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266  structures 1953  species 0  interactions 7483  sequences 122  architectures

Family: TFIIS_C (PF01096)

Summary: Transcription factor S-II (TFIIS)

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Transcription factor S-II (TFIIS) Provide feedback

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This tab holds annotation information from the InterPro database.

InterPro entry IPR001222

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [ PUBMED:10529348 , PUBMED:15963892 , PUBMED:15718139 , PUBMED:17210253 , PUBMED:12665246 ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [ PUBMED:11179890 ]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS [ PUBMED:3346229 ]. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites [ PUBMED:10723030 ]. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre.

TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [ PUBMED:7626141 ] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site [ PUBMED:12914699 ].

Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor [ PUBMED:2398897 ].

Gene Ontology

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Domain organisation

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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.

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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.

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Seed source: Prosite
Previous IDs: TFIIS;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Bateman A
Number in seed: 92
Number in full: 7483
Average length of the domain: 38.90 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 18.69 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 39
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 TFIIS_C domain has been found. There are 266 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.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0G2K4V8 View 3D Structure Click here
A0A0R0FQZ5 View 3D Structure Click here
A0A0R0IXK5 View 3D Structure Click here
A0A1D6EF90 View 3D Structure Click here
A0A1D6FI80 View 3D Structure Click here
A0A1D6L1V3 View 3D Structure Click here
A0A1D8PHV8 View 3D Structure Click here
A0A2R8Q7Y8 View 3D Structure Click here
A1ZBX4 View 3D Structure Click here
A4HY64 View 3D Structure Click here
A4I9C2 View 3D Structure Click here
A4IE59 View 3D Structure Click here
B4F8B1 View 3D Structure Click here
B4FDM3 View 3D Structure Click here
B6T798 View 3D Structure Click here
B6TRW3 View 3D Structure Click here
C6SXF5 View 3D Structure Click here
C6T4H3 View 3D Structure Click here
D4A531 View 3D Structure Click here
E9AH32 View 3D Structure Click here
F1QTS2 View 3D Structure Click here
F1R4I1 View 3D Structure Click here
I1JYC9 View 3D Structure Click here
I1KB67 View 3D Structure Click here
I1KJX9 View 3D Structure Click here
I1KMS4 View 3D Structure Click here
I1MGG3 View 3D Structure Click here
I1N2G1 View 3D Structure Click here
I1NA71 View 3D Structure Click here
K7KWE4 View 3D Structure Click here
K7LQV0 View 3D Structure Click here
O13896 View 3D Structure Click here
O17587 View 3D Structure Click here
O27369 View 3D Structure Click here
O29033 View 3D Structure Click here
O74635 View 3D Structure Click here
O75764 View 3D Structure Click here
O94703 View 3D Structure Click here
O96159 View 3D Structure Click here
P07273 View 3D Structure Click here