Transcriptional repressor NF-X1, R3H domain (IPR034076)

Short name: R3H_NF-X1

Overlapping homologous superfamilies

Domain relationships

  • R3H domain (IPR001374)
    • Transcriptional repressor NF-X1, R3H domain (IPR034076)


This entry includes the R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes [PMID: 7964459, PMID: 8413274]. The Drosophila homologue shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system [PMID: 8524296].

The R3H domain is a conserved sequence motif found in proteins from a diverse range of organisms including eubacteria, green plants, fungi and various groups of metazoans, but not in archaea and Escherichia coli. The domain is named R3H because it contains an invariant arginine and a highly conserved histidine, that are separated by three residues. It also displays a conserved pattern of hydrophobic residues, prolines and glycines. It can be found alone, in association with AAA domain or with various DNA/RNA binding domains like DSRM, KH, G-patch, PHD, DEAD box, or RRM. The functions of these domains indicate that the R3H domain might be involved in polynucleotide-binding, including DNA, RNA and single-stranded DNA [PMID: 9787637].

The 3D structure of the R3H domain has been solved. The fold presents a small motif, consisting of a three-stranded antiparallel beta-sheet, against which two alpha-helices pack from one side. This fold is related to the structures of the YhhP protein and the C-terminal domain of the translational initiation factor IF3. Three conserved basic residues cluster on the same face of the R3H domain and could play a role in nucleic acid recognition. An extended hydrophobic area at a different site of the molecular surface could act as a protein-binding site [PMID: 12547203].

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0003676 nucleic acid binding

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.