regulation of invasive growth in response to glucose limitation	Any process that activates or increases the frequency, rate or extent of invasive growth in response to glucose limitation.
	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:0070202	regulation of establishment of protein localization to chromosome	Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates 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:0070847	core mediator complex	A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The core mediator complex has a stimulatory effect on basal transcription, and contains most of the same subdomains as the larger form of mediator complex -- a head domain comprising proteins known in Saccharomyces as Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; and a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p -- but lacks the regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan core mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
	GO:0016592	mediator complex	A protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The mediator complex is required for activation of transcription of most protein-coding genes, but can also act as a transcriptional corepressor. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
	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.

Chain 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: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: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: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:0001135	transcription factor activity, RNA polymerase II transcription factor recruiting	The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II.
	GO:0001084	transcription factor activity, TFIID-class binding	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: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:0001190	transcriptional activator activity, RNA polymerase II transcription factor binding	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	transcriptional repressor activity, RNA polymerase II transcription factor binding	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.
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 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: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 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: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.

NMR Structure
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