Summary: CCR4-NOT transcription complex subunit 1 CAF1-binding domain
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
This is the Wikipedia entry entitled "CNOT1". More...
CNOT1 Edit Wikipedia article
| CCR4-Not complex component, Not1 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | Not1 | ||||||||
| Pfam | PF04054 | ||||||||
| InterPro | IPR007196 | ||||||||
| |||||||||
CCR4-NOT transcription complex subunit 1 is a protein that in humans is encoded by the CNOT1 gene.[5][6]
It is a part of the Ccr4-Not complex, which deadenylates mRNAs.[7] CNOT1 acts as a scaffold protein, binding other subunits of the complex.[8][9][10]
Interactions
CNOT1 has been shown to interact with CNOT8.[11][12]
References
- ^ a b c GRCh38: Ensembl release 89: ENSG00000125107 - Ensembl, May 2017
- ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000036550 - Ensembl, May 2017
- ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- ^ Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, et al. (January 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nature Genetics. 36 (1): 40–5. doi:10.1038/ng1285. PMID 14702039.
- ^ "Entrez Gene: CNOT1 CCR4-NOT transcription complex, subunit 1".
- ^ Garneau NL, Wilusz J, Wilusz CJ (Feb 2007). "The highways and byways of mRNA decay". Nat. Rev. Mol. Cell Biol. 8 (2): 113–26. doi:10.1038/nrm2104. PMID 17245413.
- ^ Sandler H, Kreth J, Timmers HT, Stoecklin G (May 2011). "Not1 mediates recruitment of the deadenylase Caf1 to mRNAs targeted for degradation by tristetraprolin". Nucleic Acids Res. 39 (10): 4373–86. doi:10.1093/nar/gkr011. PMC 3105394. PMID 21278420.
- ^ Petit AP, Wohlbold L, Bawankar P, Huntzinger E, Schmidt S, Izaurralde E, Weichenrieder O (Nov 2012). "The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex". Nucleic Acids Res. 40 (21): 11058–72. doi:10.1093/nar/gks883. PMC 3510486. PMID 22977175.
- ^ Basquin J, Roudko VV, Rode M, Basquin C, Séraphin B, Conti E (Oct 26, 2012). "Architecture of the nuclease module of the yeast Ccr4-not complex: the Not1-Caf1-Ccr4 interaction". Mol. Cell. 48 (2): 207–18. doi:10.1016/j.molcel.2012.08.014. PMID 22959269.
- ^ Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D (2007). "Large-scale mapping of human protein-protein interactions by mass spectrometry". Mol. Syst. Biol. 3 (1): 89. doi:10.1038/msb4100134. PMC 1847948. PMID 17353931.
- ^ Albert TK, Lemaire M, van Berkum NL, Gentz R, Collart MA, Timmers HT (February 2000). "Isolation and characterization of human orthologs of yeast CCR4-NOT complex subunits". Nucleic Acids Res. 28 (3): 809–17. doi:10.1093/nar/28.3.809. PMC 102560. PMID 10637334.
Further reading
- Bonaldo MF, Lennon G, Soares MB (1996). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome Res. 6 (9): 791–806. doi:10.1101/gr.6.9.791. PMID 8889548.
- Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosawa M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O (1999). "Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 6 (1): 63–70. doi:10.1093/dnares/6.1.63. PMID 10231032.
- Chen J, Rappsilber J, Chiang YC, Russell P, Mann M, Denis CL (2001). "Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex". J. Mol. Biol. 314 (4): 683–94. doi:10.1006/jmbi.2001.5162. PMID 11733989.
- Laveder P, De Pittà C, Toppo S, Valle G, Lanfranchi G (2002). "A two-step strategy for constructing specifically self-subtracted cDNA libraries". Nucleic Acids Res. 30 (9): 38e–38. doi:10.1093/nar/30.9.e38. PMC 113861. PMID 11972353.
- Winkler GS, Mulder KW, Bardwell VJ, Kalkhoven E, Timmers HT (2006). "Human Ccr4-Not complex is a ligand-dependent repressor of nuclear receptor-mediated transcription". EMBO J. 25 (13): 3089–99. doi:10.1038/sj.emboj.7601194. PMC 1500986. PMID 16778766.
External links
- Eukaryotic Linear Motif resource motif class LIG_CNOT1_NIM_1
- Human CNOT1 genome location and CNOT1 gene details page in the UCSC Genome Browser.
- Overview of all the structural information available in the PDB for UniProt: A5YKK6 (CCR4-NOT transcription complex subunit 1) at the PDBe-KB.
 | This article on a gene on human chromosome 16 is a stub. You can help Wikipedia by expanding it. |
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
CCR4-NOT transcription complex subunit 1 CAF1-binding domain Provide feedback
This is the CAF1-binding domain of CCR4-NOT transcription complex. It adopts a MIF4G (middle portion of eIF4G) fold [1].
Literature references
-
Petit AP, Wohlbold L, Bawankar P, Huntzinger E, Schmidt S, Izaurralde E, Weichenrieder O;, Nucleic Acids Res. 2012;40:11058-11072.: The structural basis for the interaction between the CAF1 nuclease and the NOT1 scaffold of the human CCR4-NOT deadenylase complex. PUBMED:22977175 EPMC:22977175
This tab holds annotation information from the InterPro database.
InterPro entry IPR032191
This is the CAF1-binding domain of CCR4-NOT transcription complex subunit 1, which is a scaffolding component of the CCR4-NOT complex. This domain adopts a MIF4G (middle portion of eIF4G) fold [PUBMED:22977175].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
Loading domain graphics...
Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
View options
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
| Seed (81) |
Full (1937) |
Representative proteomes | UniProt (3252) |
NCBI (5140) |
Meta (3) |
||||
|---|---|---|---|---|---|---|---|---|---|
| RP15 (302) |
RP35 (941) |
RP55 (1472) |
RP75 (1967) |
||||||
| Jalview | |||||||||
| HTML | |||||||||
| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
Download options
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
| Seed (81) |
Full (1937) |
Representative proteomes | UniProt (3252) |
NCBI (5140) |
Meta (3) |
||||
|---|---|---|---|---|---|---|---|---|---|
| RP15 (302) |
RP35 (941) |
RP55 (1472) |
RP75 (1967) |
||||||
| Raw Stockholm | |||||||||
| Gzipped | |||||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | PDB:4gml |
| Previous IDs: | CNOT_CAF1_bind; |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Eberhardt R 
|
| Number in seed: | 81 |
| Number in full: | 1937 |
| Average length of the domain: | 212.80 aa |
| Average identity of full alignment: | 45 % |
| Average coverage of the sequence by the domain: | 10.64 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
| Model details: |
|
||||||||||||
| Model length: | 225 | ||||||||||||
| Family (HMM) version: | 6 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
Archea
|
Eukaryota
|
Bacteria
|
Other sequences
|
Viruses
|
Unclassified
|
Viroids
|
Unclassified sequence
|
Selections
Align selected sequences to HMM
Generate a FASTA-format file
Clear selection
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the CNOT1_CAF1_bind domain has been found. There are 19 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
Loading structure mapping...
