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22  structures 302  species 2  interactions 1824  sequences 43  architectures

Family: PBD (PF00786)

Summary: P21-Rho-binding domain

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

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


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000095

The molecular bases of the versatile functions of Rho-like GTPases are still unknown. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB). The Cdc42/Rac interactive binding (CRIB) region has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway [PUBMED:9119069]. In fission yeast pak1+ encodes a protein kinase that interacts with Cdc42p and is involved in the control of cell polarity and mating [PUBMED:8846783].

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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Alignments

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...

View options

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.

  Seed
(44)
Full
(1824)
Representative proteomes NCBI
(1667)
Meta
(2)
RP15
(294)
RP35
(490)
RP55
(775)
RP75
(1078)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(44)
Full
(1824)
Representative proteomes NCBI
(1667)
Meta
(2)
RP15
(294)
RP35
(490)
RP55
(775)
RP75
(1078)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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.

  Seed
(44)
Full
(1824)
Representative proteomes NCBI
(1667)
Meta
(2)
RP15
(294)
RP35
(490)
RP55
(775)
RP75
(1078)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

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.

Pfam alignments:

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...

Trees

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: Alignment kindly provided by SMART
Previous IDs: none
Type: Domain
Author: SMART
Number in seed: 44
Number in full: 1824
Average length of the domain: 56.30 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 11.27 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.0 21.1
Noise cut-off 20.9 20.9
Model length: 59
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 2 interactions for this family. More...

Pkinase PBD

Structures

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 22 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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