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NMR Structure - model 1 (Jmol Viewer)

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Title :   NMR STRUCTURE OF A COMPLEX CONTAINING THE TFIIF SUBUNIT RAP74 AND THE RNAP II CTD PHOSPHATASE FCP1

Authors :   B. D. Nguyen, K. L. Abbott, K. Potempa, M. S. Kobor, J. Archambault, J. Greenblatt, P. Legault, J. G. Omichinski

Date :   02 Mar 03 (Deposition) - 20 May 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (20x)

Keywords :   Transcription Factor, Human General Transcription Factor Tfiif, Rap74, Rna Polymerase Ii Ctd Phosphatase, Tfiif- Associating Ctd Phosphatase, Fcp1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. D. Nguyen, K. L. Abbott, K. Potempa, M. S. Kobor, J. Archambault, J. Greenblatt, P. Legault, J. G. Omichinski
Nmr Structure Of A Complex Containing The Tfiif Subunit Rap74 And The Rna Polymerase Ii Carboxyl-Terminal Domain Phosphatase Fcp1
Proc. Natl. Acad. Sci. Usa V. 100 5688 2003
PubMed-ID: 12732728 | Reference-DOI: 10.1073/PNAS.1031524100
(for further references see the PDB file header)

Molecule 1 - TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	GST-2T
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PGEX
	Fragment	:	C-TERMINAL DOMAIN OF RAP74, SEQUENCE DATABASE RESIDUES 436-517
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TFIIF-ALFA, TRANSCRIPTION INITIATION FACTOR RAP74

Molecule 2 - SERINE PHOSPHATASE FCP1A
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	GST-3X
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PGEX
	Fragment	:	C-TERMINAL DOMAIN OF FCP1, SEQUENCE DATABASE RESIDUES 760-842
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ONV)

(no "Site" information available for 1ONV)

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

(no "Cis Peptide Bond" information available for 1ONV)

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

(no "PROSITE Motif" information available for 1ONV)

NMR Structure (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000394456	1	ENSE00002168237	chr19:6393291-6392995	297	T2FA_HUMAN	1-4	4	0	-	-
1.2	ENST00000394456	2	ENSE00001664061	chr19:6392914-6392868	47	T2FA_HUMAN	5-20	16	0	-	-
1.3	ENST00000394456	3	ENSE00001720340	chr19:6391985-6391913	73	T2FA_HUMAN	20-44	25	0	-	-
1.4	ENST00000394456	4	ENSE00000666056	chr19:6389648-6389455	194	T2FA_HUMAN	45-109	65	0	-	-
1.5	ENST00000394456	5	ENSE00000666058	chr19:6387570-6387400	171	T2FA_HUMAN	109-166	58	0	-	-
1.6	ENST00000394456	6	ENSE00000666060	chr19:6383506-6383322	185	T2FA_HUMAN	166-228	63	0	-	-
1.7	ENST00000394456	7	ENSE00001060029	chr19:6381861-6381708	154	T2FA_HUMAN	228-279	52	0	-	-
1.8	ENST00000394456	8	ENSE00001060032	chr19:6381626-6381565	62	T2FA_HUMAN	279-300	22	0	-	-
1.9	ENST00000394456	9	ENSE00001060028	chr19:6381489-6381370	120	T2FA_HUMAN	300-340	41	0	-	-
1.10	ENST00000394456	10	ENSE00000666066	chr19:6381206-6381133	74	T2FA_HUMAN	340-364	25	0	-	-
1.11	ENST00000394456	11	ENSE00000666068	chr19:6381053-6380915	139	T2FA_HUMAN	365-411	47	0	-	-
1.12	ENST00000394456	12	ENSE00000666070	chr19:6380701-6380584	118	T2FA_HUMAN	411-450	40	0	-	-
1.13	ENST00000394456	13	ENSE00001518517	chr19:6380496-6379580	917	T2FA_HUMAN	450-517	68	1	A:451-517	67

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)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:67
 aligned with T2FA_HUMAN | P35269 from UniProtKB/Swiss-Prot  Length:517

