2D5R - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A TOB-HCAF1 COMPLEX

Authors :   M. Horiuchi, N. N. Suzuki, N. Muroya, K. Takahasi, M. Nishida, Y. Yoshida, N. Ikematsu, T. Nakamura, J. Kawamura-Tsuzuku, T. Yamamoto, F. Inagaki

Date :   04 Nov 05 (Deposition) - 12 Dec 06 (Release) - 06 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Poly(A) Deadenylase, Antiproliferative Protein, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Horiuchi, K. Takeuchi, N. Noda, N. Muroya, T. Suzuki, T. Nakamura, J. Kawamura-Tsuzuku, K. Takahasi, T. Yamamoto, F. Inagaki
Structural Basis For The Antiproliferative Activity Of The Tob-Hcaf1 Complex.
J. Biol. Chem. V. 284 13244 2009
PubMed-ID: 19276069 | Reference-DOI: 10.1074/JBC.M809250200
(for further references see the PDB file header)

Molecule 1 - CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 7
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BLR (DE3)/PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	POLY(A) DEADENYLASE
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CCR4-ASSOCIATED FACTOR 1, CAF1, BTG1 BINDING FACTOR 1

Molecule 2 - TOB1 PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BLR (DE3)/PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BTG/TOB DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TRANSDUCER OF ERBB-2 1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2D5R)

(no "Site" information available for 2D5R)

(no "SS Bond" information available for 2D5R)

(no "Cis Peptide Bond" information available for 2D5R)

(no "SAP(SNP)/Variant" information available for 2D5R)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BTG_1	PS00960	BTG family signature 1.	TOB1_HUMAN	40-60	1	B:64-84
2	BTG_2	PS01203	BTG family signature 2.	TOB1_HUMAN	86-105	1	B:110-129

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000268957	1	ENSE00001757872	chr17:48945339-48945166	174	TOB1_HUMAN	-	0	0	-	-
1.2	ENST00000268957	2	ENSE00001685727	chr17:48944963-48944855	109	TOB1_HUMAN	-	0	0	-	-
1.4a	ENST00000268957	4a	ENSE00000947126	chr17:48941524-48940341	1184	TOB1_HUMAN	1-394	394	1	B:25-139	115

2.1a	ENST00000361272	1a	ENSE00001299172	chr8:17104387-17104184	204	CNOT7_HUMAN	-	0	0	-	-
2.5a	ENST00000361272	5a	ENSE00002152109	chr8:17102756-17102545	212	CNOT7_HUMAN	1-39	39	1	A:11-39	29
2.8c	ENST00000361272	8c	ENSE00000681996	chr8:17100694-17100501	194	CNOT7_HUMAN	40-104	65	1	A:40-104	65
2.9c	ENST00000361272	9c	ENSE00000681993	chr8:17094882-17094721	162	CNOT7_HUMAN	104-158	55	1	A:104-158	55
2.10b	ENST00000361272	10b	ENSE00000681990	chr8:17092369-17092225	145	CNOT7_HUMAN	158-206	49	1	A:158-206	49
2.11b	ENST00000361272	11b	ENSE00000681987	chr8:17090046-17089936	111	CNOT7_HUMAN	207-243	37	1	A:207-243	37
2.12b	ENST00000361272	12b	ENSE00001321978	chr8:17088357-17086737	1621	CNOT7_HUMAN	244-285	42	1	A:244-262	19

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
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Chain A from PDB  Type:PROTEIN  Length:252
 aligned with CNOT7_HUMAN | Q9UIV1 from UniProtKB/Swiss-Prot  Length:285

    Alignment length:252
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260  
          CNOT7_HUMAN    11 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGL 262
               SCOP domains d2d5ra1 A:11-262 CCR4-NOT transcription complex subunit 7, CAF1                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhh.eeeeeee.............hhhhhhhhhhhhhhh.....eeeeeee...........eeeee..........hhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhh.........eeee..hhhhhhhhhhhhhh.....hhhhhhhhhhhhh..eeehhhhhhhh.....hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 2 (1) Exon 2.5a  PDB: A:11-39      Exon 2.8c  PDB: A:40-104 UniProt: 40-104                         -----------------------------------------------------Exon 2.10b  PDB: A:158-206 UniProt: 158-206      Exon 2.11b  PDB: A:207-243           Exon 2.12b          Transcript 2 (1)
           Transcript 2 (2) ---------------------------------------------------------------------------------------------Exon 2.9c  PDB: A:104-158 UniProt: 104-158             -------------------------------------------------------------------------------------------------------- Transcript 2 (2)
                 2d5r A  11 RICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDLLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELLMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGL 262
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with TOB1_HUMAN | P50616 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:116
                             1                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109      
           TOB1_HUMAN     - -MQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVD 115
               SCOP domains d2d5rb1 B:24-139 TOB1, N-terminal domain                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..........hhhhhheee....hhhhhhhhhh...hhhhhhhhh...eeeeee..eeeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------BTG_1  PDB: B:64-84  -------------------------BTG_2  PDB: B:110-12---------- PROSITE
               Transcript 1 -Exon 1.4a  PDB: B:25-139 UniProt: 1-394 [INCOMPLETE]                                                                Transcript 1
                 2d5r B  24 HMQLEIQVALNFIISYLYNKLPRRRVNIFGEELERLLKKKYEGHWYPEKPYKGSGFRCIHIGEKVDPVIEQASKESGLDIDDVRGNLPQDLSVWIDPFEVSYQIGEKGPVKVLYVD 139
                                    33        43        53        63        73        83        93       103       113       123       133

