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568  structures 8496  species 0  interactions 35586  sequences 218  architectures

Family: ClpB_D2-small (PF10431)

Summary: C-terminal, D2-small domain, of ClpB protein

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C-terminal, D2-small domain, of ClpB protein Provide feedback

This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, PF00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly [1]. The domain is associated with two Clp_N, PF02861 at the N-terminus as well as AAA, PF00004 and AAA_2, PF07724.

Literature references

  1. Lee S, Sowa ME, Watanabe YH, Sigler PB, Chiu W, Yoshida M, Tsai FT; , Cell. 2003;115:229-240.: The structure of ClpB: a molecular chaperone that rescues proteins from an aggregated state. PUBMED:14567920 EPMC:14567920


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019489

Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation [ PUBMED:16879409 ]. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain ( INTERPRO ) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [ PUBMED:14567920 ].

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 AAA_lid (CL0671), which has the following description:

Many AAA+ proteins have a C-terminal alpha-helical bundle in addition to the AAA core [1]. The functional roles of the helical bundle are varied and include the formation of a lid over the nucleotide binding site and mediation of subunit interactions in oligomeric protein complexes [1].

The clan contains the following 22 members:

AAA_assoc_2 AAA_lid_1 AAA_lid_10 AAA_lid_11 AAA_lid_2 AAA_lid_3 AAA_lid_4 AAA_lid_5 AAA_lid_6 AAA_lid_7 AAA_lid_8 AAA_lid_9 CbbQ_C ClpB_D2-small Dpoe2NT MCM_lid Mg_chelatase_C ORC4_C PCP_red TIP49_C UVR Vps4_C

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 (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.

  Seed
(485)
Full
(35586)
Representative proteomes UniProt
(159856)
RP15
(5100)
RP35
(17371)
RP55
(34851)
RP75
(58928)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(485)
Full
(35586)
Representative proteomes UniProt
(159856)
RP15
(5100)
RP35
(17371)
RP55
(34851)
RP75
(58928)
Alignment:
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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.

  Seed
(485)
Full
(35586)
Representative proteomes UniProt
(159856)
RP15
(5100)
RP35
(17371)
RP55
(34851)
RP75
(58928)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Gene3D. pdb_1qvr
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Coggill P
Number in seed: 485
Number in full: 35586
Average length of the domain: 81.50 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 11.94 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.9 21.9
Trusted cut-off 21.9 21.9
Noise cut-off 21.8 21.8
Model length: 81
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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 ClpB_D2-small domain has been found. There are 568 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
A0A0B4LID7 View 3D Structure Click here
A0A0G2KJF1 View 3D Structure Click here
A0A0N7KFF5 View 3D Structure Click here
A0A0N7KFI2 View 3D Structure Click here
A0A0P0VHW4 View 3D Structure Click here
A0A0P0VHW9 View 3D Structure Click here
A0A0P0WPU2 View 3D Structure Click here
A0A0R0GIY4 View 3D Structure Click here
A0A0R0HUU5 View 3D Structure Click here
A0A0R0IX14 View 3D Structure Click here
A0A0R0JI83 View 3D Structure Click here
A0A0R0K0U9 View 3D Structure Click here
A0A140KXW9 View 3D Structure Click here
A0A1D6EC46 View 3D Structure Click here
A0A1D6G7E2 View 3D Structure Click here
A0A1D6H2L6 View 3D Structure Click here
A0A1D6H4P1 View 3D Structure Click here
A0A1D6H9K3 View 3D Structure Click here
A0A1D6K5Y7 View 3D Structure Click here
A0A1D6MA59 View 3D Structure Click here
A0A1D6Q3F7 View 3D Structure Click here
A0A1D8PTP9 View 3D Structure Click here
A0A381MP32 View 3D Structure Click here
A4I4I4 View 3D Structure Click here
C0PDC7 View 3D Structure Click here
C0PFV4 View 3D Structure Click here
C0PFZ0 View 3D Structure Click here
E7F9J1 View 3D Structure Click here
F4K7F6 View 3D Structure Click here
I1JU82 View 3D Structure Click here
I1JXP9 View 3D Structure Click here
I1JXT1 View 3D Structure Click here
I1JYR4 View 3D Structure Click here
I1K6S6 View 3D Structure Click here
I1KAS9 View 3D Structure Click here
I1KBU6 View 3D Structure Click here
I1KBY3 View 3D Structure Click here
I1KP32 View 3D Structure Click here
I1L3L8 View 3D Structure Click here
I1MQ99 View 3D Structure Click here
I1N4I0 View 3D Structure Click here
I1N6A2 View 3D Structure Click here
I1NID3 View 3D Structure Click here
K7TSX2 View 3D Structure Click here
K7VD78 View 3D Structure Click here
O74402 View 3D Structure Click here
O76031 View 3D Structure Click here
O94641 View 3D Structure Click here
P0A6H1 View 3D Structure Click here
P0A6H5 View 3D Structure Click here
P0ABH9 View 3D Structure Click here
P31539 View 3D Structure Click here
P33416 View 3D Structure Click here
P38323 View 3D Structure Click here
P42730 View 3D Structure Click here
P42762 View 3D Structure Click here
P63284 View 3D Structure Click here
P90788 View 3D Structure Click here
P9WPB9 View 3D Structure Click here
P9WPC9 View 3D Structure Click here
P9WPD1 View 3D Structure Click here
Q0E3C8 View 3D Structure Click here
Q25823 View 3D Structure Click here
Q2FV74 View 3D Structure Click here
Q2FXQ7 View 3D Structure Click here
Q2FZ28 View 3D Structure Click here
Q2FZS8 View 3D Structure Click here
Q2G0P5 View 3D Structure Click here
Q2QVG9 View 3D Structure Click here
Q4CLP1 View 3D Structure Click here
Q4CRW0 View 3D Structure Click here
Q4CX68 View 3D Structure Click here
Q4DRN5 View 3D Structure Click here
Q4DTH5 View 3D Structure Click here
Q4E408 View 3D Structure Click here
Q53LY0 View 3D Structure Click here
Q53N47 View 3D Structure Click here
Q54EV3 View 3D Structure Click here
Q54I27 View 3D Structure Click here
Q54IQ2 View 3D Structure Click here
Q5N8G6 View 3D Structure Click here
Q5U2U0 View 3D Structure Click here
Q60649 View 3D Structure Click here
Q65XY4 View 3D Structure Click here
Q66GN9 View 3D Structure Click here
Q6F2Y7 View 3D Structure Click here
Q6H795 View 3D Structure Click here
Q75GT3 View 3D Structure Click here
Q7F9I1 View 3D Structure Click here
Q7XL03 View 3D Structure Click here
Q8I0E1 View 3D Structure Click here
Q8I377 View 3D Structure Click here
Q8IB03 View 3D Structure Click here
Q8IIJ8 View 3D Structure Click here
Q8IM28 View 3D Structure Click here
Q8VYJ7 View 3D Structure Click here
Q96UX5 View 3D Structure Click here
Q9FI56 View 3D Structure Click here
Q9FK07 View 3D Structure Click here
Q9H078 View 3D Structure Click here
Q9JHS4 View 3D Structure Click here
Q9LF37 View 3D Structure Click here
Q9SXJ7 View 3D Structure Click here
Q9WTT2 View 3D Structure Click here