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103  structures 1809  species 0  interactions 4735  sequences 45  architectures

Family: TF_Zn_Ribbon (PF08271)

Summary: TFIIB zinc-binding

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TFIIB zinc-binding Provide feedback

The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure [1].

Literature references

  1. Chen HT, Legault P, Glushka J, Omichinski JG, Scott RA; , Protein Sci 2000;9:1743-1752.: Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. PUBMED:11045620 EPMC:11045620

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013137

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 IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (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 seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH [ PUBMED:1633439 ].

TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [ PUBMED:8516312 , PUBMED:8504927 ].

The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites [ PUBMED:8564536 ]. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site [ PUBMED:15024075 ]. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I [ PUBMED:15024075 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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: Pfam-B_1298 (release 17.0)
Previous IDs: TFIIB_Zn_Ribbon;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 58
Number in full: 4735
Average length of the domain: 43.10 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 11.19 %

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 29.0 29.0
Trusted cut-off 29.0 29.0
Noise cut-off 28.9 28.9
Model length: 43
Family (HMM) version: 15
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 TF_Zn_Ribbon domain has been found. There are 103 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
A0A0R0JYX3 View 3D Structure Click here
A0A0R4IRB5 View 3D Structure Click here
A0A131MCT5 View 3D Structure Click here
A0A1D6ETX0 View 3D Structure Click here
A0A1D6I9Y0 View 3D Structure Click here
A0A1D6L5K1 View 3D Structure Click here
A0A1D6MBN6 View 3D Structure Click here
A0A1D6MM72 View 3D Structure Click here
A0A1D6NEY5 View 3D Structure Click here
A0A1D6NEY6 View 3D Structure Click here
A0A1D8PT00 View 3D Structure Click here
A0B5T8 View 3D Structure Click here
A1RY32 View 3D Structure Click here
A2SQM6 View 3D Structure Click here
A6QLI8 View 3D Structure Click here
A6UW60 View 3D Structure Click here
A7IAR4 View 3D Structure Click here
A8MCX6 View 3D Structure Click here
B8GJQ9 View 3D Structure Click here
D4A8W8 View 3D Structure Click here
F1R9S3 View 3D Structure Click here
G3V992 View 3D Structure Click here
I1JG98 View 3D Structure Click here
I1JNB0 View 3D Structure Click here
I1N8Y6 View 3D Structure Click here
K7KNC5 View 3D Structure Click here
O13749 View 3D Structure Click here
O16991 View 3D Structure Click here
O26971 View 3D Structure Click here
O28970 View 3D Structure Click here
O29501 View 3D Structure Click here
O34434 View 3D Structure Click here
O81787 View 3D Structure Click here
O82494 View 3D Structure Click here
P0CW15 View 3D Structure Click here
P29052 View 3D Structure Click here
P29055 View 3D Structure Click here
P29056 View 3D Structure Click here
P29083 View 3D Structure Click here
P36100 View 3D Structure Click here