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 '\|'

(no "CATH Domain" information available for 2D5R)

(no "Pfam Domain" information available for 2D5R)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CNOT7_HUMAN | Q9UIV1)

molecular function
	GO:0000175	3'-5'-exoribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0004532	exoribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 5' or 3' terminus of an RNA molecule.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0004535	poly(A)-specific ribonuclease activity	Catalysis of the exonucleolytic cleavage of poly(A) to 5'-AMP.
	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:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	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.
biological process
	GO:0006977	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest	A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
	GO:0090503	RNA phosphodiester bond hydrolysis, exonucleolytic	The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0033962	cytoplasmic mRNA processing body assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a cytoplasmic mRNA processing body.
	GO:0000290	deadenylation-dependent decapping of nuclear-transcribed mRNA	Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length.
	GO:0043928	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay	The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 3'-poly(A) tail.
	GO:0031047	gene silencing by RNA	Any process in which RNA molecules inactivate expression of target genes.
	GO:0035195	gene silencing by miRNA	Downregulation of gene expression through the action of microRNAs (miRNAs), endogenous 21-24 nucleotide small RNAs processed from stem-loop RNA precursors (pre-miRNAs). Once incorporated into a RNA-induced silencing complex (RISC), miRNAs can downregulate gene expression by either of two posttranscriptional mechanisms: endolytic cleavage of mRNA cleavage or translational repression, usually accompanied by poly-A tail shortening and subsequent degradation of the mRNA.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding 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:0000289	nuclear-transcribed mRNA poly(A) tail shortening	Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0061014	positive regulation of mRNA catabolic process	Any process that increases the rate, frequency, or extent of a mRNA catabolic process, the chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:1900153	positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
	GO:0060213	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
	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:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0030014	CCR4-NOT complex	The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

Chain B (TOB1_HUMAN | P50616)

molecular function
	GO:0005070	SH3/SH2 adaptor activity	Interacting selectively and non-covalently and simultaneously with one or more signal transduction molecules, usually acting as a scaffold to bring these molecules into close proximity either using their own SH2/SH3 domains (e.g. Grb2) or those of their target molecules (e.g. SAM68).
	GO:0046332	SMAD binding	Interacting selectively and non-covalently with a SMAD signaling protein.
	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:0030971	receptor tyrosine kinase binding	Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
	GO:0003714	transcription corepressor activity	Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
	GO:0007184	SMAD protein import into nucleus	The directed movement of a SMAD proteins from the cytoplasm into the nucleus. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
	GO:0030514	negative regulation of BMP signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0060212	negative regulation of nuclear-transcribed mRNA poly(A) tail shortening	Any process that decreases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
	GO:1903507	negative regulation of nucleic acid-templated transcription	Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
	GO:0045668	negative regulation of osteoblast differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:1900153	positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	Any process that activates or increases the frequency, rate or extent of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay.
	GO:0060213	positive regulation of nuclear-transcribed mRNA poly(A) tail shortening	Any process that increases the frequency, rate or extent of poly(A) tail shortening of a nuclear-transcribed mRNA. Poly(A) tail shortening is the decrease in length of the poly(A) tail of an mRNA from full length to an oligo(A) length.
	GO:0009967	positive regulation of signal transduction	Any process that activates or increases the frequency, rate or extent of signal transduction.
cellular component
	GO:0030014	CCR4-NOT complex	The evolutionarily conserved CCR4-NOT complex is involved in several aspects of mRNA metabolism, including repression and activation of mRNA initiation, control of mRNA elongation, and the deadenylation and subsequent degradation of mRNA. In Saccharomyces the CCR4-NOT complex comprises a core complex of 9 proteins (Ccr4p, Caf1p, Caf40p, Caf130p, Not1p, Not2p, Not3p, Not4p, and Not5p), Caf4p, Caf16p, and several less well characterized proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Asymmetric/Biological Unit
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	2d5r
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