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Title :   MODEL FOR VP16 BINDING TO PC4

Authors :   H. R. A. Jonker, R. W. Wechselberger, R. Boelens, G. E. Folkers, R. Kaptein

Date :   11 Apr 07 (Deposition) - 24 Apr 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C  (10x)

Keywords :   Pc4, Vp16, Transcription, Cofactor, Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. R. A. Jonker, R. W. Wechselberger, R. Boelens, G. E. Folkers, R. Kaptein
Structural Properties Of The Promiscuous Vp16 Activation Domain
Biochemistry V. 44 827 2005
PubMed-ID: 15654739 | Reference-DOI: 10.1021/BI0482912
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTIONAL COACTIVATOR PC4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL CORE DOMAIN
	Gene	:	SUB1, PC4, RPO2TC1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SUB1 HOMOLOG, POSITIVE COFACTOR 4, P15, P14

Molecule 2 - ALPHA TRANS-INDUCING PROTEIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PART OF ACTIVATION DOMAIN
	Gene	:	UL48
	Organism Scientific	:	HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
	Organism Taxid	:	10299
	Strain	:	17
	Synonym	:	VMW65, ICP25, VP16 PROTEIN, ALPHA- TIF


NMR Structure (10x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2PHE)

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

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

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

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

NMR Structure (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.4a	ENST00000265073	4a	ENSE00001164444	chr5:32585605-32585731	127	TCP4_HUMAN	-	0	0	-	-
1.6a	ENST00000265073	6a	ENSE00002195559	chr5:32588618-32588690	73	TCP4_HUMAN	1-24	24	0	-	-
1.7b	ENST00000265073	7b	ENSE00001164441	chr5:32591669-32591791	123	TCP4_HUMAN	25-65	41	2	A:61-64 B:61-64	4 4
1.9b	ENST00000265073	9b	ENSE00001200257	chr5:32599067-32599175	109	TCP4_HUMAN	66-102	37	2	A:65-101 B:65-101	37 37
1.10k	ENST00000265073	10k	ENSE00001563086	chr5:32601111-32604185	3075	TCP4_HUMAN	102-127	26	2	A:101-126 B:101-126	26 26

NMR Structure

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:66
 aligned with TCP4_HUMAN | P53999 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:66
                                    71        81        91       101       111       121      
           TCP4_HUMAN    62 NMFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL 127
               SCOP domains d2phea1 A:61-126 Transcriptional coactivator PC4 C-terminal domain SCOP domains
               CATH domains 2pheA00 A:61-126 Transcriptional Coactivator Pc4; Chain A          CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeeeeee..eeeeeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.7b------------------------------------Exon 1.10k  PDB: A:101-126 Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.9b  PDB: A:65-101             ------------------------- Transcript 1 (2)
                 2phe A  61 AMFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL 126
                                    70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:66
 aligned with TCP4_HUMAN | P53999 from UniProtKB/Swiss-Prot  Length:127

    Alignment length:66
                                    71        81        91       101       111       121      
           TCP4_HUMAN    62 NMFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL 127
               SCOP domains d2pheb1 B:61-126 Transcriptional coactivator PC4 C-terminal domain SCOP domains
               CATH domains 2pheB00 B:61-126 Transcriptional Coactivator Pc4; Chain A          CATH domains
           Pfam domains (1) -PC4-2pheB01 B:62-123                                          --- Pfam domains (1)
           Pfam domains (2) -PC4-2pheB02 B:62-123                                          --- Pfam domains (2)
         Sec.struct. author .eee....eeeeeee....eeeeeeeeee.....eeeeeeeeeehhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.7b------------------------------------Exon 1.10k  PDB: B:101-126 Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.9b  PDB: B:65-101             ------------------------- Transcript 1 (2)
                 2phe B  61 AMFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL 126
                                    70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:26
 aligned with VP16_HHV11 | P06492 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:26
                                   474       484      
           VP16_HHV11   465 YGALDMADFEFEQMFTDALGIDEYGG 490
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains HSV_VP16_C-2pheC01         Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                 2phe C 465 YGALDMADFEFEQMFTDALGIDEYGG 490
                                   474       484

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 '\|'

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Transcriptional Co-activator pc4; Chain A (6)

Homologous Superfamily: Transcriptional Coactivator Pc4; Chain A (6)

Human (Homo sapiens) (3)

1a	2pheA00	A:61-126
1b	2pheB00	B:61-126

NMR Structure(hide GO term definitions)

Chain A,B (TCP4_HUMAN | P53999)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
	GO:0003713	transcription coactivator activity	Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0001205	transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
	GO:0060395	SMAD protein signal transduction	The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
	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: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: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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.

Chain C (VP16_HHV11 | P06492)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	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).
biological process
	GO:0039695	DNA-templated viral transcription	A transcription process that uses a viral DNA as a template.
	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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0019033	viral tegument	A structure lying between the capsid and envelope of a virus, varying in thickness and often distributed asymmetrically.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

NMR Structure
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	2phe
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	TCP4_HUMAN \| P53999
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	VP16_HHV11 \| P06492
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	VP16_HHV11 \| P06492
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UniProtKB/Swiss-Prot
	TCP4_HUMAN \| P53999	:	1pcf 2c62 4usg
	VP16_HHV11 \| P06492	:	16vp 2phg

6099	BACKBONE CHEMICAL SHIFT ASSIGNMENTS FOR THE ACTIVATION DOMAIN OF THE TRANSCRIPTIONAL ACTIVATOR VP16
1pcf	CRYSTAL STRUCTURE OF THE HUMAN TRANSCRIPTIONAL COACTIVATOR PC4 C-TERMINAL CORE DOMAIN
2phg

Description

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Ligands, Modified Residues, Ions (0, 0)

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Exons (3, 6)

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SCOP Domains (1, 2)

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