    Alignment length:67
                                   460       470       480       490       500       510       
           T2FA_HUMAN   451 DVQVTEDAVRRYLTRKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRLNPERKMINDKMHFSLKE 517
               SCOP domains d1onva_ A: C-terminal domain of the rap74 subunit of TFIIF          SCOP domains
               CATH domains 1onvA00 A:451-517 'winged helix' repressor DNA binding domain       CATH domains
               Pfam domains TFIIF_alpha-1onvA01 A:451-517                                       Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhhhh.eeee....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.13  PDB: A:451-517 UniProt: 450-517 [INCOMPLETE]             Transcript 1
                 1onv A 451 DVQVTEDAVRRYLTRKPMTTKDLLKKFQTKKTGLSSEQTVNVLAQILKRLNPERKMINDKMHFSLKE 517
                                   460       470       480       490       500       510

Chain B from PDB  Type:PROTEIN  Length:21
 aligned with CTDP1_HUMAN | Q9Y5B0 from UniProtKB/Swiss-Prot  Length:961

    Alignment length:21
                                   950       960 
          CTDP1_HUMAN   941 GSSSEADEMAKALEAELNDLM 961
               SCOP domains --------------------- SCOP domains
               CATH domains 1onvB00 B:941-961     CATH domains
               Pfam domains FCP1_C-1onvB01        Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 1onv B 941 GSSSEADEMAKALEAELNDLM 961
                                   950       960

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: C-terminal domain of the rap74 subunit of TFIIF (4)

Protein domain: C-terminal domain of the rap74 subunit of TFIIF (4)

Human (Homo sapiens) [TaxId: 9606] (4)

d1onva_

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: FCP1_C] (1)

Family: FCP1_C (1)

Homo sapiens (Human) (1)

FCP1_C-1onvB01

B:941-961

Clan: no clan defined [family: TFIIF_alpha] (3)

Family: TFIIF_alpha (3)

Homo sapiens (Human) (3)

TFIIF_alpha-1onvA01

A:451-517

NMR Structure(hide GO term definitions)

Chain A (T2FA_HUMAN | P35269)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0019211	phosphatase activator activity	Increases the activity of a phosphatase, an enzyme which catalyzes of the removal of a phosphate group from a substrate molecule.
	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: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:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
	GO:0006370	7-methylguanosine mRNA capping	Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
	GO:0008543	fibroblast growth factor receptor signaling pathway	The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
	GO:0010467	gene expression	The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0000398	mRNA splicing, via spliceosome	The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
	GO:0043085	positive regulation of catalytic activity	Any process that activates or increases the activity of an enzyme.
	GO:0032968	positive regulation of transcription elongation from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
	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:0050434	positive regulation of viral transcription	Any process that activates or increases the frequency, rate or extent of viral transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009615	response to virus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
	GO:0042795	snRNA transcription from RNA polymerase II promoter	The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	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:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0005674	transcription factor TFIIF complex	A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.

Chain B (CTDP1_HUMAN | Q9Y5B0)

molecular function
	GO:0008420	CTD phosphatase activity	Catalysis of the reaction: phospho-(DNA-directed RNA polymerase) + H2O = (DNA-directed RNA polymerase) + phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	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:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0070940	dephosphorylation of RNA polymerase II C-terminal domain	The process of removing a phosphate group from an amino acid residue in the C-terminal domain of RNA polymerase II. Some dephosphorylation occurs during transcription while some may occur after the enzyme is released from the template in order to prepare it for the beginning of the transcription cycle again. RNA polymerase II with little or no phosphorylation is referred to as the hypophosphorylated or II(A) form.
	GO:0010458	exit from mitosis	The cell cycle transition where a cell leaves M phase and enters a new G1 phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
	GO:0061052	negative regulation of cell growth involved in cardiac muscle cell development	Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
	GO:0050434	positive regulation of viral transcription	Any process that activates or increases the frequency, rate or extent of viral transcription.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	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).
cellular component
	GO:0016591	DNA-directed RNA polymerase II, holoenzyme	A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters.
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0030496	midbody	A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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:0005819	spindle	The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
	GO:0051233	spindle midzone	The area in the center of the spindle where the spindle microtubules from opposite poles overlap.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

NMR Structure
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