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1  structure 170  species 0  interactions 39716  sequences 2435  architectures

Family: KRAB (PF01352)

Summary: KRAB box

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This is the Wikipedia entry entitled "Kruppel associated box". More...

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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.

KRAB box Provide feedback

The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions [2,3]. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation [4].

Literature references

  1. Thiesen HJ, Bellefroid E, Revelant O, Martial JA; , Nucleic Acids Res 1991;19:3996-3996.: Conserved KRAB protein domain identified upstream from the zinc finger region of Kox 8. PUBMED:1861988 EPMC:1861988

  2. Kim SS, Chen YM, O'Leary E, Witzgall R, Vidal M, Bonventre JV; , Proc Natl Acad Sci U S A 1996;93:15299-15304.: A novel member of the RING finger family, KRIP-1, associates with the KRAB-A transcriptional repressor domain of zinc finger proteins. PUBMED:8986806 EPMC:8986806

  3. Friedman JR, Fredericks WJ, Jensen DE, Speicher DW, Huang XP, Neilson EG, Rauscher FJ; , Genes Dev 1996;10:2067-2078.: KAP-1, a novel corepressor for the highly conserved KRAB repression domain. PUBMED:8769649 EPMC:8769649

  4. Urrutia R; , Genome Biol 2003;4:231.: KRAB-containing zinc-finger repressor proteins. PUBMED:14519192 EPMC:14519192

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001909

The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) [ PUBMED:14519192 ]. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box [ PUBMED:2023909 ].

The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [ PUBMED:8183939 , PUBMED:8183940 ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [ PUBMED:10653693 , PUBMED:10748030 ].

KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome [ PUBMED:10360839 ]. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta, KRAB-A interacting protein and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation [ PUBMED:25609696 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

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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 and the UniProtKB sequence database. More...

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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.

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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...


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.

Curation View help on the curation process

Seed source: Bateman A
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 427
Number in full: 39716
Average length of the domain: 41.10 aa
Average identity of full alignment: 52 %
Average coverage of the sequence by the domain: 7.92 %

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 20.4 20.4
Trusted cut-off 20.4 20.4
Noise cut-off 20.3 20.3
Model length: 42
Family (HMM) version: 30
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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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...

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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 KRAB domain has been found. There are 1 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
A0A087WNP1 View 3D Structure Click here
A0A087WNP5 View 3D Structure Click here
A0A087WPN2 View 3D Structure Click here
A0A087WQI7 View 3D Structure Click here
A0A087WQW2 View 3D Structure Click here
A0A087WR25 View 3D Structure Click here
A0A087WRH0 View 3D Structure Click here
A0A087WRJ1 View 3D Structure Click here
A0A087WRR7 View 3D Structure Click here
A0A087WS64 View 3D Structure Click here
A0A087WSP8 View 3D Structure Click here
A0A096MJ30 View 3D Structure Click here
A0A096MKA8 View 3D Structure Click here
A0A0G2JEM5 View 3D Structure Click here
A0A0G2JT46 View 3D Structure Click here
A0A0G2JUN3 View 3D Structure Click here
A0A0G2JV17 View 3D Structure Click here
A0A0G2JV23 View 3D Structure Click here
A0A0G2JWU0 View 3D Structure Click here
A0A0G2JWY4 View 3D Structure Click here
A0A0G2JX65 View 3D Structure Click here
A0A0G2JXW3 View 3D Structure Click here
A0A0G2JXX2 View 3D Structure Click here
A0A0G2JY97 View 3D Structure Click here
A0A0G2JZA5 View 3D Structure Click here
A0A0G2JZD8 View 3D Structure Click here
A0A0G2JZW8 View 3D Structure Click here
A0A0G2K029 View 3D Structure Click here
A0A0G2K073 View 3D Structure Click here
A0A0G2K0K0 View 3D Structure Click here
A0A0G2K1C7 View 3D Structure Click here
A0A0G2K1H6 View 3D Structure Click here
A0A0G2K279 View 3D Structure Click here
A0A0G2K2G3 View 3D Structure Click here
A0A0G2K2R7 View 3D Structure Click here
A0A0G2K390 View 3D Structure Click here
A0A0G2K3T8 View 3D Structure Click here
A0A0G2K5Q4 View 3D Structure Click here
A0A0G2K690 View 3D Structure Click here
A0A0G2K6B4 View 3D Structure Click here