2C62 | PD0931 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE HUMAN TRANSCRIPTION COFACTOR PC4 IN COMPLEX WITH SINGLE-STRANDED DNA

Authors :   S. Werten, D. Moras

Date :   07 Nov 05 (Deposition) - 11 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Transcription Cofactor, Single-Stranded Dna, Protein-Dna Complex, Dna Unwinding, Activator, Dna-Binding, Nuclear Protein, Phosphorylation, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Werten, D. Moras
A Global Transcription Cofactor Bound To Juxtaposed Strands Of Unwound Dna
Nat. Struct. Mol. Biol. V. 13 181 2006
PubMed-ID: 16415882 | Reference-DOI: 10.1038/NSMB1044

Molecule 1 - ACTIVATED RNA POLYMERASE II TRANSCRIPTIONAL COACTIVATOR P15
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	DE3
	Fragment	:	C-TERMINAL SSDNA-BINDING DOMAIN, RESIDUES 62-126
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	N-TERMINAL ALA RESIDUE RESULTS FROM VECTOR SEQUENCE
	Synonym	:	PC4, POSITIVE COFACTOR 4, P14

*Molecule 2 - 5'-D(TPTPTPTPTPTPTPTPTPTP TPTPTPTPTPTPTPTPTPG)-3'*
	Chains	:	C
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:62 , HOH A:2054	BINDING SITE FOR RESIDUE SO4 A1128
2	AC2	SOFTWARE	DG C:20 , HOH C:2049	BINDING SITE FOR RESIDUE SO4 C1021

(no "SS Bond" information available for 2C62)

(no "Cis Peptide Bond" information available for 2C62)

(no "SAP(SNP)/Variant" information available for 2C62)

(no "PROSITE Motif" information available for 2C62)

Asymmetric/Biological Unit (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:62-65 B:62-65	4 4
1.9b	ENST00000265073	9b	ENSE00001200257	chr5:32599067-32599175	109	TCP4_HUMAN	66-102	37	2	A:66-102 B:66-102	37 37
1.10k	ENST00000265073	10k	ENSE00001563086	chr5:32601111-32604185	3075	TCP4_HUMAN	102-127	26	2	A:102-127 B:102-127	26 26

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: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 d2c62a_ A: Transcriptional coactivator PC4 C-terminal domain       SCOP domains
               CATH domains 2c62A00 A:62-127 Transcriptional Coactivator Pc4; Chain A          CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeeeeee..eeeeeeeeeee.....eeeeeeeeeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.7b------------------------------------Exon 1.10k  PDB: A:102-127 Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.9b  PDB: A:66-102             ------------------------- Transcript 1 (2)
                 2c62 A  62 AMFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL 127
                                    71        81        91       101       111       121

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 d2c62b_ B: Transcriptional coactivator PC4 C-terminal domain       SCOP domains
               CATH domains 2c62B00 B:62-127 Transcriptional Coactivator Pc4; Chain A          CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeeeeee..eeeeeeeeeee.....eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.7b------------------------------------Exon 1.10k  PDB: B:102-127 Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.9b  PDB: B:66-102             ------------------------- Transcript 1 (2)
                 2c62 B  62 AMFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL 127
                                    71        81        91       101       111       121

Chain C from PDB  Type:DNA  Length:16
                                                
                 2c62 C   5 TTTTTTTTTTTTTTTG  20
                                    14

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(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

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	2c62A00	A:62-127
1b	2c62B00	B:62-127

(no "Pfam Domain" information available for 2C62)

Asymmetric/Biological Unit(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.

Asymmetric/Biological Unit
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	2c62
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	TCP4_HUMAN \| P53999
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	TCP4_HUMAN \| P53999	:	1pcf 2phe 4usg

1pcf	HUMAN TRANSCRIPTIONAL COACTIVATOR PC4 C-TERMINAL DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (3, 6)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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