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179  structures 8830  species 0  interactions 109086  sequences 849  architectures

Family: KH_1 (PF00013)

Summary: KH 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 "KH domain". More...

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.

KH domain Provide feedback

KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

Literature references

  1. Burd CG, Dreyfuss G; , Science 1994;265:615-621.: Conserved structures and diversity of functions of RNA-binding proteins. PUBMED:8036511 EPMC:8036511

  2. Musco G, Stier G, Joseph C, Castiglione Morelli MA, Nilges M, Gibson TJ, Pastore A; , Cell 1996;85:237-245.: Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. PUBMED:8612276 EPMC:8612276

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004088

The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins [ PUBMED:8036511 ]. It has been shown to bind RNA [ PUBMED:9302998 , PUBMED:10369774 ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently [ PUBMED:8036511 ].

According to structural [ PUBMED:9302998 , PUBMED:10369774 , PUBMED:11160884 ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases ( EC ); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein).

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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Pfam Clan

This family is a member of clan KH (CL0007), which has the following description:

The KH domain is thought to be the second most prevalent RNA binding motif in proteins. The motif is characterised by a conserved GXXXGXXG in the middle of the domain. Structures of KH reveal that the KH domain is arranged as either a beta-alpha-alpha-beta-beta (mini-KH domain) or beta-alpha-alpha-beta-beta-alpha (maxi-KH domain). The secondary elements are separated by at least four loop segments. The second loop is located between beta-1 and al The KH domain can be found either as single or multiple copies. The KH domain usually binds RNA as a multimer.

The clan contains the following 14 members:

DUF2096 DUF370 KH_1 KH_10 KH_2 KH_4 KH_5 KH_6 KH_7 KH_8 KH_9 MOEP19 MRP-S24 SLS


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.

Representative proteomes UniProt
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Representative proteomes UniProt

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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.

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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.

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 View help on the curation process

Seed source: Published_alignment
Previous IDs: KH-domain; KH;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Eddy SR , Finn RD
Number in seed: 783
Number in full: 109086
Average length of the domain: 65.1 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 22.52 %

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 21.5 21.5
Trusted cut-off 21.5 21.5
Noise cut-off 21.4 21.4
Model length: 66
Family (HMM) version: 32
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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The tree shows the occurrence of this domain across different species. 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 KH_1 domain has been found. There are 179 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
A0A044RAF6 View 3D Structure Click here
A0A044SHG8 View 3D Structure Click here
A0A044SKT1 View 3D Structure Click here
A0A044SMY6 View 3D Structure Click here
A0A044SNL8 View 3D Structure Click here
A0A044SP97 View 3D Structure Click here
A0A044TEI6 View 3D Structure Click here
A0A044TV22 View 3D Structure Click here
A0A044U3F5 View 3D Structure Click here
A0A044U9P0 View 3D Structure Click here
A0A044UNL3 View 3D Structure Click here
A0A044UQ63 View 3D Structure Click here
A0A044V1C4 View 3D Structure Click here
A0A044V3B3 View 3D Structure Click here
A0A044V667 View 3D Structure Click here
A0A077Z180 View 3D Structure Click here
A0A077Z251 View 3D Structure Click here
A0A077Z2M7 View 3D Structure Click here
A0A077Z350 View 3D Structure Click here
A0A077Z459 View 3D Structure Click here
A0A077Z797 View 3D Structure Click here
A0A077Z7E0 View 3D Structure Click here
A0A077Z807 View 3D Structure Click here
A0A077Z815 View 3D Structure Click here
A0A077Z914 View 3D Structure Click here
A0A077Z9C8 View 3D Structure Click here
A0A077ZB11 View 3D Structure Click here
A0A077ZC04 View 3D Structure Click here
A0A077ZE09 View 3D Structure Click here
A0A077ZFX6 View 3D Structure Click here
A0A077ZGV0 View 3D Structure Click here
A0A077ZHU7 View 3D Structure Click here
A0A077ZIB7 View 3D Structure Click here
A0A0B4J1B0 View 3D Structure Click here
A0A0B4KGY6 View 3D Structure Click here
A0A0D2DMD3 View 3D Structure Click here
A0A0D2DN49 View 3D Structure Click here
A0A0D2EUG0 View 3D Structure Click here
A0A0D2GCE9 View 3D Structure Click here
A0A0D2GUI4 View 3D Structure Click here