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33  structures 555  species 6  interactions 3073  sequences 73  architectures

Family: PBD (PF00786)

Summary: P21-Rho-binding domain

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P21-Rho-binding domain Provide feedback

Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB).

Literature references

  1. Ottilie S, Miller PJ, Johnson DI, Creasy CL, Sells MA, Bagrodia S, Forsburg SL, Chernoff J; , EMBO J 1995;14:5908-5919.: Fission yeast pak1+ encodes a protein kinase that interacts with Cdc42p and is involved in the control of cell polarity and mating. PUBMED:8846783 EPMC:8846783

  2. Leberer E, Wu C, Leeuw T, Fourest-Lieuvin A, Segall JE, Thomas DY; , EMBO J 1997;16:83-97.: Functional characterization of the Cdc42p binding domain of yeast Ste20p protein kinase. PUBMED:9009270 EPMC:9009270

  3. Osada S, Izawa M, Koyama T, Hirai S, Ohno S; , FEBS Lett 1997;404:227-233.: A domain containing the Cdc42/Rac interactive binding (CRIB) region of p65PAK inhibits transcriptional activation and cell transformation mediated by the Ras-Rac pathway. PUBMED:9119069 EPMC:9119069

  4. Burbelo PD, Drechsel D, Hall A; , J Biol Chem 1995;270:29071-29074.: A conserved binding motif defines numerous candidate target proteins for both Cdc42 and Rac GTPases. PUBMED:7493928 EPMC:7493928

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000095

This entry represents the CRIB domain.

Many putative downstream effectors of the small GTPases Cdc42 and Rac contain a GTPase binding domain (GBD), also called p21 binding domain (PBD), which has been shown to specifically bind the GTP bound form of Cdc42 or Rac, with a preference for Cdc42 [PUBMED:8107774, PUBMED:8625410]. The most conserved region of GBD/PBD domains is the N-terminal Cdc42/Rac interactive binding motif (CRIB), which consists of about 16 amino acids with the consensus sequence I-S-x-P-x(2,4)-F-x-H-x(2)-H-V-G [PUBMED:7493928].

Although the CRIB motif is necessary for the binding to Cdc42 and Rac, it is not sufficient to give high-affinity binding [PUBMED:9660763, PUBMED:9601050]. A less well conserved inhibitory switch (IS) domain responsible for maintaining the proteins in a basal (autoinhibited) state is located C-terminaly of the CRIB-motif [PUBMED:10724160, PUBMED:10975528, PUBMED:10966102].

GBD domains can adopt related but distinct folds depending on context. Although GBD domains are largely unstructured in the free state, the IS domain forms an N-terminal beta; hairpin that immediately follows the conserved CRIB motif and a central bundle of three alpha; helices in the autoinhibited state. The interaction between GBD domains and their respective G proteins leads to the formation of a high-affinity complex in which unstructured regions of both the effector and the G protein become rigid. CRIB motifs from various GBD domains interact with Cdc42 in a similar manner, forming an intermolecular beta;-sheet with strand beta;-2 of Cdc42. Outside the CRIB motif, the C-termini of the various GBD domains are very divergent and show variation in their mode of binding to Cdc42, perhaps determining the specificity of the interaction. Binding of Cdc42 or Rac to the GBD domain causes a dramatic conformational change, refolding part of the IS domain and unfolding the rest [PUBMED:9660763, PUBMED:10724160, PUBMED:10975528, PUBMED:10966102, PUBMED:10360579].

Some proteins known to contain a CRIB domain are listed below:

  • Mammalian activated Cdc42-associated kinases (ACKs), nonreceptor tyrosine kinases implicated in integrin-coupled pathways.
  • Mammalian p21-activated kinases (PAK1 to PAK4), serine/threonine kinases that modulate cytoskeletal assembly and activate MAP-kinase pathways.
  • Mammalian Wiskott-Aldrich Symdrom Proteins (WASPs), non-kinase proteins involved in the organisation of the actin cytoskeleton.
  • Yeast STE20 and CLA4, the homologues of mammalian PAKs. STE20 is involved in the mating/pheromone MAP kinase cascade.

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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Representative proteomes NCBI

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

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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.

Curation View help on the curation process

Seed source: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Author: SMART
Number in seed: 31
Number in full: 3073
Average length of the domain: 54.10 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 10.77 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -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: 59
Family (HMM) version: 24
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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There are 6 interactions for this family. More...

EspF EspG Ras Pkinase PBD Pkinase


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 PBD domain has been found. There are 33 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 seqence.

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